A small trip in the untranquil world of genomes A survey on the detection and analysis of genome rearrangement breakpoints
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paper_title: Are molecular cytogenetics and bioinformatics suggesting diverging models of ancestral mammalian genomes?

paper_content:

Excavating ancestral genomes The recent release of the chicken genome sequence (Hillier et al. 2004Go) provided exciting news for the comparative genomics community as it allows insights into the early evolution of the human genome. A bird species can now be used as an outgroup to model early mammalian genome organization and reshuffling. The genome sequence data have already been incorporated in a computational analysis of chicken, mouse, rat, and human genome sequences for the reconstruction of the ancestral genome organization of both a mammalian ancestor as well as a murid rodent ancestor (Hillier et al. 2004Go; Bourque et al. 2005Go). This bioinformatic effort joins a molecular cytogenetic model (Richard et al. 2003Go; Yang et al. 2003Go; Robinson et al. 2004Go; Svartman et al. 2004Go; Wienberg 2004Go; Froenicke 2005Go) as the second global approach to explore the architecture of the ancestral eutherian karyotype—a fundamental question in comparative genomics. Since both models use the human genome as reference, they are readily comparable. Surprisingly, however, they share few similarities. Only two small autosomes and the sex chromosomes of the hypothesized ancestral karyotypes are common to both. Unfortunately, given its significance, neither the extent of these differences nor their impact on comparative genomics have been discussed by Bourque and colleagues (2005Go). In an attempt to redress this, we compare the two methods of ancestral genome reconstruction, verify the resulting models, and discuss reasons for their apparent divergence.
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paper_title: Human and mouse genomic sequences reveal extensive breakpoint reuse in mammalian evolution

paper_content:

The human and mouse genomic sequences provide evidence for a larger number of rearrangements than previously thought and reveal extensive reuse of breakpoints from the same short fragile regions. Breakpoint clustering in regions implicated in cancer and infertility have been reported in previous studies; we report here on breakpoint clustering in chromosome evolution. This clustering reveals limitations of the widely accepted random breakage theory that has remained unchallenged since the mid-1980s. The genome rearrangement analysis of the human and mouse genomes implies the existence of a large number of very short “hidden” synteny blocks that were invisible in the comparative mapping data and ignored in the random breakage model. These blocks are defined by closely located breakpoints and are often hard to detect. Our results suggest a model of chromosome evolution that postulates that mammalian genomes are mosaics of fragile regions with high propensity for rearrangements and solid regions with low propensity for rearrangements.
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paper_title: The Fragile Breakage versus Random Breakage Models of Chromosome Evolution

paper_content:

For many years, studies of chromosome evolution were dominated by the random breakage theory, which implies that there are no rearrangement hot spots in the human genome. In 2003, Pevzner and Tesler argued against the random breakage model and proposed an alternative "fragile breakage" model of chromosome evolution. In 2004, Sankoff and Trinh argued against the fragile breakage model and raised doubts that Pevzner and Tesler provided any evidence of rearrangement hot spots. We investigate whether Sankoff and Trinh indeed revealed a flaw in the arguments of Pevzner and Tesler. We show that Sankoff and Trinh's synteny block identification algorithm makes erroneous identifications even in small toy examples and that their parameters do not reflect the realities of the comparative genomic architecture of human and mouse. We further argue that if Sankoff and Trinh had fixed these problems, their arguments in support of the random breakage model would disappear. Finally, we study the link between rearrangements and regulatory regions and argue that long regulatory regions and inhomogeneity of gene distribution in mammalian genomes may be responsible for the breakpoint reuse phenomenon.
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paper_title: Evolution's cauldron: duplication, deletion, and rearrangement in the mouse and human genomes.

paper_content:

This study examines genomic duplications, deletions, and rearrangements that have happened at scales ranging from a single base to complete chromosomes by comparing the mouse and human genomes. From whole-genome sequence alignments, 344 large (>100-kb) blocks of conserved synteny are evident, but these are further fragmented by smaller-scale evolutionary events. Excluding transposon insertions, on average in each megabase of genomic alignment we observe two inversions, 17 duplications (five tandem or nearly tandem), seven transpositions, and 200 deletions of 100 bases or more. This includes 160 inversions and 75 duplications or transpositions of length >100 kb. The frequencies of these smaller events are not substantially higher in finished portions in the assembly. Many of the smaller transpositions are processed pseudogenes; we define a "syntenic" subset of the alignments that excludes these and other small-scale transpositions. These alignments provide evidence that approximately 2% of the genes in the human/mouse common ancestor have been deleted or partially deleted in the mouse. There also appears to be slightly less nontransposon-induced genome duplication in the mouse than in the human lineage. Although some of the events we detect are possibly due to misassemblies or missing data in the current genome sequence or to the limitations of our methods, most are likely to represent genuine evolutionary events. To make these observations, we developed new alignment techniques that can handle large gaps in a robust fashion and discriminate between orthologous and paralogous alignments.
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paper_title: The convergence of cytogenetics and rearrangement-based models for ancestral genome reconstruction.

paper_content:

Froenicke et al. (2006) asked the question “Are molecular cytogenetics and bioinformatics suggesting diverging models of ancestral mammalian genomes?” Their commentary seems to imply that cytogenetics is superior to “bioinformatics” when it comes to studies of ancestral mammalian genomes. But, comparing cytogenetics with other approaches to deriving ancestral genomic architectures (like MGR developed by Bourque and Pevzner 2002) on two very different data sets (80+ cytogenetic maps vs. four distantly related sequenced genomes) does not say much about the merits and demerits of the approaches; instead, it indirectly evaluates the quality of the input data sets. In this context, the main conclusion of Froenicke et al. (2006) amounts to the statement that 80+ cytogenetic maps lead to a more definitive reconstruction than four divergent genomes when it comes to low-resolution ancestral architectures. We never argued against this point in our publications and even advocated for the use of radiation hybrid mapping (as a trade-off in resolution between cytogenetic and sequencing data) to extend the number of analyzed genomes (Murphy et al. 2003, 2005). Indeed, with more taxon sampling, a rearrangementbased reconstruction with just seven genomes (Murphy et al. 2005) is already highly consistent with the cytogenetics reconstruction. Before we substantiate this convergence, we clarify the notion of weak associations, which was used in Bourque et al. (2005) to alert the reader that some of the adjacencies were left as unresolved in the ancestor. The discrepancies identified by Froenicke et al. (2006) all involve weak associations and point toward a misunderstanding more than a contradiction. Finally, we underline some of the important strengths exclusive to rearrangement-based approaches, such as the ability to detect smaller genomic segments, to handle fast evolving lineages, and to orient conserved segments in the ancestors.
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paper_title: Hotspots of mammalian chromosomal evolution

paper_content:

Background ::: Chromosomal evolution is thought to occur through a random process of breakage and rearrangement that leads to karyotype differences and disruption of gene order. With the availability of both the human and mouse genomic sequences, detailed analysis of the sequence properties underlying these breakpoints is now possible.
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paper_title: Chromosomal breakpoint reuse in genome sequence rearrangement

paper_content:

In order to apply gene-order rearrangement algorithms to the comparison of genome sequences, Pevzner and Tesler bypass gene finding and ortholog identification and use the order of homologous blocks of unannotated sequence as input. The method excludes blocks shorter than a threshold length. Here we investigate possible biases introduced by eliminating short blocks, focusing on the notion of breakpoint reuse introduced by these authors. Analytic and simulation methods show that reuse is very sensitive to the proportion of blocks excluded. As is pertinent to the comparison of mammalian genomes, this exclusion risks randomizing the comparison partially or entirely.
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paper_title: Mechanism and regulation of human non-homologous DNA end-joining

paper_content:

In multicellular eukaryotes, non-homologous DNA end-joining (NHEJ) is the primary pathway for repairing double-stranded DNA breaks (DSBs). The other important pathway for the repair of such breaks is homologous recombination, which is restricted to late S and G2 phases in dividing cells. ::: Pathological DSBs result when there is replication across a nick, when ionizing radiation passes near the DNA, and when reactive-oxygen species contact DNA. Such breaks are repaired by NHEJ when they occur in G0, G1 or early S phases of the cell cycle, and often even during late S and G2 phases. ::: Physiological DSBs result during V(D)J recombination and class-switch recombination. The rejoining phase of these two processes uses NHEJ. ::: NHEJ is typically imprecise in multicellular eukaryotes, making it the only main DNA-repair pathway that is error prone. ::: Because of its error-prone nature, NHEJ might contribute to cancer and ageing. ::: Defects in NHEJ result in sensitivity to ionizing radiation and in a lack of lymphocytes. The lack of lymphocytes results from the loss of the ability to complete V(D)J recombination. In humans, mutations in Artemis are responsible for about 15% of cases of severe combined immune deficiency syndrome. Artemis, in complex with the DNA-dependent protein kinase catalytic subunit (DNA-PKcs), is responsible for trimming the DNA ends in NHEJ. ::: In multicellular eukaryotes, non-homologous DNA end-joining (NHEJ) is the primary pathway for repairing double-stranded DNA breaks (DSBs). The other important pathway for the repair of such breaks is homologous recombination, which is restricted to late S and G2 phases in dividing cells. Pathological DSBs result when there is replication across a nick, when ionizing radiation passes near the DNA, and when reactive-oxygen species contact DNA. Such breaks are repaired by NHEJ when they occur in G0, G1 or early S phases of the cell cycle, and often even during late S and G2 phases. Physiological DSBs result during V(D)J recombination and class-switch recombination. The rejoining phase of these two processes uses NHEJ. NHEJ is typically imprecise in multicellular eukaryotes, making it the only main DNA-repair pathway that is error prone. Because of its error-prone nature, NHEJ might contribute to cancer and ageing. Defects in NHEJ result in sensitivity to ionizing radiation and in a lack of lymphocytes. The lack of lymphocytes results from the loss of the ability to complete V(D)J recombination. In humans, mutations in Artemis are responsible for about 15% of cases of severe combined immune deficiency syndrome. Artemis, in complex with the DNA-dependent protein kinase catalytic subunit (DNA-PKcs), is responsible for trimming the DNA ends in NHEJ.
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paper_title: Structural variation in the human genome

paper_content:

The first wave of information from the analysis of the human genome revealed SNPs to be the main source of genetic and phenotypic human variation. However, the advent of genome-scanning technologies has now uncovered an unexpectedly large extent of what we term 'structural variation' in the human genome. This comprises microscopic and, more commonly, submicroscopic variants, which include deletions, duplications and large-scale copy-number variants - collectively termed copy-number variants or copy-number polymorphisms - as well as insertions, inversions and translocations. Rapidly accumulating evidence indicates that structural variants can comprise millions of nucleotides of heterogeneity within every genome, and are likely to make an important contribution to human diversity and disease susceptibility.
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paper_title: Nonhomologous end joining in yeast.

paper_content:

AbstractNonhomologous end joining (NHEJ), the direct rejoining of DNA double-strand breaks, is closely associated with illegitimate recombination and chromosomal rearrangement. This has led to the concept that NHEJ is error prone. Studies with the yeast Saccharomyces cerevisiae have revealed that this model eukaryote has a classical NHEJ pathway dependent on Ku and DNA ligase IV, as well as alternative mechanisms for break rejoining. The evolutionary conservation of the Ku-dependent process includes several genes dedicated to this pathway, indicating that classical NHEJ at least is a strong contributor to fitness in the wild. Here we review how double-strand break structure, the yeast NHEJ proteins, and alternative rejoining mechanisms influence the accuracy of break repair. We also consider how the balance between NHEJ and homologous repair is regulated by cell state to promote genome preservation. The principles discussed are instructive to NHEJ in all organisms.
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paper_title: Structure of chromosomal duplicons and their role in mediating human genomic disorders.

paper_content:

Chromosome-specific low-copy repeats, or duplicons, occur in multiple regions of the human genome. Homologous recombination between different duplicon copies leads to chromosomal rearrangements, such as deletions, duplications, inversions, and inverted duplications, depending on the orientation of the recombining duplicons. When such rearrangements cause dosage imbalance of a developmentally important gene(s), genetic diseases now termed genomic disorders result, at a frequency of 0.7-1/1000 births. Duplicons can have simple or very complex structures, with variation in copy number from 2 to >10 repeats, and each varying in size from a few kilobases in length to hundreds of kilobases. Analysis of the different duplicons involved in human genomic disorders identifies features that may predispose to recombination, including large size and high sequence identity between the recombining copies, putative recombination promoting features, and the presence of multiple genes/pseudogenes that may include genes expressed in germ cells. Most of the chromosome rearrangements involve duplicons near pericentromeric regions, which may relate to the propensity of such regions to accumulate duplicons. Detailed analyses of the structure, polymorphic variation, and mechanisms of recombination in genomic disorders, as well as the evolutionary origin of various duplicons will further our understanding of the structure, function, and fluidity of the human genome.
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paper_title: Pathological consequences of sequence duplications in the human genome.

paper_content:

As large-scale sequencing accumulates momentum, an increasing number of instances are being revealed in which genes or other relatively rare sequences are duplicated, either in tandem or at nearby locations. Such duplications are a source of considerable polymorphism in populations, and also increase the evolutionary possibilities for the coregulation of juxtaposed sequences. As a further consequence, they promote inversions and deletions that are responsible for significant inherited pathology. Here we review known examples of genomic duplications present on the human X chromosome and autosomes.
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paper_title: Genome architecture, rearrangements and genomic disorders.

paper_content:

An increasing number of human diseases are recognized to result from recurrent DNA rearrangements involving unstable genomic regions. These are termed genomic disorders, in which the clinical phenotype is a consequence of abnormal dosage of gene(s) located within the rearranged genomic fragments. Both inter- and intrachromosomal rearrangements are facilitated by the presence of region-specific low-copy repeats (LCRs) and result from nonallelic homologous recombination (NAHR) between paralogous genomic segments. LCRs usually span approximately 10-400 kb of genomic DNA, share >or= 97% sequence identity, and provide the substrates for homologous recombination, thus predisposing the region to rearrangements. Moreover, it has been suggested that higher order genomic architecture involving LCRs plays a significant role in karyotypic evolution accompanying primate speciation.
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paper_title: Molecular-evolutionary mechanisms for genomic disorders

paper_content:

Molecular studies of unstable regions in the human genome have identified region-specific low-copy repeats (LCRs). Unlike highly repetitive sequences (e.g. Alus and LINEs), LCRs are usually of 10–400 kb in size and exhibit ≥ 95–97% similarity. According to computer analyses of available sequencing data, LCRs may constitute >5% of the human genome. Through the process of non-allelic homologous recombination using paralogous genomic segments as substrates, LCRs have been shown to facilitate meiotic DNA rearrangements associated with disease traits, referred to as genomic disorders. In addition, this LCR-based complex genome architecture appears to play a major role in both primate karyotype evolution and human tumorigenesis.
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paper_title: Origins of primate chromosomes – as delineated by Zoo-FISH and alignments of human and mouse draft genome sequences

paper_content:

This review examines recent advances in comparative eutherian cytogenetics, including Zoo-FISH data from 30 non-primate species. These data provide insights into the nature of karyotype evolution and
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paper_title: Are molecular cytogenetics and bioinformatics suggesting diverging models of ancestral mammalian genomes?

paper_content:

Excavating ancestral genomes The recent release of the chicken genome sequence (Hillier et al. 2004Go) provided exciting news for the comparative genomics community as it allows insights into the early evolution of the human genome. A bird species can now be used as an outgroup to model early mammalian genome organization and reshuffling. The genome sequence data have already been incorporated in a computational analysis of chicken, mouse, rat, and human genome sequences for the reconstruction of the ancestral genome organization of both a mammalian ancestor as well as a murid rodent ancestor (Hillier et al. 2004Go; Bourque et al. 2005Go). This bioinformatic effort joins a molecular cytogenetic model (Richard et al. 2003Go; Yang et al. 2003Go; Robinson et al. 2004Go; Svartman et al. 2004Go; Wienberg 2004Go; Froenicke 2005Go) as the second global approach to explore the architecture of the ancestral eutherian karyotype—a fundamental question in comparative genomics. Since both models use the human genome as reference, they are readily comparable. Surprisingly, however, they share few similarities. Only two small autosomes and the sex chromosomes of the hypothesized ancestral karyotypes are common to both. Unfortunately, given its significance, neither the extent of these differences nor their impact on comparative genomics have been discussed by Bourque and colleagues (2005Go). In an attempt to redress this, we compare the two methods of ancestral genome reconstruction, verify the resulting models, and discuss reasons for their apparent divergence.
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paper_title: Molecular cytotaxonomy of primates by chromosomal in situ suppression hybridization

paper_content:

A new strategy for analyzing chromosomal evolution in primates is presented using chromosomal in situ suppression (CISS) hybridization. Biotin-labeled DNA libraries from flow-sorted human chromosomes are hybridized to chromosome preparations of catarrhines, platyrrhines, and prosimians. By this approach rearrangements of chromosomes that occurred during hominoid evolution are visualized directly at the level of DNA sequences, even in primate species with pronounced chromosomal shuffles.
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paper_title: Reconstruction of genomic rearrangements in great apes and gibbons by chromosome painting.

paper_content:

The homology between hylobatid chromosomes and other primates has long remained elusive. We used chromosomal in situ suppression hybridization of all human chromosome-specific DNA libraries to "paint" the chromosomes of primates and establish homologies between the human, great ape (chimpanzee, gorilla, and orangutan), and gibbon karyotypes (Hylobates lar species group, 2n = 44). The hybridization patterns unequivocally demonstrate the high degree of chromosomal homology and synteny of great ape and human chromosomes. Relative to human, no translocations were detected in great apes, except for the well-known fusion-origin of human chromosome 2 and a 5;17 translocation in the gorilla. In contrast, numerous translocations were detected that have led to the massive reorganization of the gibbon karyotype: the 22 autosomal human chromosomes have been divided into 51 elements to compose the 21 gibbon autosomes. Molecular cytogenetics promises to finally allow hylobatids to be integrated into the overall picture of chromosomal evolution in the primates.
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paper_title: The convergence of cytogenetics and rearrangement-based models for ancestral genome reconstruction.

paper_content:

Froenicke et al. (2006) asked the question “Are molecular cytogenetics and bioinformatics suggesting diverging models of ancestral mammalian genomes?” Their commentary seems to imply that cytogenetics is superior to “bioinformatics” when it comes to studies of ancestral mammalian genomes. But, comparing cytogenetics with other approaches to deriving ancestral genomic architectures (like MGR developed by Bourque and Pevzner 2002) on two very different data sets (80+ cytogenetic maps vs. four distantly related sequenced genomes) does not say much about the merits and demerits of the approaches; instead, it indirectly evaluates the quality of the input data sets. In this context, the main conclusion of Froenicke et al. (2006) amounts to the statement that 80+ cytogenetic maps lead to a more definitive reconstruction than four divergent genomes when it comes to low-resolution ancestral architectures. We never argued against this point in our publications and even advocated for the use of radiation hybrid mapping (as a trade-off in resolution between cytogenetic and sequencing data) to extend the number of analyzed genomes (Murphy et al. 2003, 2005). Indeed, with more taxon sampling, a rearrangementbased reconstruction with just seven genomes (Murphy et al. 2005) is already highly consistent with the cytogenetics reconstruction. Before we substantiate this convergence, we clarify the notion of weak associations, which was used in Bourque et al. (2005) to alert the reader that some of the adjacencies were left as unresolved in the ancestor. The discrepancies identified by Froenicke et al. (2006) all involve weak associations and point toward a misunderstanding more than a contradiction. Finally, we underline some of the important strengths exclusive to rearrangement-based approaches, such as the ability to detect smaller genomic segments, to handle fast evolving lineages, and to orient conserved segments in the ancestors.
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paper_title: Reconstruction of the ancestral karyotype of eutherian mammals

paper_content:

Applying the parsimony principle, i.e. that chromosomes identical in species belonging to different taxa were likely to be present in their common ancestor, the ancestral karyotype of eutherian mammals (about 100 million years old) was tentatively reconstructed. Comparing chromosome banding with all ZOO-FISH data from literature or studied by us, this reconstruction can be proposed with only limited uncertainties. This karyotype comprised 50 chromosomes of which 40-42 were acrocentrics. Ten ancestral pairs of chromosomes were homologous to a single human chromosome: 5, 6, 9, 11, 13, 17, 18, 20, X and Y (human nomenclature). Nine others were homologous to a part of a human chromosome: 1p + q (proximal), 1q, 2p + q (proximal), 2q, part of 7, 8q, 10p, 10q and 19p (human nomenclature). Finally, seven pairs of chromosomes, homologs to human chromosomes 3 + 21, 4 + 8p, part of 7 + 16p, part of 12 + part of 22 (twice), 14 + 15, 16q + 19q, formed syntenies disrupted in man.
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paper_title: Mauve: Multiple alignment of conserved genomic sequence with rearrangements. Genome Res

paper_content:

As genomes evolve, they undergo large-scale evolutionary processes that present a challenge to sequence comparison not posed by short sequences. Recombination causes frequent genome rearrangements, horizontal transfer introduces new sequences into bacterial chromosomes, and deletions remove segments of the genome. Consequently, each genome is a mosaic of unique lineage-specific segments, regions shared with a subset of other genomes and segments conserved among all the genomes under consideration. Furthermore, the linear order of these segments may be shuffled among genomes. We present methods for identification and alignment of conserved genomic DNA in the presence of rearrangements and horizontal transfer. Our methods have been implemented in a software package called Mauve. Mauve has been applied to align nine enterobacterial genomes and to determine global rearrangement structure in three mammalian genomes. We have evaluated the quality of Mauve alignments and drawn comparison to other methods through extensive simulations of genome evolution.
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paper_title: A General Method Applicable to the Search for Similarities in the Amino Acid Sequence of Two Proteins

paper_content:

A computer adaptable method for finding similarities in the amino acid sequences of two proteins has been developed. From these findings it is possible to determine whether significant homology exists between the proteins. This information is used to trace their possible evolutionary development. The maximum match is a number dependent upon the similarity of the sequences. One of its definitions is the largest number of amino acids of one protein that can be matched with those of a second protein allowing for all possible interruptions in either of the sequences. While the interruptions give rise to a very large number of comparisons, the method efficiently excludes from consideration those comparisons that cannot contribute to the maximum match. Comparisons are made from the smallest unit of significance, a pair of amino acids, one from each protein. All possible pairs are represented by a two-dimensional array, and all possible comparisons are represented by pathways through the array. For this maximum match only certain of the possible pathways must, be evaluated. A numerical value, one in this case, is assigned to every cell in the array representing like amino acids. The maximum match is the largest number that would result from summing the cell values of every
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paper_title: Evolution's cauldron: duplication, deletion, and rearrangement in the mouse and human genomes.

paper_content:

This study examines genomic duplications, deletions, and rearrangements that have happened at scales ranging from a single base to complete chromosomes by comparing the mouse and human genomes. From whole-genome sequence alignments, 344 large (>100-kb) blocks of conserved synteny are evident, but these are further fragmented by smaller-scale evolutionary events. Excluding transposon insertions, on average in each megabase of genomic alignment we observe two inversions, 17 duplications (five tandem or nearly tandem), seven transpositions, and 200 deletions of 100 bases or more. This includes 160 inversions and 75 duplications or transpositions of length >100 kb. The frequencies of these smaller events are not substantially higher in finished portions in the assembly. Many of the smaller transpositions are processed pseudogenes; we define a "syntenic" subset of the alignments that excludes these and other small-scale transpositions. These alignments provide evidence that approximately 2% of the genes in the human/mouse common ancestor have been deleted or partially deleted in the mouse. There also appears to be slightly less nontransposon-induced genome duplication in the mouse than in the human lineage. Although some of the events we detect are possibly due to misassemblies or missing data in the current genome sequence or to the limitations of our methods, most are likely to represent genuine evolutionary events. To make these observations, we developed new alignment techniques that can handle large gaps in a robust fashion and discriminate between orthologous and paralogous alignments.
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paper_title: Strategies and Tools for Whole-Genome Alignments

paper_content:

The availability of the assembled mouse genome makes possible, for the first time, an alignment and comparison of two large vertebrate genomes. We investigated different strategies of alignment for the subsequent analysis of conservation of genomes that are effective for assemblies of different quality. These strategies were applied to the comparison of the working draft of the human genome with the Mouse Genome Sequencing Consortium assembly, as well as other intermediate mouse assemblies. Our methods are fast and the resulting alignments exhibit a high degree of sensitivity, covering more than 90% of known coding exons in the human genome. We obtained such coverage while preserving specificity. With a view towards the end user, we developed a suite of tools and Web sites for automatically aligning and subsequently browsing and working with whole-genome comparisons. We describe the use of these tools to identify conserved non-coding regions between the human and mouse genomes, some of which have not been identified by other methods.
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paper_title: Choosing the best heuristic for seeded alignment of DNA sequences

paper_content:

BackgroundSeeded alignment is an important component of algorithms for fast, large-scale DNA similarity search. A good seed matching heuristic can reduce the execution time of genomic-scale sequence comparison without degrading sensitivity. Recently, many types of seed have been proposed to improve on the performance of traditional contiguous seeds as used in, e.g., NCBI BLASTN. Choosing among these seed types, particularly those that use information besides the presence or absence of matching residue pairs, requires practical guidance based on a rigorous comparison, including assessment of sensitivity, specificity, and computational efficiency. This work performs such a comparison, focusing on alignments in DNA outside widely studied coding regions.ResultsWe compare seeds of several types, including those allowing transition mutations rather than matches at fixed positions, those allowing transitions at arbitrary positions ("BLASTZ" seeds), and those using a more general scoring matrix. For each seed type, we use an extended version of our Mandala seed design software to choose seeds with optimized sensitivity for various levels of specificity. Our results show that, on a test set biased toward alignments of noncoding DNA, transition information significantly improves seed performance, while finer distinctions between different types of mismatches do not. BLASTZ seeds perform especially well. These results depend on properties of our test set that are not shared by EST-based test sets with a strong bias toward coding DNA.ConclusionPractical seed design requires careful attention to the properties of the alignments being sought. For noncoding DNA sequences, seeds that use transition information, especially BLASTZ-style seeds, are particularly useful. The Mandala seed design software can be found at http://www.cse.wustl.edu/~yanni/mandala/.
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paper_title: Comparative architectures of mammalian and chicken genomes reveal highly variable rates of genomic rearrangements across different lineages

paper_content:

Molecular evolution studies are usually based on the analysis of individual genes and thus reflect only small-range variations in genomic sequences. A complementary approach is to study the evolutionary history of rearrangements in entire genomes based on the analysis of gene orders. The progress in whole genome sequencing provides an unprecedented level of detailed sequence data to infer genome rearrangements through comparative approaches. The comparative analysis of recently sequenced rodent genomes with the human genome revealed evidence for a larger number of rearrangements than previously thought and led to the reconstruction of the putative genomic architecture of the murid rodent ancestor, while the architecture of the ancestral mammalian genome and the rate of rearrangements in the human lineage remained unknown. Sequencing the chicken genome provides an opportunity to reconstruct the architecture of the ancestral mammalian genome by using chicken as an outgroup. Our analysis reveals a very low rate of rearrangements and, in particular, interchromosomal rearrangements in chicken, in the early mammalian ancestor, or in both. The suggested number of interchromosomal rearrangements between the mammalian ancestor and chicken, during an estimated 500 million years of evolution, only slightly exceeds the number of interchromosomal rearrangements that happened in the mouse lineage, over the course of about 87 million years.
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paper_title: Comparative architectures of mammalian and chicken genomes reveal highly variable rates of genomic rearrangements across different lineages

paper_content:

Molecular evolution studies are usually based on the analysis of individual genes and thus reflect only small-range variations in genomic sequences. A complementary approach is to study the evolutionary history of rearrangements in entire genomes based on the analysis of gene orders. The progress in whole genome sequencing provides an unprecedented level of detailed sequence data to infer genome rearrangements through comparative approaches. The comparative analysis of recently sequenced rodent genomes with the human genome revealed evidence for a larger number of rearrangements than previously thought and led to the reconstruction of the putative genomic architecture of the murid rodent ancestor, while the architecture of the ancestral mammalian genome and the rate of rearrangements in the human lineage remained unknown. Sequencing the chicken genome provides an opportunity to reconstruct the architecture of the ancestral mammalian genome by using chicken as an outgroup. Our analysis reveals a very low rate of rearrangements and, in particular, interchromosomal rearrangements in chicken, in the early mammalian ancestor, or in both. The suggested number of interchromosomal rearrangements between the mammalian ancestor and chicken, during an estimated 500 million years of evolution, only slightly exceeds the number of interchromosomal rearrangements that happened in the mouse lineage, over the course of about 87 million years.
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paper_title: Chaining Multiple-Alignment Blocks

paper_content:

ABSTRACT We derive a time-efficient method for building a multiple alignment consisting of a highestscoring chain of “blocks,” i.e., short gap-free alignments. Besides executing faster than a general-purpose multiple-alignment program, the method may be particularly appropriate when discovery of blocks meeting a certain criterion is the main reason for aligning the sequences. Utility of the method is illustrated by locating a chain of “phylogenetic footprints” (specifically, exact matches of length 6 or more) in the 5'-flanking regions of six mammalian e-globin genes.
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paper_title: Transforming men into mice: the Nadeau-Taylor chromosomal breakage model revisited

paper_content:

Although analysis of genome rearrangements was pioneered by Dobzhansky and Sturtevant 65 years ago, we still know very little about the rearrangement events that produced the existing varieties of genomic architectures. The genomic sequences of human and mouse provide evidence for a larger number of rearrangements than previously thought and shed some light on previously unknown features of mammalian evolution. In particular, they reveal extensive re-use of breakpoints from the same relatively short regions. Our analysis implies the existence of a large number of very short "hidden" synteny blocks that were invisible in comparative mapping data and were not taken into account in previous studies of chromosome evolution. These blocks are defined by closely located breakpoints and are often hard to detect. Our result is in conflict with the widely accepted random breakage model of chromosomal evolution. We suggest a new "fragile breakage" model of chromosome evolution that postulates that breakpoints are chosen from relatively short fragile regions that have much higher propensity for rearrangements than the rest of the genome.
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paper_title: AVID: A Global Alignment Program

paper_content:

In this paper we describe a new global alignment method called AVID. The method is designed to be fast, memory efficient, and practical for sequence alignments of large genomic regions up to megabases long. We present numerous applications of the method, ranging from the comparison of assemblies to alignment of large syntenic genomic regions and whole genome human/mouse alignments. We have also performed a quantitative comparison of AVID with other popular alignment tools. To this end, we have established a format for the representation of alignments and methods for their comparison. These formats and methods should be useful for future studies. The tools we have developed for the alignment comparisons, as well as the AVID program, are publicly available. See Web Site References section for AVID Web address and Web addresses for other programs discussed in this paper.
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paper_title: Computing the Assignment of Orthologous Genes via Genome Rearrangement

paper_content:

The assignment of orthologous genes between a pair of genomes is a fundamental and challenging problem in comparative genomics. Existing methods that assign orthologs based on the similarity between DNA or protein sequences may make erroneous assignments when sequence similarity does not clearly delineate the evolutionary relationship among genes of the same families. In this paper, we present a new approach to ortholog assignment that takes into account both sequence similarity and evolutionary events at genome level, where orthologous genes are assumed to correspond to each other in the most parsimonious evolving scenario under genome rearrangement. It is then formulated as a problem of computing the signed reversal distance with duplicates between two genomes of interest, for which an efcient heuristic algorithm was given by introducing two new optimization problems, minimum common partition and maximum cycle decomposition. Following this approach, we have implemented a high-throughput system for assigning orthologs on a genome scale, called SOAR, and tested it on both simulated data and real genome sequence data. Compared to a recent ortholog assignment method based entirely on homology search (called INPARANOID), SOAR shows a marginally better performance in terms of sensitivity on the real data set because it was able to identify several correct orthologous pairs that were missed by INPARANOID. The simulation results demonstrate that SOAR in general performs better than the iterated exemplar algorithm in terms of computing the reversal distance and assigning correct orthologs.
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paper_title: Automated Whole-Genome Multiple Alignment of Rat, Mouse, and Human

paper_content:

We have built a whole-genome multiple alignment of the three currently available mammalian genomes using a fully automated pipeline that combines the local/global approach of the Berkeley Genome Pipeline and the LAGAN program. The strategy is based on progressive alignment and consists of two main steps: (1) alignment of the mouse and rat genomes, and (2) alignment of human to either the mouse-rat alignments from step 1, or the remaining unaligned mouse and rat sequences. The resulting alignments demonstrate high sensitivity, with 87% of all human gene-coding areas aligned in both mouse and rat. The specificity is also high: <7% of the rat contigs are aligned to multiple places in human, and 97% of all alignments with human sequence >100 kb agree with a three-way synteny map built independently, using predicted exons in the three genomes. At the nucleotide level <1% of the rat nucleotides are mapped to multiple places in the human sequence in the alignment, and 96.5% of human nucleotides within all alignments agree with the synteny map. The alignments are publicly available online, with visualization through the novel Multi-VISTA browser that we also present.
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paper_title: Mauve: Multiple alignment of conserved genomic sequence with rearrangements. Genome Res

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As genomes evolve, they undergo large-scale evolutionary processes that present a challenge to sequence comparison not posed by short sequences. Recombination causes frequent genome rearrangements, horizontal transfer introduces new sequences into bacterial chromosomes, and deletions remove segments of the genome. Consequently, each genome is a mosaic of unique lineage-specific segments, regions shared with a subset of other genomes and segments conserved among all the genomes under consideration. Furthermore, the linear order of these segments may be shuffled among genomes. We present methods for identification and alignment of conserved genomic DNA in the presence of rearrangements and horizontal transfer. Our methods have been implemented in a software package called Mauve. Mauve has been applied to align nine enterobacterial genomes and to determine global rearrangement structure in three mammalian genomes. We have evaluated the quality of Mauve alignments and drawn comparison to other methods through extensive simulations of genome evolution.
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paper_title: Genome sequence of the Brown Norway rat yields insights into mammalian evolution

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The laboratory rat (Rattus norvegicus) is an indispensable tool in experimental medicine and drug development, having made inestimable contributions to human health. We report here the genome sequence of the Brown Norway (BN) rat strain. The sequence represents a high-quality 'draft' covering over 90% of the genome. The BN rat sequence is the third complete mammalian genome to be deciphered, and three-way comparisons with the human and mouse genomes resolve details of mammalian evolution. This first comprehensive analysis includes genes and proteins and their relation to human disease, repeated sequences, comparative genome-wide studies of mammalian orthologous chromosomal regions and rearrangement breakpoints, reconstruction of ancestral karyotypes and the events leading to existing species, rates of variation, and lineage-specific and lineage-independent evolutionary events such as expansion of gene families, orthology relations and protein evolution.
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paper_title: Reconstructing an ancestral genome using minimum segments duplications and reversals

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We consider a particular model of genomic rearrangements that takes paralogous and orthologous genes into account. Given a particular model of evolution and an optimization criterion, the problem is to recover an ancestor of a modern genome modeled as an ordered sequence of signed genes. One direct application is to infer gene orders at the ancestral nodes of a phylogenetic tree.Implicit in the rearrangement literature is that each gene has exactly one copy in each genome. This hypothesis is clearly false for species containing several copies of highly paralogous genes, e.g. multigene families. One of the most important regional event by which gene duplication can occur has been referred to as duplication transposition. Our model of evolution takes such duplications into account. For a genome G with gene families of different sizes, the implicit hypothesis is that G has an ancestor containing exactly one copy of each gene, and that G has evolved from this ancestor through a series of duplication transpositions and substring reversals. The question is: how can we reconstruct an ancestral genome giving rise to the minimal number of duplication transpositions and reversals? The key idea is to reduce the problem to a series of subproblems involving genomes containing at most two copies of each gene. For this simpler version, we provide tight bounds, and we describe an algorithm, based on Hannenhalli and Pevzner graph and result, that is exact when certain conditions are verified. We then show how to use this algorithm to recover gene orders at the ancestral nodes of a phylogenetic tree.
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paper_title: A General Method Applicable to the Search for Similarities in the Amino Acid Sequence of Two Proteins

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A computer adaptable method for finding similarities in the amino acid sequences of two proteins has been developed. From these findings it is possible to determine whether significant homology exists between the proteins. This information is used to trace their possible evolutionary development. The maximum match is a number dependent upon the similarity of the sequences. One of its definitions is the largest number of amino acids of one protein that can be matched with those of a second protein allowing for all possible interruptions in either of the sequences. While the interruptions give rise to a very large number of comparisons, the method efficiently excludes from consideration those comparisons that cannot contribute to the maximum match. Comparisons are made from the smallest unit of significance, a pair of amino acids, one from each protein. All possible pairs are represented by a two-dimensional array, and all possible comparisons are represented by pathways through the array. For this maximum match only certain of the possible pathways must, be evaluated. A numerical value, one in this case, is assigned to every cell in the array representing like amino acids. The maximum match is the largest number that would result from summing the cell values of every
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paper_title: Glocal alignment : finding rearrangements during alignment

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Motivation: To compare entire genomes from different species, biologists increasingly need alignment methods that are efficient enough to handle long sequences, and accurate enough to correctly align the conserved biological features between distant species. The two main classes of pairwise alignments are global alignment, where one string is transformed into the other, and local alignment, where all locations of similarity between the two strings are returned. Global alignments are less prone to demonstrating false homology as each letter of one sequence is constrained to being aligned to only one letter of the other. Local alignments, on the other hand, can cope with rearrangements between non-syntenic, orthologous sequences by identifying similar regions in sequences; this, however, comes at the expense of a higher false positive rate due to the inability of local aligners to take into account overall conservation maps. Results: In this paper we introduce the notion of glocal alignment, a combination of global and local methods, where one creates a map that transforms one sequence into the other while allowing for rearrangement events. We present Shuffle-LAGAN, a glocal alignment algorithm that is based on the CHAOS local alignment algorithm and the LAGAN global aligner, and is able to align long genomic sequences. To test Shuffle-LAGAN we split the mouse genome into BAC-sized pieces, and aligned these pieces to the human genome. We demonstrate that ShuffleLAGAN compares favorably in terms of sensitivity and specificity with standard local and global aligners. From the alignments we conclude that about 9% of human/mouse homology may be attributed to small rearrangements, 63% of which are duplications. Availability: Our systems, supplemental information, and the alignment of the human and mouse genomes using ∗ To whom correspondence should be addressed.
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paper_title: Lengths of chromosomal segments conserved since divergence of man and mouse.

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Linkage relationships of homologous loci in man and mouse were used to estimate the mean length of autosomal segments conserved during evolution. Comparison of the locations of greater than 83 homologous loci revealed 13 conserved segments. Map distances between the outermost markers of these 13 segments are known for the mouse and range from 1 to 24 centimorgans. Methods were developed for using this sample of conserved segments to estimate the mean length of all conserved autosomal segments in the genome. This mean length was estimated to be 8.1 +/- 1.6 centimorgans. Evidence is presented suggesting that chromosomal rearrangements that determine the lengths of these segments are randomly distributed within the genome. The estimated mean length of conserved segments was used to predict the probability that certain loci, such as peptidase-3 and renin, are linked in man given that homologous loci are chi centimorgans apart in the mouse. The mean length of conserved segments was also used to estimate the number of chromosomal rearrangements that have disrupted linkage since divergence of man and mouse. This estimate was shown to be 178 +/- 39 rearrangements.
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paper_title: Chromosomal distributions of breakpoints in cancer, infertility, and evolution.

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We extract 11 genome-wide sets of breakpoint positions from databases on reciprocal translocations, inversions and deletions in neoplasms, reciprocal translocations and inversions in families carrying rearrangements and the human-mouse comparative map, and for each set of positions construct breakpoint distributions for the 44 autosomal arms. We identify and interpret four main types of distribution: (i) a uniform distribution associated both with families carrying translocations or inversions, and with the comparative map, (ii) telomerically skewed distributions of translocations or inversions detected consequent to births with malformations, (iii) medially clustered distributions of translocation and deletion breakpoints in tumor karyotypes, and (iv) bimodal translocation breakpoint distributions for chromosome arms containing telomeric proto-oncogenes.
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paper_title: Human and mouse genomic sequences reveal extensive breakpoint reuse in mammalian evolution

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The human and mouse genomic sequences provide evidence for a larger number of rearrangements than previously thought and reveal extensive reuse of breakpoints from the same short fragile regions. Breakpoint clustering in regions implicated in cancer and infertility have been reported in previous studies; we report here on breakpoint clustering in chromosome evolution. This clustering reveals limitations of the widely accepted random breakage theory that has remained unchallenged since the mid-1980s. The genome rearrangement analysis of the human and mouse genomes implies the existence of a large number of very short “hidden” synteny blocks that were invisible in the comparative mapping data and ignored in the random breakage model. These blocks are defined by closely located breakpoints and are often hard to detect. Our results suggest a model of chromosome evolution that postulates that mammalian genomes are mosaics of fragile regions with high propensity for rearrangements and solid regions with low propensity for rearrangements.
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paper_title: Hotspots of mammalian chromosomal evolution

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Background ::: Chromosomal evolution is thought to occur through a random process of breakage and rearrangement that leads to karyotype differences and disruption of gene order. With the availability of both the human and mouse genomic sequences, detailed analysis of the sequence properties underlying these breakpoints is now possible.
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paper_title: Human and mouse genomic sequences reveal extensive breakpoint reuse in mammalian evolution

paper_content:

The human and mouse genomic sequences provide evidence for a larger number of rearrangements than previously thought and reveal extensive reuse of breakpoints from the same short fragile regions. Breakpoint clustering in regions implicated in cancer and infertility have been reported in previous studies; we report here on breakpoint clustering in chromosome evolution. This clustering reveals limitations of the widely accepted random breakage theory that has remained unchallenged since the mid-1980s. The genome rearrangement analysis of the human and mouse genomes implies the existence of a large number of very short “hidden” synteny blocks that were invisible in the comparative mapping data and ignored in the random breakage model. These blocks are defined by closely located breakpoints and are often hard to detect. Our results suggest a model of chromosome evolution that postulates that mammalian genomes are mosaics of fragile regions with high propensity for rearrangements and solid regions with low propensity for rearrangements.
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paper_title: The Signal in the Genomes

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Nostra culpa. Not only did we foist a hastily conceived and incorrectly executed simulation on an overworked RECOMB conference program committee, but worse—nostra maxima culpa—we obliged a team of high-powered researchers to clean up after us! It was never our intention to introduce an alternative way of constructing synteny blocks; the so-called ST-synteny was only a (bungled) attempt to mimic Pevzner and Tesler's method, based on our reading or misreading of their paper [1]. Moreover, shortly after the conference, before preparing the full journal version of our article, we recognized through a back-of-an-envelope calculation that realistic values of the parameters in our simulations would not produce much increase in reuse rate. Consequently, our published article [2] develops only the main part of our communication, modeling and simulating the artifactual increase in reuse rates due to deleting synteny blocks but not that due to the construction of synteny blocks. ::: ::: Unfortunately, our makeshift work distracted from the main point of our communication. The theme in our full article [2], in the RECOMB extended abstract, and elsewhere is not substantially confronted in the recently published PLoS Computational Biology paper by Glenn Tesler and colleagues [3]. Wherever high rates of breakpoint reuse are inferred, whether they are due to bona fide reuse or rather to violations in the assumptions justifying the use of particular algorithms (relating to the construction of synteny blocks or their size thresholds, or to the unrealistically limited repertoire of rearrangement processes recognized by the algorithm), there is a correspondingly high rate of loss in the historical signal. ::: ::: While two genomes diverge without breakpoint reuse, the historical signal is conserved in the breakpoint graph, which consists entirely of four-vertex cycles, specifying exactly which pairs of breakpoints must be healed by reversals or translocations. As breakpoints are reused—as they eventually must be for finite gene orders, or for genomic sequence, where there are criteria for deciding when two breakpoints are too close together to be considered distinct—the four-vertex cycles are merged into larger structures, and the breakpoint graph becomes ambiguous concerning the rearrangements that produced it. The two divergent genomes eventually become randomized with respect to each other. But this randomization also occurs, even if divergence involves only distinct breakpoints, when the assumptions underlying the use of genome rearrangement algorithms are violated, which can happen in many possible ways [4,5]. And we cannot infer whether mutually randomized synteny block orderings derived from two divergent genomes were created through bona fide breakpoint reuse or rather through noise introduced in block construction or through processes other than reversal and translocation. ::: ::: I illustrate this point with data on the human/mouse comparison from Pevzner and Tesler's more detailed paper [6]. We simulated 100 pairs of genomes constructed of 22 and 19 human and mouse autosomes, with 270 blocks distributed exactly as in the human and mouse genomes, except that the blocks were randomly permuted and sign—or strandedness—was assigned randomly to each block. Permutations are within, not between, chromosomes, assuring a realistic reversals/translocations ratio. Output from the standard rearrangement algorithm [7] is summarized in Table 1. ::: ::: ::: ::: Table 1 ::: ::: Human/Mouse Comparison Resembles Randomized Genome Comparison ::: ::: ::: ::: The human/mouse comparison parallels the randomized genomes, and both deviate drastically from the hypothetical case of 270 blocks evolving without breakpoint reuse. There is an excess of 22 four-cycles and three other small cycles in the real data, largely due to reversals within concatenated blocks from a single chromosome in both human and mouse, largely dispersed in the randomized chromosomes. These 25 are what remains of the detailed evolutionary signal; they account for the small differences in distance, in breakpoint reuse, and in the total number of cycles. The giant cycles celebrated in Pevzner and Tesler's paper [6] and Tesler and colleagues' paper [3] have almost identical structure in the human/mouse and randomized comparisons. ::: ::: Note that in contrast to the autosomes, the rearrangement analysis of the human and mouse X chromosomes involves only short cycles, a breakpoint reuse rate close to 1.0 and a clear evolutionary signal. ::: ::: In conclusion, I take issue neither with Pevzner and Tesler's ingenious method for constructing synteny blocks nor with the notion that genomes are spatially heterogeneous in their susceptibility to rearrangement; many types of genomic regions, as reviewed in a previously published paper [5], have documented elevated rates of rearrangement. Nevertheless, a high reuse rate in the output of rearrangement algorithms, which simply indicates loss of signal, is not good evidence for fragile regions. The output of comparisons of randomized genomes has the same characteristics—namely, similar rearrangement distance, similar cycle/path sizes, similar number of chromosomes touched by each large cycle, similar reuse rates, and similar estimates [8] of the number of translocations and reversals.
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paper_title: Chromosomal Speciation and Molecular Divergence--Accelerated Evolution in Rearranged Chromosomes

paper_content:

Humans and their closest evolutionary relatives, the chimpanzees, differ in approximately 1.24% of their genomic DNA sequences. The fraction of these changes accumulated during the speciation processes that have separated the two lineages may be of special relevance in understanding the basis of their differences. We analyzed human and chimpanzee sequence data to search for the patterns of divergence and polymorphism predicted by a theoretical model of speciation. According to the model, positively selected changes should accumulate in chromosomes that present fixed structural differences, such as inversions, between the two species. Protein evolution was more than 2.2 times faster in chromosomes that had undergone structural rearrangements compared with colinear chromosomes. Also, nucleotide variability is slightly lower in rearranged chromosomes. These patterns of divergence and polymorphism may be, at least in part, the molecular footprint of speciation events in the human and chimpanzee lineages.
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paper_title: The Fragile Breakage versus Random Breakage Models of Chromosome Evolution

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For many years, studies of chromosome evolution were dominated by the random breakage theory, which implies that there are no rearrangement hot spots in the human genome. In 2003, Pevzner and Tesler argued against the random breakage model and proposed an alternative "fragile breakage" model of chromosome evolution. In 2004, Sankoff and Trinh argued against the fragile breakage model and raised doubts that Pevzner and Tesler provided any evidence of rearrangement hot spots. We investigate whether Sankoff and Trinh indeed revealed a flaw in the arguments of Pevzner and Tesler. We show that Sankoff and Trinh's synteny block identification algorithm makes erroneous identifications even in small toy examples and that their parameters do not reflect the realities of the comparative genomic architecture of human and mouse. We further argue that if Sankoff and Trinh had fixed these problems, their arguments in support of the random breakage model would disappear. Finally, we study the link between rearrangements and regulatory regions and argue that long regulatory regions and inhomogeneity of gene distribution in mammalian genomes may be responsible for the breakpoint reuse phenomenon.
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paper_title: Evolution's cauldron: duplication, deletion, and rearrangement in the mouse and human genomes.

paper_content:

This study examines genomic duplications, deletions, and rearrangements that have happened at scales ranging from a single base to complete chromosomes by comparing the mouse and human genomes. From whole-genome sequence alignments, 344 large (>100-kb) blocks of conserved synteny are evident, but these are further fragmented by smaller-scale evolutionary events. Excluding transposon insertions, on average in each megabase of genomic alignment we observe two inversions, 17 duplications (five tandem or nearly tandem), seven transpositions, and 200 deletions of 100 bases or more. This includes 160 inversions and 75 duplications or transpositions of length >100 kb. The frequencies of these smaller events are not substantially higher in finished portions in the assembly. Many of the smaller transpositions are processed pseudogenes; we define a "syntenic" subset of the alignments that excludes these and other small-scale transpositions. These alignments provide evidence that approximately 2% of the genes in the human/mouse common ancestor have been deleted or partially deleted in the mouse. There also appears to be slightly less nontransposon-induced genome duplication in the mouse than in the human lineage. Although some of the events we detect are possibly due to misassemblies or missing data in the current genome sequence or to the limitations of our methods, most are likely to represent genuine evolutionary events. To make these observations, we developed new alignment techniques that can handle large gaps in a robust fashion and discriminate between orthologous and paralogous alignments.
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paper_title: Chromosomal breakpoint reuse in genome sequence rearrangement

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In order to apply gene-order rearrangement algorithms to the comparison of genome sequences, Pevzner and Tesler bypass gene finding and ortholog identification and use the order of homologous blocks of unannotated sequence as input. The method excludes blocks shorter than a threshold length. Here we investigate possible biases introduced by eliminating short blocks, focusing on the notion of breakpoint reuse introduced by these authors. Analytic and simulation methods show that reuse is very sensitive to the proportion of blocks excluded. As is pertinent to the comparison of mammalian genomes, this exclusion risks randomizing the comparison partially or entirely.
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paper_title: Genomic features in the breakpoint regions between syntenic blocks

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MOTIVATION ::: We study the largely unaligned regions between the syntenic blocks conserved in humans and mice, based on data extracted from the UCSC genome browser. These regions contain evolutionary breakpoints caused by inversion, translocation and other processes. ::: ::: ::: RESULTS ::: We suggest explanations for the limited amount of genomic alignment in the neighbourhoods of breakpoints. We discount inferences of extensive breakpoint reuse as artefacts introduced during the reconstruction of syntenic blocks. We find that the number, size and distribution of small aligned fragments in the breakpoint regions depend on the origin of the neighbouring blocks and the other blocks on the same chromosome. We account for this and for the generalized loss of alignment in the regions partially by artefacts due to alignment protocols and partially by mutational processes operative only after the rearrangement event. These results are consistent with breakpoints occurring randomly over virtually the entire genome.
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paper_title: Molecular mechanisms for constitutional chromosomal rearrangements in humans.

paper_content:

Cytogenetic imbalance in the newborn is a frequent cause of mental retardation and birth defects. Although aneuploidy accounts for the majority of imbalance, structural aberrations contribute to a significant fraction of recognized chromosomal anomalies. This review describes the major classes of constitutional, structural cytogenetic abnormalities and recent studies that explore the molecular mechanisms that bring about their de novo occurrence. Genomic features flanking the sites of recombination may result in susceptibility to chromosomal rearrangement. One such substrate for recombination is low-copy region-specific repeats. The identification of genome architectural features conferring susceptibility to rearrangements has been accomplished using methods that enable investigation of regions of the genome that are too small to be visualized by traditional cytogenetics and too large to be resolved by conventional gel electrophoresis. These investigations resulted in the identification of previously unrecognized structural cytogenetic anomalies, which are associated with genetic syndromes and allowed for the molecular basis of some chromosomal rearrangements to be delineated.
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paper_title: Segmental duplications and the evolution of the primate genome

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Initial human genome sequence analysis has revealed large segments of nearly identical sequence in particular chromosomal regions. The recent origin of these segments and their abundance (∼5%) has challenged investigators to elucidate their underlying mechanism and role in primate genome evolution. Although the precise fraction is unknown, some of these duplicated segments have recently been shown to be associated with rapid gene innovation and chromosomal rearrangement in the genomes of man and the great apes.
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paper_title: Murine segmental duplications are hot spots for chromosome and gene evolution

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Mouse and rat genomic sequences permit us to obtain a global view of evolutionary rearrangements that have occurred between the two species and to define hallmarks that might underlie these events. We present a comparative study of the sequence assemblies of mouse and rat genomes and report an enrichment of rodent-specific segmental duplications in regions where synteny is not preserved. We show that segmental duplications present higher rates of molecular evolution and that genes in rearranged regions have evolved faster than those located elsewhere. Previous studies have shown that synteny breakpoints between the mouse and the human genomes are enriched in human segmental duplications, suggesting a causative connection between such structures and evolutionary rearrangements. Our work provides further evidence to support the role of segmental duplications in chromosomal rearrangements in the evolution of the architecture of mammalian chromosomes and in the speciation processes that separate the mouse and the rat.
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paper_title: Enrichment of segmental duplications in regions of breaks of synteny between the human and mouse genomes suggest their involvement in evolutionary rearrangements.

paper_content:

The sequence of the mouse genome allows one to compare the conservation of synteny between the human and mouse genome and exploration of regions that might have been involved in major rearrangements during the evolution of these two species (evolutionary genome rearrangements). Recent segmental duplications (or duplicons) are paralogous DNA sequences with high sequence identity that account for about 3.5-5% of the human genome and have emerged during the past approximately 35 million years of evolution. These regions are susceptible to illegitimate recombination leading to rearrangements that result in genomic disorders or genomic mutations. A catalogue of several hundred segmental duplications potentially leading to genomic rearrangements has been reported. The authors and others have observed that some chromosome regions involved in genomic disorders are shuffled in orientation and order in the mouse genome and that regions flanked by segmental duplications are often polymorphic. We have compared the human and mouse genome sequences and demonstrate here that recent segmental duplications correlate with breaks of synteny between these two species. We also observed that nine primary regions involved in human genomic disorders show changes in the order or the orientation of mouse/human synteny segments, were often flanked by segmental duplications in the human sequence. We found that 53% of all evolutionary rearrangement breakpoints associate with segmental duplications, as compared with 18% expected in a random location of breaks along the chromosome (P<0.0001). Our data suggest that segmental duplications have participated in the recent evolution of the human genome, as driving forces for evolutionary rearrangements, chromosome structure polymorphisms and genomic disorders.
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paper_title: Structure of chromosomal duplicons and their role in mediating human genomic disorders.

paper_content:

Chromosome-specific low-copy repeats, or duplicons, occur in multiple regions of the human genome. Homologous recombination between different duplicon copies leads to chromosomal rearrangements, such as deletions, duplications, inversions, and inverted duplications, depending on the orientation of the recombining duplicons. When such rearrangements cause dosage imbalance of a developmentally important gene(s), genetic diseases now termed genomic disorders result, at a frequency of 0.7-1/1000 births. Duplicons can have simple or very complex structures, with variation in copy number from 2 to >10 repeats, and each varying in size from a few kilobases in length to hundreds of kilobases. Analysis of the different duplicons involved in human genomic disorders identifies features that may predispose to recombination, including large size and high sequence identity between the recombining copies, putative recombination promoting features, and the presence of multiple genes/pseudogenes that may include genes expressed in germ cells. Most of the chromosome rearrangements involve duplicons near pericentromeric regions, which may relate to the propensity of such regions to accumulate duplicons. Detailed analyses of the structure, polymorphic variation, and mechanisms of recombination in genomic disorders, as well as the evolutionary origin of various duplicons will further our understanding of the structure, function, and fluidity of the human genome.
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paper_title: Dynamics of Mammalian Chromosome Evolution Inferred from Multispecies Comparative Maps

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The genome organizations of eight phylogenetically distinct species from five mammalian orders were compared in order to address fundamental questions relating to mammalian chromosomal evolution. Rates of chromosome evolution within mammalian orders were found to increase since the Cretaceous-Tertiary boundary. Nearly 20% of chromosome breakpoint regions were reused during mammalian evolution; these reuse sites are also enriched for centromeres. Analysis of gene content in and around evolutionary breakpoint regions revealed increased gene density relative to the genome-wide average. We found that segmental duplications populate the majority of primate-specific breakpoints and often flank inverted chromosome segments, implicating their role in chromosomal rearrangement.
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paper_title: Recent duplication, domain accretion and the dynamic mutation of the human genome

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An estimated 5% of the human genome consists of interspersed duplications that have arisen over the past 35 million years of evolution. Two categories of such recently duplicated segments can be distinguished: segmental duplications between nonhomologous chromosomes (transchromosomal duplications) and duplications mainly restricted to a particular chromosome (chromosome-specific duplications). Many of these duplications exhibit an extraordinarily high degree of sequence identity at the nucleotide level (>95%) and span large genomic distances (1–100 kb). Preliminary analyses indicate that these same regions are targets for rapid evolutionary turnover among the genomes of closely related primates. The dynamic nature of these regions because of recurrent chromosomal rearrangement, and their ability to create fusion genes from juxtaposed cassettes suggest that duplicative transposition was an important force in the evolution of our genome.
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paper_title: Hotspots of mammalian chromosomal evolution

paper_content:

Background ::: Chromosomal evolution is thought to occur through a random process of breakage and rearrangement that leads to karyotype differences and disruption of gene order. With the availability of both the human and mouse genomic sequences, detailed analysis of the sequence properties underlying these breakpoints is now possible.
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paper_title: Pathological consequences of sequence duplications in the human genome.

paper_content:

As large-scale sequencing accumulates momentum, an increasing number of instances are being revealed in which genes or other relatively rare sequences are duplicated, either in tandem or at nearby locations. Such duplications are a source of considerable polymorphism in populations, and also increase the evolutionary possibilities for the coregulation of juxtaposed sequences. As a further consequence, they promote inversions and deletions that are responsible for significant inherited pathology. Here we review known examples of genomic duplications present on the human X chromosome and autosomes.
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paper_title: Molecular-evolutionary mechanisms for genomic disorders

paper_content:

Molecular studies of unstable regions in the human genome have identified region-specific low-copy repeats (LCRs). Unlike highly repetitive sequences (e.g. Alus and LINEs), LCRs are usually of 10–400 kb in size and exhibit ≥ 95–97% similarity. According to computer analyses of available sequencing data, LCRs may constitute >5% of the human genome. Through the process of non-allelic homologous recombination using paralogous genomic segments as substrates, LCRs have been shown to facilitate meiotic DNA rearrangements associated with disease traits, referred to as genomic disorders. In addition, this LCR-based complex genome architecture appears to play a major role in both primate karyotype evolution and human tumorigenesis.
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paper_title: Fourfold Faster Rate of Genome Rearrangement in Nematodes Than in Drosophila

paper_content:

The genes of Caenorhabditis elegans appear to have an unusually rapid rate of evolution. The substitution rates of many C. elegans genes are twice those of their orthologs in non-nematode metazoans (Aguinaldo et al. 1997; see Fig. 3 in Mushegian et al. 1998). Even among nematodes, the C. elegans small subunit ribosomal RNA gene evolves faster than its orthologs in most of the major clades (see Fig. 1 in Blaxter et al. 1998). It has been estimated that two-thirds of C. elegans protein-coding genes evolve more rapidly than their Drosophila orthologs (Mushegian et al. 1998). In vertebrates at least, the rate of nucleotide substitution is correlated with that of chromosomal rearrangement (Burt et al. 1999). ::: ::: Ranz et al. (2001) reported that Drosophila chromosomes rearrange at least 175 times faster than those of other metazoans, and at a rate at least five times greater than the rate of the fastest plant genomes. However, no Caenorhabditis rate data existed to compare with the Drosophila data. Given their fast rate of nucleotide substitution, we guessed that Caenorhabditis genomes might have a fast rate of rearrangement. Here, we have estimated the rate of rearrangement since the divergence of C. elegans from its sister species Caenorhabditis briggsae, using the complete C. elegans genome sequence (The C. elegans Sequencing Consortium 1998) and 13 Mb of sequence from C. briggsae released by the Washington University Genome Sequencing Center (http://genome.wustl.edu/gsc/). Previous studies have shown that C. elegans and C. briggsae have conservation of gene order over stretches of chromosome that can be up to six genes long (Kuwabara and Shah 1994; Thacker et al. 1999). ::: ::: To calculate the rate, we estimated the number of chromosomal rearrangements since the speciation of C. elegans and C. briggsae. Because both species have six chromosomes (Nigon and Dougherty 1949), we assumed that there have not been any fusions or fissions of whole chromosomes since they diverged. Kececioglu and Ravi (1995) and Hannenhalli (1996) have developed computer algorithms that deduce the historical order and sizes of the reciprocal translocations (whereby two nonhomologous chromosomes exchange chunks of DNA by recombination) and/or inversions that have occurred since the divergence of two multichromosomal genomes. However, the C. elegans genome evolves not only by reciprocal translocations and inversions, but also by transpositions (whereby a chunk of DNA excises from one chromosome and inserts into a nonhomologous chromosome) and duplications (Robertson 2001). We designed a simple algorithm to calculate the number and sizes of such mutations, although not the order in which they occurred. Our method starts by finding all perfectly conserved segments between two species, in which gene content, order, and orientation are conserved. Next, these segments are fused into larger segments that have been splintered by duplications, inversions, or transpositions. When no more segments can be merged, the final fused segments are assumed to have resulted from fissure of chromosomes by reciprocal translocations. ::: ::: To convert the observed number of rearrangements into a rate, it is necessary to have an accurate estimate of the briggsae–elegans divergence date. Emmons et al. (1979) were the first to estimate this date, using restriction fragment data, venturing that it must be “tens of millions of years” ago. Butler et al. (1981) speculated that the date was 10–100 million years ago (Mya), judging from 5S rRNA sequences, anatomical differences, and protein electrophoretic mobilities. Subsequent estimates based on sequence data were 30–60 Mya (Prasad and Baillie 1989; one gene), 23–32 Mya (Heschl and Baillie 1990; one gene), 54–58 Mya (Lee et al. 1992; two genes), and 40 Mya (Kennedy et al. 1993; seven genes). Nematode fossils are extremely scarce (Poinar 1983). Therefore, to calibrate the molecular clock, these studies either assumed that all organisms have the same silent substitution rate (Prasad and Baillie 1989; Heschl and Baillie 1990) or nonsilent substitution rate (Lee et al. 1992), or that C. elegans has the same silent rate as Drosophila (Kennedy et al. 1993). These are dubious assumptions; for example, Mushegian et al. (1998) showed that about two-thirds of C. elegans genes have a higher rate of nonsilent substitution than their orthologs in Drosophila. To gain a more reliable interval estimate of the briggsae–elegans speciation date, we used phylogenetic analysis of all genes for which orthologous sequences were available from C. elegans, C. briggsae, Drosophila, and human. Only those genes that did not have a significantly different amino acid substitution rate in the four taxa were used to produce date estimates. ::: ::: The briggsae–elegans sequence data set is the largest available for any pair of congeneric eukaryotes. Such a big sample has a high power for detecting genome-wide trends. For example, the breakpoints of reciprocal translocations and inversions are frequently near repetitive DNA. This has been observed in bacteria (Romero et al. 1999), yeast (Fischer et al. 2000), insects (Caceres et al. 1999), mammals (Dehal et al. 2001), and plants (Zhang and Peterson 1999), but not yet in nematodes. Rearrangements near transposable elements may happen when the element is transposing (Zhang and Peterson 1999), but most rearrangements are hypothesized to occur by homologous recombination between nontransposing transposable elements, dispersed repeats, or gene family members. We find that translocation and transposition breakpoints are strongly associated with repeats in the C. elegans genome.
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paper_title: Genomic rearrangements by LINE-1 insertion-mediated deletion in the human and chimpanzee lineages

paper_content:

Long INterspersed Elements (LINE-1s or L1s) are abundant non-LTR retrotransposons in mammalian genomes that are capable of insertional mutagenesis. They have been associated with target site deletions upon insertion in cell culture studies of retrotransposition. Here, we report 50 deletion events in the human and chimpanzee genomes directly linked to the insertion of L1 elements, resulting in the loss of � 18 kb of sequence from the human genome and � 15 kb from the chimpanzee genome. Our data suggest that during the primate radiation, L1 insertions may have deleted up to 7.5 Mb of target genomic sequences. While the results of our in vivo analysis differ from those of previous cell culture assays of L1 insertion-mediated deletions in terms of the size and rate of sequence deletion, evolutionary factors can reconcile the differences. We report a pattern of genomic deletion sizes similar to those created during the retrotransposition of Alu elements. Our study provides support for the existence of different mechanisms for small and large L1mediated deletions, and we present a model for the correlation of L1 element size and the corresponding deletion size. In addition, we show that internal rearrangements can modify L1 structure during retrotransposition events associated with large deletions.
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paper_title: Human Chromosome 19 and Related Regions in Mouse: Conservative and Lineage-Specific Evolution

paper_content:

To illuminate the function and evolutionary history of both genomes, we sequenced mouse DNA related to human chromosome 19. Comparative sequence alignments yielded confirmatory evidence for hypothetical genes and identified exons, regulatory elements, and candidate genes that were missed by other predictive methods. Chromosome-wide comparisons revealed a difference between single-copy HSA19 genes, which are overwhelmingly conserved in mouse, and genes residing in tandem familial clusters, which differ extensively in number, coding capacity, and organization between the two species. Finally, we sequenced breakpoints of all 15 evolutionary rearrangements, providing a view of the forces that drive chromosome evolution in mammals.
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paper_title: Response to Comment on "Chromosomal Speciation and Molecular Divergence-Accelerated Evolution in Rearranged Chromosomes"

paper_content:

By clever use of outgroups, Lu et al . ([ 1 ][1]) tackle some of the questions raised by Navarro and Barton ([ 2 ][2]). Beyond confirming the previous result that rapidly evolving genes tend to be associated with chromosomes that have been rearranged between humans and chimpanzees ([ 2 ][2]), Lu et
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paper_title: Murine segmental duplications are hot spots for chromosome and gene evolution

paper_content:

Mouse and rat genomic sequences permit us to obtain a global view of evolutionary rearrangements that have occurred between the two species and to define hallmarks that might underlie these events. We present a comparative study of the sequence assemblies of mouse and rat genomes and report an enrichment of rodent-specific segmental duplications in regions where synteny is not preserved. We show that segmental duplications present higher rates of molecular evolution and that genes in rearranged regions have evolved faster than those located elsewhere. Previous studies have shown that synteny breakpoints between the mouse and the human genomes are enriched in human segmental duplications, suggesting a causative connection between such structures and evolutionary rearrangements. Our work provides further evidence to support the role of segmental duplications in chromosomal rearrangements in the evolution of the architecture of mammalian chromosomes and in the speciation processes that separate the mouse and the rat.
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paper_title: Chromosomal Speciation and Molecular Divergence--Accelerated Evolution in Rearranged Chromosomes

paper_content:

Humans and their closest evolutionary relatives, the chimpanzees, differ in approximately 1.24% of their genomic DNA sequences. The fraction of these changes accumulated during the speciation processes that have separated the two lineages may be of special relevance in understanding the basis of their differences. We analyzed human and chimpanzee sequence data to search for the patterns of divergence and polymorphism predicted by a theoretical model of speciation. According to the model, positively selected changes should accumulate in chromosomes that present fixed structural differences, such as inversions, between the two species. Protein evolution was more than 2.2 times faster in chromosomes that had undergone structural rearrangements compared with colinear chromosomes. Also, nucleotide variability is slightly lower in rearranged chromosomes. These patterns of divergence and polymorphism may be, at least in part, the molecular footprint of speciation events in the human and chimpanzee lineages.
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paper_title: Effects of chromosomal rearrangements on human-chimpanzee molecular evolution

paper_content:

Many chromosomes are rearranged between humans and chimpanzees while others remain colinear. It was recently observed, based on over 100 genes, that the rates of protein evolution are substantially higher on rearranged than on colinear chromosomes during human-chimpanzee evolution. This finding led to the conclusion, since debated in the literature, that chromosomal rearrangements had played a key role in human-chimpanzee speciation. Here we re-examine this important conclusion by employing larger a data set (over 7000 genes), as well as alternative analyses. We show that the higher rates of protein evolution on rearranged chromosomes observed in the earlier study are not reproduced by our survey of the larger data set. We further show that the conclusion of the earlier study is likely confounded by two factors introduced by the relatively limited sample size: (1) nonuniform distribution of genes in the genome, and (2) stochastic noise in substitution rates inherent to short lineages such as the human-chimpanzee lineage. Our results offer a general cautionary note on the importance of controlling for hidden factors in studies involving bioinformatic surveys.
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paper_title: Chromosomal rearrangements are associated with higher rates of molecular evolution in mammals.

paper_content:

Abstract Evolutionary rates are not uniformly distributed across the genome. Knowledge about the biological causes of this observation is still incomplete, but its exploration has provided valuable insight into the genomical, historical and demographical variables that influence rates of genetic divergence. Recent studies suggest a possible association between chromosomal rearrangements and regions of greater divergence, but evidence is limited and contradictory. Here, we test the hypothesis of a relationship between chromosomal rearrangements and higher rates of molecular evolution by studying the genomic distribution of divergence between 12 000 human–mouse orthologous genes. Our results clearly show that genes located in genomic regions that have been highly rearranged between the two species present higher rates of synonymous (0.7686 vs. 0.7076) and non-synonymous substitution (0.1014 vs. 0.0871), and that synonymous substitution rates are higher in genes close to the breakpoints of individual rearrangements. The many potential causes of such striking are discussed, particularly in the light of speciation models suggesting that chromosomal rearrangements may have contributed to some of the speciation processes along the human and mouse lineages. Still, there are other possible causes and further research is needed to properly explore them.
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paper_title: The molecular basis of common and rare fragile sites.

paper_content:

Fragile sites are specific loci that form gaps and constrictions on chromosomes exposed to partial replication stress. Fragile sites are classified as rare or common, depending on their induction and frequency within the population. These loci are known to be involved in chromosomal rearrangements in tumors and are associated with human diseases. Therefore, the understanding of the molecular basis of fragile sites is of high significance. Here we discuss the works performed in recent years that investigated the characteristics of fragile sites which underlie their inherent instability.
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paper_title: Evolutionary conserved chromosomal segments in the human karyotype are bounded by unstable chromosome bands

paper_content:

In this paper an ancestral karyotype for primates, defining for the first time the ancestral chromosome morphology and the banding patterns, is proposed, and the ancestral syntenic chromosomal segments are identified in the human karyotype. The chromosomal bands that are boundaries of ancestral segments are identified. We have analyzed from data published in the literature 35 different primate species from 19 genera, using the order Scandentia, as well as other published mammalian species as out-groups, and propose an ancestral chromosome number of 2n = 54 for primates, which includes the following chromosomal forms: 1(a+c(1)), 1(b+c(2)), 2a, 2b, 3/21, 4, 5, 6, 7a, 7b, 8, 9, 10a, 10b, 11, 12a/22a, 12b/22b, 13, 14/15, 16a, 16b, 17, 18, 19a, 19b, 20 and X and Y. From this analysis, we have been able to point out the human chromosome bands more "prone" to breakage during the evolutionary pathways and/or pathology processes. We have observed that 89.09% of the human chromosome bands, which are boundaries for ancestral chromosome segments, contain common fragile sites and/or intrachromosomal telomeric-like sequences. A more in depth analysis of twelve different human chromosomes has allowed us to determine that 62.16% of the chromosomal bands implicated in inversions and 100% involved in fusions/fissions correspond to fragile sites, intrachromosomal telomeric-like sequences and/or bands significantly affected by X irradiation. In addition, 73% of the bands affected in pathological processes are co-localized in bands where fragile sites, intrachromosomal telomeric-like sequences, bands significantly affected by X irradiation and/or evolutionary chromosomal bands have been described. Our data also support the hypothesis that chromosomal breakages detected in pathological processes are not randomly distributed along the chromosomes, but rather concentrate in those important evolutionary chromosome bands which correspond to fragile sites and/or intrachromosomal telomeric-like sequences.
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paper_title: Fragile Sites in Human and Macaca Fascicularis Chromosomes are Breakpoints in Chromosome Evolution

paper_content:

We have analysed the expression of aphidicolin-induced common fragile sites at two different aphidicolin concentrations (0.1 µmol/L and 0.2 µmol/L) in three female and one male crab-eating macaques (Macaca fascicularis, Cercopithecidae, Catarrhini). A total of 3948 metaphases were analysed: 1754 in cultures exposed to 0.1 µmol/L aphidicolin, 1261 in cultures exposed to 0.2 µmol/L aphidicolin and 933 in controls. The number of breaks and gaps detected ranged from 439 in cultures exposed to 0.1 µmol/L aphidicolin to 2061 in cultures exposed to 0.2 µmol/L aphidicolin. The use of a multinomial FSM statistical model allowed us to identify 95 fragile sites in the chromosomes of M. fascicularis, of which only 16 are expressed in all four specimens. A comparative study between the chromosomes of M. fascicularis and man has demonstrated that 38 human common fragile sites (50%) are found in the equivalent location in M. fascicularis. The analysis of the rearrangements that have taken place during chromosome evolution has revealed that the breakpoints involved in these rearrangements correspond significantly (p < 0.025) to the location of M. fascicularis fragile sites.
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paper_title: Evolutionary breakpoints are co-localized with fragile sites and intrachromosomal telomeric sequences in primates

paper_content:

The concentration of evolutionary breakpoints in primate karyotypes in some particular regions or chromosome bands suggests that these chromosome regions are more prone to breakage. This is the first extensive comparative study which investigates a possible relationship of two genetic markers (intrachromosomal telomeric sequences [TTAGGG]n, [ITSs] and fragile sites [FSs]), which are implicated in the evolutionary process as well as in chromosome rearrangements. For this purpose, we have analyzed: (a) the cytogenetic expression of aphidicolin-induced FSs in Cebus apella and Cebus nigrivittatus (F. Cebidae, Platyrrhini) and Mandrillus sphinx (F. Cercopithecidae, Catarrhini), and (b) the intrachromosomal position of telomeric-like sequences by FISH with a synthetic (TTAGGG)n probe in C. apella chromosomes. The multinomial FSM statistical model allowed us to determinate 53 FSs in C. apella, 16 FSs in C. nigrivittatus and 50 FSs in M. sphinx. As expected, all telomeres hybridized with the probe, and 55 intrachromosomal loci were also detected in the Cebus apella karyotype. The chi(2) test indicates that the coincidence of the location of Cebus and Mandrillus FSs with the location of human FSs is significant (P < 0.005). Based on a comparative cytogenetic study among different primate species we have identified (or described) the chromosome bands in the karyotypes of Papionini and Cebus species implicated in evolutionary reorganizations. More than 80% of these evolutionary breakpoints are located in chromosome bands that express FSs and/or contain ITSs.
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paper_title: Translocation and gross deletion breakpoints in human inherited disease and cancer II: Potential involvement of repetitive sequence elements in secondary structure formation between DNA ends

paper_content:

Translocations and gross deletions are responsible for a significant proportion of both cancer and inherited disease. Although such gene rearrangements are nonuniformly distributed in the human genome, the underlying mutational mechanisms remain unclear. We have studied the potential involvement of various types of repetitive sequence elements in the formation of secondary structure intermediates between the single-stranded DNA ends that recombine during rearrangements. Complexity analysis was used to assess the potential of these ends to form secondary structures, the maximum decrease in complexity consequent to a gross rearrangement being used as an indicator of the type of repeat and the specific DNA ends involved. A total of 175 pairs of deletion/translocation breakpoint junction sequences available from the Gross Rearrangement Breakpoint Database [GRaBD; www.uwcm.ac.uk/uwcm/mg/grabd/grabd.html] were analyzed. Potential secondary structure was noted between the 5' flanking sequence of the first breakpoint and the 3' flanking sequence of the second breakpoint in 49% of rearrangements and between the 5' flanking sequence of the second breakpoint and the 3' flanking sequence of the first breakpoint in 36% of rearrangements. Inverted repeats, inversions of inverted repeats, and symmetric elements were found in association with gross rearrangements at approximately the same frequency. However, inverted repeats and inversions of inverted repeats accounted for the vast majority (83%) of deletions plus small insertions, symmetric elements for one-half of all antigen receptor-mediated translocations, while direct repeats appear only to be involved in mediating simple deletions. These findings extend our understanding of illegitimate recombination by highlighting the importance of secondary structure formation between single-stranded DNA ends at breakpoint junctions.
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paper_title: Non-B DNA conformations, genomic rearrangements, and human disease

paper_content:

The history of investigations on non-B DNA conformations as related to genetic diseases dates back to the mid-1960s. Studies with high molecular weight DNA polymers of defined repeating nucleotide sequences demonstrated the role of sequence in their properties and conformations (1). Investigations with repeating homo-, di-, tri-, and tetranucleotide repeating motifs revealed the powerful role of sequence in molecular behaviors. At that time, this concept was heretical because numerous prior investigations with naturally occurring DNA sequences masked the effect of sequence (1). It may be noted that these studies in the 1960s predated DNA sequencing by at least a decade. Early studies were followed by a number of innovative discoveries on DNA conformational features in synthetic oligomers, restriction fragments, and recombinant DNAs. The DNA polymorphisms were a function of sequence, topology (supercoil density), ionic conditions, protein binding, methylation, carcinogen binding, and other factors (2). A number of non-B DNA structures have been discovered (approximately one new conformation every 3 years for the past 35 years) and include the following: triplexes, left-handed DNA, bent DNA, cruciforms, nodule DNA, flexible and writhed DNA, G4 tetrad (tetraplexes), slipped structures, and sticky DNA (Fig. 1). From the outset, it was realized (1, 2) that these sequence effects probably have profound biological implications, and indeed their role in transcription (3) and in the maintenance of telomere ends (4) has recently been reviewed. However, in the past few years dramatic advances from genomics, human genetics, medicine, and DNA structural biology have revealed the role of non-B conformations in the etiology of at least 46 human genetic diseases (Table I) that involve genomic rearrangements as well as other types of mutation events.
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paper_title: Breakpoints of gross deletions coincide with non-B DNA conformations.

paper_content:

Genomic rearrangements are a frequent source of instability, but the mechanisms involved are poorly understood. A 2.5-kbp poly(purine.pyrimidine) sequence from the human PKD1 gene, known to form non-B DNA structures, induced long deletions and other instabilities in plasmids that were mediated by mismatch repair and, in some cases, transcription. The breakpoints occurred at predicted non-B DNA structures. Distance measurements also indicated a significant proximity of alternating purine-pyrimidine and oligo(purine.pyrimidine) tracts to breakpoint junctions in 222 gross deletions and translocations, respectively, involved in human diseases. In 11 deletions analyzed, breakpoints were explicable by non-B DNA structure formation. We conclude that alternative DNA conformations trigger genomic rearrangements through recombination-repair activities.
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paper_title: Translocation and gross deletion breakpoints in human inherited disease and cancer I: Nucleotide composition and recombination-associated motifs

paper_content:

Translocations and gross deletions are important causes of both cancer and inherited disease. Such gene rearrangements are nonrandomly distributed in the human genome as a consequence of selection for growth advantage and/or the inherent potential of some DNA sequences to be frequently involved in breakage and recombination. Using the Gross Rearrangement Breakpoint Database [GRaBD; www.uwcm.ac.uk/uwcm/mg/grabd/grabd.html] (containing 397 germ-line and somatic DNA breakpoint junction sequences derived from 219 different rearrangements underlying human inherited disease and cancer), we have analyzed the sequence context of translocation and deletion breakpoints in a search for general characteristics that might have rendered these sequences prone to rearrangement. The oligonucleotide composition of breakpoint junctions and a set of reference sequences, matched for length and genomic location, were compared with respect to their nucleotide composition. Deletion breakpoints were found to be AT-rich whereas by comparison, translocation breakpoints were GC-rich. Alternating purine-pyrimidine sequences were found to be significantly over-represented in the vicinity of deletion breakpoints while polypyrimidine tracts were over-represented at translocation breakpoints. A number of recombination-associated motifs were found to be over-represented at translocation breakpoints (including DNA polymerase pause sites/frameshift hotspots, immunoglobulin heavy chain class switch sites, heptamer/nonamer V(D)J recombination signal sequences, translin binding sites, and the χ element) but, with the exception of the translin-binding site and immunoglobulin heavy chain class switch sites, none of these motifs were over-represented at deletion breakpoints. Alu sequences were found to span both breakpoints in seven cases of gross deletion that may thus be inferred to have arisen by homologous recombination. Our results are therefore consistent with a role for homologous unequal recombination in deletion mutagenesis and a role for nonhomologous recombination in the generation of translocations. Hum Mutat 22:229–244, 2003. © 2003 Wiley-Liss, Inc.
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paper_title: Dynamics of Mammalian Chromosome Evolution Inferred from Multispecies Comparative Maps

paper_content:

The genome organizations of eight phylogenetically distinct species from five mammalian orders were compared in order to address fundamental questions relating to mammalian chromosomal evolution. Rates of chromosome evolution within mammalian orders were found to increase since the Cretaceous-Tertiary boundary. Nearly 20% of chromosome breakpoint regions were reused during mammalian evolution; these reuse sites are also enriched for centromeres. Analysis of gene content in and around evolutionary breakpoint regions revealed increased gene density relative to the genome-wide average. We found that segmental duplications populate the majority of primate-specific breakpoints and often flank inverted chromosome segments, implicating their role in chromosomal rearrangement.
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paper_title: The Evolutionary Chromosome Translocation 4;19 in Gorilla gorilla is Associated with Microduplication of the Chromosome Fragment Syntenic to Sequences Surrounding the Human Proximal CMT1A-REP

paper_content:

Many genomic disorders occur as a result of chromosome rearrangements involving low-copy repeats (LCRs). To better understand the molecular basis of chromosome rearrangements, including translocations, we have investigated the mechanism of evolutionary rearrangements. In contrast to several intrachromosomal rearrangements, only two evolutionary translocations have been identified by cytogenetic analyses of humans and greater apes. Human chromosome 2 arose as a result of a telomeric fusion between acrocentric chromosomes, whereas chromosomes 4 and 19 in Gorilla gorilla are the products of a reciprocal translocation between ancestral chromosomes, syntenic to human chromosomes 5 and 17, respectively. Fluorescence in situ hybridization (FISH) was used to characterize the breakpoints of the latter translocation at the molecular level. We identified three BAC clones that span translocation breakpoints. One breakpoint occurred in the region syntenic to human chromosome 5q13.3, between the HMG-CoA reductase gene (HMGCR) and RAS p21 protein activator 1 gene (RASA1). The second breakpoint was in a region syntenic to human chromosome 17p12 containing the 24 kb region-specific low-copy repeat-proximal CMT1A-REP. Moreover, we found that the t(4;19) is associated with a submicroscopic chromosome duplication involving a 19p chromosome fragment homologous to the human chromosome region surrounding the proximal CMT1A-REP. These observations further indicate that higher order genomic architecture involving low-copy repeats resulting from genomic duplication plays a significant role in karyotypic evolution.
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paper_title: Molecular Characterization of the Pericentric Inversion That Causes Differences Between Chimpanzee Chromosome 19 and Human Chromosome 17

paper_content:

A comparison of the human genome with that of the chimpanzee is an attractive approach to attempts to understand the specificity of a certain phenotype's development. The two karyotypes differ by one chromosome fusion, nine pericentric inversions, and various additions of heterochromatin to chromosomal telomeres. Only the fusion, which gave rise to human chromosome 2, has been characterized at the sequence level. During the present study, we investigated the pericentric inversion by which chimpanzee chromosome 19 differs from human chromosome 17. Fluorescence in situ hybridization was used to identify breakpoint-spanning bacterial artificial chromosomes (BACs) and plasmid artificial chromosomes (PACs). By sequencing the junction fragments, we localized breakpoints in intergenic regions rich in repetitive elements. Our findings suggest that repeat-mediated nonhomologous recombination has facilitated inversion formation. No addition or deletion of any sequence element was detected at the breakpoints or in the surrounding sequences. Next to the break, at a distance of 10.2-39.1 kb, the following genes were found: NGFR and NXPH3 (on human chromosome 17q21.3) and GUC2D and ALOX15B (on human chromosome 17p13). The inversion affects neither the genomic structure nor the gene-activity state with regard to replication timing of these genes.
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paper_title: Molecular characterisation of the pericentric inversion that distinguishes human chromosome 5 from the homologous chimpanzee chromosome

paper_content:

Human and chimpanzee karyotypes differ by virtue of nine pericentric inversions that serve to distinguish human chromosomes 1, 4, 5, 9, 12, 15, 16, 17, and 18 from their chimpanzee orthologues. In this study, we have analysed the breakpoints of the pericentric inversion characteristic of chimpanzee chromosome 4, the homologue of human chromosome 5. Breakpoint-spanning BAC clones were identified from both the human and chimpanzee genomes by fluorescence in situ hybridisation, and the precise locations of the breakpoints were determined by sequence comparisons. In stark contrast to some other characterised evolutionary rearrangements in primates, this chimpanzee-specific inversion appears not to have been mediated by either gross segmental duplications or low-copy repeats, although micro-duplications were found adjacent to the breakpoints. However, alternating purine-pyrimidine (RY) tracts were detected at the breakpoints, and such sequences are known to adopt non-B DNA conformations that are capable of triggering DNA breakage and genomic rearrangements. Comparison of the breakpoint region of human chromosome 5q15 with the orthologous regions of the chicken, mouse, and rat genomes, revealed similar but non-identical syntenic disruptions in all three species. The clustering of evolutionary breakpoints within this chromosomal region, together with the presence of multiple pathological breakpoints in the vicinity of both 5p15 and 5q15, is consistent with the non-random model of chromosomal evolution and suggests that these regions may well possess intrinsic features that have served to mediate a variety of genomic rearrangements, including the pericentric inversion in chimpanzee chromosome 4.
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paper_title: Refinement of a chimpanzee pericentric inversion breakpoint to a segmental duplication cluster

paper_content:

BackgroundPericentric inversions are the most common euchromatic chromosomal differences among humans and the great apes. The human and chimpanzee karyotype differs by nine such events, in addition to several constitutive heterochromatic increases and one chromosomal fusion event. Reproductive isolation and subsequent speciation are thought to be the potential result of pericentric inversions, as reproductive boundaries form as a result of hybrid sterility.ResultsHere we employed a comparative fluorescence in situ hybridization approach, using probes selected from a combination of physical mapping, genomic sequence, and segmental duplication analyses to narrow the breakpoint interval of a pericentric inversion in chimpanzee involving the orthologous human 15q11-q13 region. We have refined the inversion breakpoint of this chimpanzee-specific rearrangement to a 600 kilobase (kb) interval of the human genome consisting of entirely duplicated material. Detailed analysis of the underlying sequence indicated that this region comprises multiple segmental duplications, including a previously characterized duplication of the alpha7 neuronal nicotinic acetylcholine receptor subunit gene (CHRNA7) in 15q13.3 and several Golgin-linked-to-PML, or LCR15, duplications.ConclusionsWe conclude that, on the basis of experimental data excluding the CHRNA7 duplicon as the site of inversion, and sequence analysis of regional duplications, the most likely rearrangement site is within a GLP/LCR15 duplicon. This study further exemplifies the genomic plasticity due to the presence of segmental duplications and highlights their importance for a complete understanding of genome evolution.
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paper_title: Breakpoint analysis of the pericentric inversion distinguishing human chromosome 4 from the homologous chromosome in the chimpanzee (Pan troglodytes).

paper_content:

The study of breakpoints that occurred during primate evolution promises to yield valuable insights into the mechanisms underlying chromosome rearrangements in both evolution and pathology. Karyotypic differences between humans and chimpanzees include nine pericentric inversions, which may have potentiated the parapatric speciation of hominids and chimpanzees 5-6 million years ago. Detailed analysis of the respective chromosomal breakpoints is a prerequisite for any assessment of the genetic consequences of these inversions. The breakpoints of the inversion that distinguishes human chromosome 4 (HSA4) from its chimpanzee counterpart were identified by fluorescence in situ hybridization (FISH) and comparative sequence analysis. These breakpoints, at HSA4p14 and 4q21.3, do not disrupt the protein coding region of a gene, although they occur in regions with an abundance of LINE and LTR-elements. At 30 kb proximal to the breakpoint in 4q21.3, we identified an as yet unannotated gene, C4orf12, that lacks an homologous counterpart in rodents and is expressed at a 33-fold higher level in human fibroblasts as compared to chimpanzee. Seven out of 11 genes that mapped to the breakpoint regions have been previously analyzed using oligonucleotide-microarrays. One of these genes, WDFY3, exhibits a three-fold difference in expression between human and chimpanzee. To investigate whether the genomic architecture might have facilitated the inversion, comparative sequence analysis was used to identify an approximately 5-kb inverted repeat in the breakpoint regions. This inverted repeat is inexact and comprises six subrepeats with 78 to 98% complementarity. (TA)-rich repeats were also noted at the breakpoints. These findings imply that genomic architecture, and specifically high-copy repetitive elements, may have made a significant contribution to hominoid karyotype evolution, predisposing specific genomic regions to rearrangements.
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paper_title: Chromosome evolution: the junction of mammalian chromosomes in the formation of mouse chromosome 10.

paper_content:

During evolution, chromosomes are rearranged and become fixed into new patterns in new species. The relatively conservative nature of this process supports predictions of the arrangement of ancestral mammalian chromosomes, but the basis for these rearrangements is unknown. Physical mapping of mouse chromosome 10 (MMU 10) previously identified a 380-kb region containing the junction of material represented in human on chromosomes 21 (HSA 21) and 22 (HSA 22) that occurred in the evolutionary lineage of the mouse. Here, acquisition of 275 kb of mouse genomic sequence from this region and comparative sequence analysis with HSA 21 and HSA 22 narrowed the junction from 380 kb to 18 kb. The minimal junction region on MMU 10 contains a variety of repeats, including an L32-like ribosomal element and low-copy sequences found on several mouse chromosomes and represented in the mouse EST database. Sequence level analysis of an interchromosomal rearrangement during evolution has not been reported previously.
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paper_title: Inversion, duplication, and changes in gene context are associated with human chromosome 18 evolution

paper_content:

Abstract Human chromosome 18 differs from its homologues in the great apes by a pericentric inversion. We have identified a chimpanzee bacterial artificial chromosome that spans a region where a break is likely to have occurred in a human progenitor and have characterized the corresponding regions in both chimpanzees and humans. Interspecies sequence comparisons indicate that the ancestral break occurred between the genes ROCK1 and USP14. In humans, the inversion places ROCK1 near centromeric heterochromatin and USP14 adjacent to highly repetitive subtelomeric repeats. In addition, we provide evidence for a human segmental duplication that may have provided a mechanism for the inversion.
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paper_title: Segmental duplication associated with the human-specific inversion of chromosome 18: a further example of the impact of segmental duplications on karyotype and genome evolution in primates

paper_content:

The human-specific pericentric inversion of chromosome 18 was analysed using breakpoint-spanning BACs from the chimpanzee and human genome. Sequence and FISH analyses disclosed that the breakpoints map to an inverted segmental duplication of 19-kb, which most likely mediated the inversion by intrachromosomal homologous recombination. The 19-kb duplication encompasses the 3' end of the ROCK1 gene and occurred in the human lineage. Only one copy of this segment is found in the chimpanzee. Due to the inversion, the genomic context of the ROCK1 and USP14 genes is altered. ROCK1 flanks USP14 in the long arm of the chimpanzee chromosome 17, which is homologous to human chromosome 18. This order is interrupted by the inversion in humans. ROCK1 is localized close to the pericentromeric region in 18q11 and USP14 is inverted to distal 18p11.3 in direct neighbourhood to LSAU-satellites, beta-satellites and telomere-associated repeats. Our findings essentially confirm the analysis of Dennehey et al. (2004). Intriguingly, USP14 is differentially expressed in human and chimpanzee cortex as well as fibroblast cell lines determined previously by the analysis of oligonucleotide arrays. Either position effects mediated by the proximity to the telomeric region or nucleotide divergence in regulatory regions might account for the differential expression of USP14. The assignment of the breakpoint region to a segmental duplication underlines the significance of the genomic architecture in the context of genome and karyotype evolution in hominoids.
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paper_title: Independent intrachromosomal recombination events underlie the pericentric inversions of chimpanzee and gorilla chromosomes homologous to human chromosome 16

paper_content:

Analyses of chromosomal rearrangements that have occurred during the evolution of the hominoids can reveal much about the mutational mechanisms underlying primate chromosome evolution. We characterized the breakpoints of the pericentric inversion of chimpanzee chromosome 18 (PTR XVI), which is homologous to human chromosome 16 (HSA 16). A conserved 23-kb inverted repeat composed of satellites, LINE and Alu elements was identified near the breakpoints and could have mediated the inversion by bringing the chromosomal arms into close proximity with each other, thereby facilitating intrachromosomal recombination. The exact positions of the breakpoints may then have been determined by local DNA sequence homologies between the inversion breakpoints, including a 22-base pair direct repeat. The similarly located pericentric inversion of gorilla (GGO) chromosome XVI, was studied by FISH and PCR analysis. The p- and q-arm breakpoints of the inversions in PTR XVI and GGO XVI were found to occur at slightly different locations, consistent with their independent origin. Further, FISH studies of the homologous chromosomal regions in macaque and orangutan revealed that the region represented by HSA BAC RP11-696P19, which spans the inversion breakpoint on HSA 16q11-12, was derived from the ancestral primate chromosome homologous to HSA 1. After the divergence of orangutan from the other great apes approximately 12 million years ago (Mya), a duplication of the corresponding region occurred followed by its interchromosomal transposition to the ancestral chromosome 16q. Thus, the most parsimonious interpretation is that the gorilla and chimpanzee homologs exhibit similar but nonidentical derived pericentric inversions, whereas HSA 16 represents the ancestral form among hominoids.
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paper_title: Human Chromosome 19 and Related Regions in Mouse: Conservative and Lineage-Specific Evolution

paper_content:

To illuminate the function and evolutionary history of both genomes, we sequenced mouse DNA related to human chromosome 19. Comparative sequence alignments yielded confirmatory evidence for hypothetical genes and identified exons, regulatory elements, and candidate genes that were missed by other predictive methods. Chromosome-wide comparisons revealed a difference between single-copy HSA19 genes, which are overwhelmingly conserved in mouse, and genes residing in tandem familial clusters, which differ extensively in number, coding capacity, and organization between the two species. Finally, we sequenced breakpoints of all 15 evolutionary rearrangements, providing a view of the forces that drive chromosome evolution in mammals.
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paper_title: Breakpoint analysis of the pericentric inversion between chimpanzee chromosome 10 and the homologous chromosome 12 in humans

paper_content:

During this study, we analysed the pericentric inversion that distinguishes human chromosome 12 (HSA12) from the homologous chimpanzee chromosome (PTR10). Two large chimpanzee-specific duplications of 86 and 23 kb were observed in the breakpoint regions, which most probably occurred associated with the inversion. The inversion break in PTR10p caused the disruption of the SLCO1B3 gene in exon 11. However, the 86-kb duplication includes the functional SLCO1B3 locus, which is thus retained in the chimpanzee, although inverted to PTR10q. The second duplication spans 23 kb and does not contain expressed sequences. Eleven genes map to a region of about 1 Mb around the breakpoints. Six of these eleven genes are not among the differentially expressed genes as determined previously by comparing the human and chimpanzee transcriptome of fibroblast cell lines, blood leukocytes, liver and brain samples. These findings imply that the inversion did not cause major expression differences of these genes. Comparative FISH analysis with BACs spanning the inversion breakpoints in PTR on metaphase chromosomes of gorilla (GGO) confirmed that the pericentric inversion of the chromosome 12 homologs in GGO and PTR have distinct breakpoints and that humans retain the ancestral arrangement. These findings coincide with the trend observed in hominoid karyotype evolution that humans have a karyotype close to an ancestral one, while African great apes present with more derived chromosome arrangements.
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paper_title: Spatial genome organization.

paper_content:

The linear sequence of genomes exists within the three-dimensional space of the cell nucleus. The spatial arrangement of genes and chromosomes within the interphase nucleus is nonrandom and gives rise to specific patterns. While recent work has begun to describe some of the positioning patterns of chromosomes and gene loci, the structural constraints that are responsible for nonrandom positioning and the relevance of spatial genome organization for genome expression are unclear. Here we discuss potential functional consequences of spatial genome organization and we speculate on the possible molecular mechanisms of how genomes are organized within the space of the mammalian cell nucleus.
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paper_title: Fine-scale structural variation of the human genome

paper_content:

Inversions, deletions and insertions are important mediators of disease and disease susceptibility1. We systematically compared the human genome reference sequence with a second genome (represented by fosmid paired-end sequences) to detect intermediate-sized structural variants >8 kb in length. We identified 297 sites of structural variation: 139 insertions, 102 deletions and 56 inversion breakpoints. Using combined literature, sequence and experimental analyses, we validated 112 of the structural variants, including several that are of biomedical relevance. These data provide a fine-scale structural variation map of the human genome and the requisite sequence precision for subsequent genetic studies of human disease.
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paper_title: Structural variation in the human genome

paper_content:

The first wave of information from the analysis of the human genome revealed SNPs to be the main source of genetic and phenotypic human variation. However, the advent of genome-scanning technologies has now uncovered an unexpectedly large extent of what we term 'structural variation' in the human genome. This comprises microscopic and, more commonly, submicroscopic variants, which include deletions, duplications and large-scale copy-number variants - collectively termed copy-number variants or copy-number polymorphisms - as well as insertions, inversions and translocations. Rapidly accumulating evidence indicates that structural variants can comprise millions of nucleotides of heterogeneity within every genome, and are likely to make an important contribution to human diversity and disease susceptibility.
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paper_title: Nuclear architecture and the induction of chromosomal aberrations.

paper_content:

Progress in fluorescence in situ hybridization, three dimensional microscopy and image analysis has provided the means to study the three-dimensional structure and distribution of chromosome territories within the cell nucleus. In this contribution, we summarize the present state of knowledge of the territorial organization of interphase chromosomes and their topological relationships with other macromolecular domains in the human cell nucleus, and present data from computer simulations of chromosome territory distributions. On this basis, we discuss models of chromosome territory and nuclear architecture and topological consequences for the formation of chromosome exchanges.
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paper_title: The evolutionary history of human chromosome 7.

paper_content:

We report on a comparative molecular cytogenetic and in silico study on evolutionary changes in human chromosome 7 homologs in all major primate lineages. The ancestral mammalian homologs comprise two chromosomes (7a and 7b/16p) and are conserved in carnivores. The subchromosomal organization of the ancestral primate segment 7a shared by a lemur and higher Old World monkeys is the result of a paracentric inversion. The ancestral higher primate chromosome form was then derived by a fission of 7b/16p, followed by a centric fusion of 7a/7b as observed in the orangutan. In hominoids two further inversions with four distinct breakpoints were described in detail: the pericentric inversion in the human/African ape ancestor and the paracentric inversion in the common ancestor of human and chimpanzee. FISH analysis employing BAC probes confined the 7p22.1 breakpoint of the pericentric inversion to 6.8 Mb on the human reference sequence map and the 7q22.1 breakpoint to 97.1 Mb. For the paracentric inversion the breakpoints were found in 7q11.23 between 76.1 and 76.3 Mb and in 7q22.1 at 101.9 Mb. All four breakpoints were flanked by large segmental duplications. Hybridization patterns of breakpoint-flanking BACs and the distribution of duplicons suggest their presence before the origin of both inversions. We propose a scenario by which segmental duplications may have been the cause rather than the result of these chromosome rearrangements.
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Title: A small trip in the untranquil world of genomes A survey on the detection and analysis of genome rearrangement breakpoints

Section 1: Introduction
Description 1: Provide an overview of the topic and explain the scope of the survey, stating the main focus areas such as detecting breakpoints and analyzing breakpoint regions.

Section 2: Biological background
Description 2: Explain genome dynamics, the different types of genome rearrangements, and the biological mechanisms underlying these rearrangements.

Section 3: Detecting breakpoints
Description 3: Discuss the available data for studying rearrangements and outline the methods used to detect conserved segments as a precursor to identifying breakpoints.

Section 4: Experimental methods
Description 4: Describe various experimental techniques used to analyze karyotypes and identify conserved segments, including karyotype comparison, chromosome banding, FISH, CGH, and gene mapping.

Section 5: Genomic alignment
Description 5: Elaborate on the types of genomic alignment algorithms and the challenges posed by whole genome alignment, including the details of specific methods used in practice.

Section 6: Anchoring
Description 6: Detail the anchoring step in alignment algorithms, comparing different models and algorithms used for identifying local similarities between genomes.

Section 7: Clustering or chaining of anchors
Description 7: Explain the methods of chaining and clustering anchors to filter out false positives and retain true homologous segments.

Section 8: Extension or recursivity
Description 8: Describe how selected anchors are used to produce final alignments, focusing on the step differences among alignment methods and their objectives.

Section 9: General comments
Description 9: Analyze the advantages and drawbacks of the discussed methods in the context of identifying breakpoint regions, covering issues like micro-rearrangements and duplications.

Section 10: Analysis of breakpoint regions
Description 10: Review what is known about rearrangement mechanisms, differentiating between systematic and punctual studies, and their findings related to evolutionary and other types of breakpoints.

Section 11: Systematic studies
Description 11: Focus on systematic analyses of breakpoint regions, exploring themes such as the randomness of breakpoints, segmental duplications, duplicated elements, evolutionary rates, and fragile sites.

Section 12: Random or not random?
Description 12: Assess the arguments and evidence for and against the random distribution model of genome rearrangements.

Section 13: Segmental duplications
Description 13: Investigate the role of segmental duplications in genome rearrangements, particularly in the context of evolutionary breakpoints.

Section 14: Various duplicated elements
Description 14: Examine associations between different types of duplicated elements and breakpoint regions, and their potential involvement in rearrangements.

Section 15: Evolutionary rates
Description 15: Discuss findings on the relationship between breakpoints and evolutionary rates, including different theories and speciation models.

Section 16: Fragile sites
Description 16: Explore the correlation between evolutionary breakpoint regions and fragile sites, and their potential role in the rearrangement process.

Section 17: Correlations with other types of breakpoints (polymorphism, inherited disease, cancer)
Description 17: Investigate common features and correlations between evolutionary breakpoints and those involved in polymorphism, inherited diseases, and cancer.

Section 18: Punctual studies
Description 18: Summarize detailed analyses of individual breakpoint regions, highlighting common trends and notable findings from such studies.

Section 19: Conclusion and open problems
Description 19: Conclude the survey by summarizing key points, presenting challenges that remain unsolved, and suggesting potential directions for future research.