Mind-Boggling Complexity in the Fruit Fly Transcriptome

The humble fruit fly that has been at the heart of genetic studies for nearly 100 years continues to amaze scientists and defy simplistic evolutionary predictions. A research team recently evaluated the diversity of gene expression across the insect's genome in much greater detail than previous studies, and the results revealed incredible complexity and design.1

One of the key features that is emerging across the spectrum of research in plant and animal genomes is the fact that nearly all DNA is expressed (copied into RNA).2 This expressed RNA makes up what is called the transcriptome. The different types of RNA molecules that are produced can be placed in a wide variety of functional categories that include noncoding RNAs (short and long) and protein-coding RNAs. The various noncoding RNA molecules greatly outnumber the protein-coding segments. Noncoding RNA regions of the genome act like an overlying informational system controlling the usage of protein-coding areas.

In this new study published in the journal Nature, the authors captured and analyzed the expressed RNA from many different fruit fly tissues using advanced sequencing technology.1 The researchers discovered more than 1,200 new genes that were previously unknown. These results show that even in well-studied, small-size genomes, much still remains to be understood and cataloged.

Another amazing discovery was the dramatic prevalence of overlapping genes encoded in two different directions. DNA is a double-stranded molecule and genes are found on both strands (running in opposite directions) with segments that can overlap each other. One strand may contain a protein-coding gene, while the other strand may encode what are labeled as antisense RNAs.3 These antisense RNAs help regulate their forward-sense protein-coding counterparts and appear to play a major role in controlling gene expression in the fruit fly genome at much higher levels than previously anticipated.

Another finding was that alternative splicing is considerably more complex and common than previously known. Both protein-coding and noncoding RNA genes contain regions called exons and introns. After a gene is copied into an RNA transcript, the introns are often spliced out and the exons are spliced together. In many genes, the exons are alternatively spliced to form variable and diverse gene products. In humans, it has been estimated that about 95 percent of genes are alternatively spliced.4,5 In fruit flies, alternative splicing was found to play a major role specifically in gene regulation during both the development and functioning of neural cells.

Much of the unexpected complexity in the fly transcriptome is due to many newly characterized control features that not only regulate gene function but also alter the RNA transcript after it is made. The authors of the study stated, "The fly transcriptome is substantially more complex than previously recognized, with this complexity arising from combinatorial usage of promoters, splice sites and polyadenylation sites."1

Even what was originally thought to be a simple animal genome continues to startle scientists with its incredible complexity. The more we discover about the genome, the more we realize that biocomplexity is much greater than ever imagined. While evolution does not predict this, a creationist view of an infinitely wise and omnipotent Creator does.


  1. Brown, J. B. et al. 2014. Diversity and dynamics of the Drosophila transcriptome. Nature. doi:10.1038/nature12962.
  2. Tomkins, J. 2013. Explaining Organismal Complexity with Non-Coding DNA. Acts & Facts. 42: (11) 19. 
  3. Pelechano, V. and L. M. Steinmetz. 2013. Gene regulation by antisense transcription. Nature Reviews Genetics. 14 (12): 880-893.
  4. Wang, E. T. et al. 2008. Alternative isoform regulation in human tissue transcriptomes. Nature. 456 (7221): 470-476.
  5. Pan, Q. et al. 2008. Deep surveying of alternative splicing complexity in the human transcriptome by high-throughput sequencing. Nature Genetics. 40: (12) 1413-1415.


Article posted on March 26, 2014.