Transcription (genetics)

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Simplified diagram of mRNA synthesis and processing. Enzymes not shown.

Transcription is the first step of gene expression, in which a particular segment of DNA is copied into RNA (mRNA, tRNA or rRNA) by the enzyme RNA polymerase.

Both RNA and DNA are nucleic acids, which use base pairs of nucleotides as a complementary language. The two can be converted back and forth from DNA to RNA by the action of the correct enzymes. During transcription, a DNA sequence is read by an RNA polymerase, which produces a complementary, antiparallel RNA strand called a primary transcript.

Transcription proceeds in the following general steps:

  1. One or more sigma factor protein binds to the RNA polymerase holoenzyme, allowing it to bind to promoter DNA.
  2. RNA polymerase creates a transcription bubble, which separates the two strands of the DNA helix. This is done by breaking the hydrogen bonds between complementary DNA nucleotides.
  3. RNA polymerase adds matching RNA nucleotides to the complementary nucleotides of one DNA strand.
  5. Hydrogen bonds of the untwisted RNA-DNA helix break, freeing the newly synthesized RNA strand.
  6. If the cell has a nucleus, the RNA may be further processed. This may include polyadenylation, capping, and splicing.
  7. The RNA may remain in the nucleus or exit to the cytoplasm through the nuclear pore complex.

The stretch of DNA transcribed into an RNA molecule is called a transcription unit and encodes at least one gene. If the gene transcribed encodes a protein, messenger RNA (mRNA) will be transcribed; the mRNA will in turn serve as a template for the protein's synthesis through translation. Alternatively, the transcribed gene may encode for either non-coding RNA (such as microRNA), ribosomal RNA (rRNA), transfer RNA (tRNA), or other enzymatic RNA molecules called ribozymes.[1] Overall, RNA helps synthesize, regulate, and process proteins; it therefore plays a fundamental role in performing functions within a cell.

In virology, the term may also be used when referring to mRNA synthesis from a RNA molecule (i.e., RNA replication). For instance, the genome of an negative-sense single-stranded RNA (ssRNA -) virus may be template a positive-sense single-stranded RNA (ssRNA +). This is since the positive-sense strand contains the information needed to translate the viral proteins for viral replication afterwards. This process is catalysed by a viral RNA replicase.[2]


A DNA transcription unit encoding for a protein may contain both a coding sequence, which will translated into the protein, and regulatory sequences, which direct and regulate the synthesis of that protein. The regulatory sequence before ("upstream" from) the coding sequence is called the five prime untranslated region (5'UTR); the sequence after ("downstream" from) the coding sequence is called the three prime untranslated region (3'UTR).[1]


Only one of the two DNA strands serve as a template for transcription. The DNA is read by RNA polymerase from the 3' end to the 5' end during transcription (3' → 5'). The complementary RNA is created in the opposite direction, in the 5' → 3' direction. This directionality is because RNA polymerase can only add nucleotides to the 3' end of the growing mRNA chain. This use of only the 3' → 5' DNA-strand eliminates the need for the Okazaki fragments that are seen in DNA replication.[1] This removes the need for an RNA primer to initiate RNA synthesis, as is the case in DNA replication.

The non-template DNA strand is called the coding strand, because its sequence is the same as the newly created RNA transcript (except for the substitution of uracil for thymine).


Major steps[edit]



In eukaryotes, RNA polymerase, and therefore the initiation of transcription, requires the presence of a core promoter sequence in the DNA. Promoters are regions of DNA that promote transcription and, in eukaryotes, are found at -30, -75, and -90 base pairs upstream from the transcription start site (abbreviated to TSS). Transcription factors are proteins that bind to these promoter sequences and facilitate the binding of RNA Polymerase.[4]


Thus, preinitiation complex contains:[citation needed].

  1. Core Promoter Sequence
  2. Transcription Factors
  3. RNA Polymerase
  4. Activators and Repressors.

The transcription preinitiation in archaea is, in essence, homologous to that of eukaryotes, but is much less complex.[5] The archaeal preinitiation complex assembles at a TATA-box binding site; however, in archaea, this complex is composed of only RNA polymerase II, TBP, and TFB (the archaeal homologue of eukaryotic transcription factor II B (TFIIB)).[6][7]


Simple diagram of transcription initiation. RNAP = RNA polymerase

In bacteria, transcription begins with the binding of RNA polymerase to the promoter in DNA. RNA polymerase is a core enzyme consisting of five subunits: 2 α subunits, 1 β subunit, 1 β' subunit, and 1 ω subunit. At the start of initiation, the core enzyme is associated with a sigma factor that aids in finding the appropriate -35 and -10 base pairs upstream of promoter sequences.[8] When the sigma factor and RNA polymerase combine, they form a holoenzyme.


Promoter clearance[edit]


In prokaryotes, abortive initiation continues to occur until an RNA product of a threshold length of approximately 10 nucleotides is synthesized, at which point promoter escape occurs and a transcription elongation complex is formed. The σ factor is released according to a stochastic model.[11] Mechanistically, promoter escape occurs through a scrunching mechanism, where the energy built up by DNA scrunching provides the energy needed to break interactions between RNA polymerase holoenzyme and the promoter.[12]

In eukaryotes, after several rounds of 10nt abortive initiation, promoter clearance coincides with the TFIIH's phosphorylation of serine 5 on the carboxy terminal domain of RNAP II, leading to the recruitment of capping enzyme (CE).[13][14] The exact mechanism of how CE induces promoter clearance in eukaryotes is not yet known.


Simple diagram of transcription elongation





Main article: Terminator (genetics)


Transcription termination in eukaryotes is less understood but involves cleavage of the new transcript followed by template-independent addition of adenines at its new 3' end, in a process called polyadenylation.[16]



Transcription factories[edit]






Measuring and detecting transcription[edit]



  • Nuclear Run-on assay: measures the relative abundance of newly formed transcripts
  • RNase protection assay and ChIP-Chip of RNAP: detect active transcription sites
  • RT-PCR: measures the absolute abundance of total or nuclear RNA levels, which may however differ from transcription rates
  • DNA microarrays: measures the relative abundance of the global total or nuclear RNA levels; however, these may differ from transcription rates
  • In situ hybridization: detects the presence of a transcript
  • MS2 tagging: by incorporating RNA stem loops, such as MS2, into a gene, these become incorporated into newly synthesized RNA. The stem loops can then be detected using a fusion of GFP and the MS2 coat protein, which has a high affinity, sequence-specific interaction with the MS2 stem loops. The recruitment of GFP to the site of transcription is visualised as a single fluorescent spot. This new approach has revealed that transcription occurs in discontinuous bursts, or pulses (see Transcriptional bursting). With the notable exception of in situ techniques, most other methods provide cell population averages, and are not capable of detecting this fundamental property of genes.[20]
  • Northern blot: the traditional method, and until the advent of RNA-Seq, the most quantitative
  • RNA-Seq: applies next-generation sequencing techniques to sequence whole transcriptomes, which allows the measurement of relative abundance of RNA, as well as the detection of additional variations such as fusion genes, post-transcriptional edits and novel splice sites

Reverse transcription[edit]

Scheme of reverse transcription





See also[edit]


  2. ^ "Tentative identification of RNA-dependent RNA polymerases of dsRNA viruses and their relationship to positive strand RNA viral polymerases". FEBS Letters 252: 42–46. doi:10.1016/0014-5793(89)80886-5. 
  4. ^ a b c Basic Medical Biochemistry, 4th edition, Marks. Chapter 14
  15. ^ Richardson, J (2002). "Rho-dependent termination and ATPases in transcript termination". Biochimica et Biophysica Acta 1577 (2): 251–260. doi:10.1016/S0167-4781(02)00456-6. 
  16. ^ Lykke-Andersen, S; Jensen, TH (2007). "Overlapping pathways dictate termination of RNA polymerase II transcription". Biochimie 89 (10): 1177–82. doi:10.1016/j.biochi.2007.05.007. 
  17. ^ 8-Hydroxyquinoline info from SIGMA-ALDRICH. Retrieved Feb 2012
  19. ^ "Chemistry 2006". Nobel Foundation. Retrieved March 29, 2007. 
  20. ^ Raj, A.; van Oudenaarden, A. (2008). "Nature, nurture, or chance: stochastic gene expression and its consequences". Cell 135: 216–26. doi:10.1016/j.cell.2008.09.050. 
  21. ^ Kolesnikova I. N. (2000 г.). "Some patterns of apoptosis mechanism during HIV-infection". Dissertation (in Russian). Retrieved February 20, 2011.  Check date values in: |date= (help)
  22. ^ ALT and Telomerase from Nature. Retrieved May 2010

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