Editing Transcription (biology) (section)

=== Elongation ===
[[File:Simple transcription elongation1.svg|thumb|400px|Simple diagram of transcription elongation]]

One strand of the DNA, the ''template strand'' (or noncoding strand), is used as a template for RNA synthesis. As transcription proceeds, RNA polymerase traverses the template strand and uses base pairing complementarity with the DNA template to create an RNA copy (which elongates during the traversal). Although RNA polymerase traverses the template strand from 3' → 5', the coding (non-template) strand and newly formed RNA can also be used as reference points, so transcription can be described as occurring 5' → 3'. This produces an RNA molecule from 5' → 3', an exact copy of the coding strand (except that [[thymine]]s are replaced with [[uracil]]s, and the nucleotides are composed of a ribose (5-carbon) sugar whereas DNA has deoxyribose (one fewer oxygen atom) in its sugar-phosphate backbone).<ref name="Clark-2005" />

mRNA transcription can involve multiple RNA polymerases on a single DNA template and multiple rounds of transcription (amplification of particular mRNA), so many mRNA molecules can be rapidly produced from a single copy of a gene.{{citation needed|date=January 2011}} The characteristic elongation rates in prokaryotes and eukaryotes are about 10–100 nts/sec.<ref>{{cite book |last1=Milo |first1=Ron |last2=Philips |first2=Rob |chapter=4. Rates and Duration: Central dogma: Which is faster:transcription or translation? |chapter-url= |title=Cell Biology by the Numbers |publisher=CRC Press |date=2015 |isbn=978-1-317-23069-4 |pages=231–6 |url={{GBurl|9NPRCgAAQBAJ|pg=PR10}} |oclc=1105558425 }}</ref> In eukaryotes, however, [[nucleosome]]s act as major barriers to transcribing polymerases during transcription elongation.<ref>{{cite journal | vauthors = Hodges C, Bintu L, Lubkowska L, Kashlev M, Bustamante C | title = Nucleosomal fluctuations govern the transcription dynamics of RNA polymerase II | journal = Science | volume = 325 | issue = 5940 | pages = 626–8 | date = July 2009 | pmid = 19644123 | pmc = 2775800 | doi = 10.1126/science.1172926| bibcode = 2009Sci...325..626H }}</ref><ref name="Fitz etal-2016" /> In these organisms, the pausing induced by nucleosomes can be regulated by transcription elongation factors such as TFIIS.<ref name="Fitz etal-2016">{{cite journal |date=2016 |title=Nucleosomal arrangement affects single-molecule transcription dynamics |journal=Proceedings of the National Academy of Sciences |volume=113 |issue=45 |pages=12733–12738 |vauthors=Fitz V, Shin J, Ehrlich C, Farnung L, Cramer P, Zaburdaev V, Grill SW |pmc=5111697 |doi=10.1073/pnas.1602764113 |pmid=27791062|bibcode=2016PNAS..11312733F |doi-access=free }}</ref>

Elongation also involves a proofreading mechanism that can replace incorrectly incorporated bases. In eukaryotes, this may correspond with short pauses during transcription that allow appropriate RNA editing factors to bind. These pauses may be intrinsic to the RNA polymerase or due to chromatin structure.{{citation needed|date=October 2019}}

Double-strand breaks in actively transcribed regions of DNA are repaired by [[homologous recombination]] during the S and G2 phases of the [[cell cycle]].<ref>{{cite journal |vauthors=Aymard F, Bugler B, Schmidt CK, Guillou E, Caron P, Briois S, Iacovoni JS, Daburon V, Miller KM, Jackson SP, Legube G |title=Transcriptionally active chromatin recruits homologous recombination at DNA double-strand breaks |journal=Nat Struct Mol Biol |volume=21 |issue=4 |pages=366–74 |date=April 2014 |pmid=24658350 |pmc=4300393 |doi=10.1038/nsmb.2796 }}</ref><ref>{{cite journal |vauthors=Ouyang J, Yadav T, Zhang JM, Yang H, Rheinbay E, Guo H, Haber DA, Lan L, Zou L |title=RNA transcripts stimulate homologous recombination by forming DR-loops |journal=Nature |volume=594 |issue=7862 |pages=283–8 |date=June 2021 |pmid=33981036 |pmc=8855348 |doi=10.1038/s41586-021-03538-8 |bibcode=2021Natur.594..283O }}</ref> Since transcription enhances the accessibility of DNA to exogenous chemicals and internal metabolites that can cause recombinogenic lesions, homologous recombination of a particular DNA sequence may be strongly stimulated by transcription.<ref>{{cite journal |vauthors=García-Rubio M, Huertas P, González-Barrera S, Aguilera A |title=Recombinogenic effects of DNA-damaging agents are synergistically increased by transcription in Saccharomyces cerevisiae. New insights into transcription-associated recombination |journal=Genetics |volume=165 |issue=2 |pages=457–66 |date=October 2003 |pmid=14573461 |pmc=1462770 |doi=10.1093/genetics/165.2.457 }}</ref>