Editing Transcription (biology) (section)

=== Promoter escape ===

After the first bond is synthesized, the RNA polymerase must escape the promoter. During this time there is a tendency to release the RNA transcript and produce truncated transcripts. This is called [[abortive initiation]], and is common for both eukaryotes and prokaryotes.<ref>{{cite journal | vauthors = Goldman SR, Ebright RH, Nickels BE | title = Direct detection of abortive RNA transcripts in vivo | journal = Science | volume = 324 | issue = 5929 | pages = 927–8 | date = May 2009 | pmid = 19443781 | pmc = 2718712 | doi = 10.1126/science.1169237 | bibcode = 2009Sci...324..927G | author-link2 = Richard H. Ebright }}</ref> 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.{{citation needed|date=April 2023}}

Mechanistically, promoter escape occurs through [[DNA scrunching]], providing the energy needed to break interactions between RNA polymerase holoenzyme and the promoter.<ref>{{cite journal | vauthors = Revyakin A, Liu C, Ebright RH, Strick TR | title = Abortive initiation and productive initiation by RNA polymerase involve DNA scrunching | journal = Science | volume = 314 | issue = 5802 | pages = 1139–43 | date = November 2006 | pmid = 17110577 | pmc = 2754787 | doi = 10.1126/science.1131398 | bibcode = 2006Sci...314.1139R }}</ref>

In bacteria, it was historically thought that the [[sigma factor]] is definitely released after promoter clearance occurs. This theory had been known as the ''obligate release model.'' However, later data showed that upon and following promoter clearance, the sigma factor is released according to a [[stochastic process|stochastic model]] known as the ''stochastic release model''.<ref>{{cite journal | vauthors = Raffaelle M, Kanin EI, Vogt J, Burgess RR, Ansari AZ | title = Holoenzyme switching and stochastic release of sigma factors from RNA polymerase in vivo | journal = Molecular Cell | volume = 20 | issue = 3 | pages = 357–66 | date = November 2005 | pmid = 16285918 | doi = 10.1016/j.molcel.2005.10.011 | doi-access = free }}</ref>

In eukaryotes, at an RNA polymerase II-dependent promoter, upon promoter clearance, TFIIH phosphorylates serine 5 on the carboxy terminal domain of RNA polymerase II, leading to the recruitment of capping enzyme (CE).<ref>{{cite journal | vauthors = Mandal SS, Chu C, Wada T, Handa H, Shatkin AJ, Reinberg D | title = Functional interactions of RNA-capping enzyme with factors that positively and negatively regulate promoter escape by RNA polymerase II | journal = Proceedings of the National Academy of Sciences of the United States of America | volume = 101 | issue = 20 | pages = 7572–7 | date = May 2004 | pmid = 15136722 | pmc = 419647 | doi = 10.1073/pnas.0401493101 | bibcode = 2004PNAS..101.7572M | doi-access = free }}</ref><ref>{{cite journal | vauthors = Goodrich JA, Tjian R | title = Transcription factors IIE and IIH and ATP hydrolysis direct promoter clearance by RNA polymerase II | journal = Cell | volume = 77 | issue = 1 | pages = 145–56 | date = April 1994 | pmid = 8156590 | doi = 10.1016/0092-8674(94)90242-9 | s2cid = 24602504 }}</ref> The exact mechanism of how CE induces promoter clearance in eukaryotes is not yet known.