Editing Sigma factor (section)

==Retention during transcription elongation==
The core RNA polymerase (consisting of 2 alpha (α), 1 beta (β), 1 beta-prime (β'), and 1 omega (ω) subunits) binds a sigma factor to form a complex called the [[RNA polymerase]] [[holoenzyme]]. It was previously believed that the RNA polymerase holoenzyme initiates transcription, while the core RNA polymerase alone synthesizes RNA. Thus, the accepted view was that sigma factor must dissociate upon transition from transcription initiation to transcription elongation (this transition is called "promoter escape"). This view was based on analysis of purified complexes of RNA polymerase stalled at initiation and at elongation. Finally, structural models of RNA polymerase complexes predicted that, as the growing RNA product becomes longer than ~15 nucleotides, sigma must be "pushed out" of the holoenzyme, since there is a steric clash between RNA and a sigma domain. However, σ<sup>70</sup> can remain attached in complex with the core RNA polymerase in early elongation<ref name=Kapanidis>{{cite journal | vauthors = Kapanidis AN, Margeat E, Laurence TA, Doose S, Ho SO, Mukhopadhyay J, Kortkhonjia E, Mekler V, Ebright RH, Weiss S | title = Retention of transcription initiation factor sigma70 in transcription elongation: single-molecule analysis | journal = Molecular Cell | volume = 20 | issue = 3 | pages = 347–56 | date = November 2005 | pmid = 16285917 | doi = 10.1016/j.molcel.2005.10.012 | doi-access = free }}</ref> and sometimes throughout elongation.<ref>{{cite journal |vauthors=Harden TT, Wells CD, Friedman LJ, Landick R, Hochschild A, Kondev J, Gelles J |title=Bacterial RNA polymerase can retain σ70 throughout transcription |journal=Proc Natl Acad Sci U S A |volume=113 |issue=3 |pages=602–7 |date=January 2016 |pmid=26733675 |pmc=4725480 |doi=10.1073/pnas.1513899113 |bibcode=2016PNAS..113..602H |doi-access=free }}</ref> Indeed, the phenomenon of promoter-proximal pausing indicates that sigma plays roles during early elongation. All studies are consistent with the assumption that promoter escape reduces the lifetime of the sigma-core interaction from very long at initiation (too long to be measured in a typical biochemical experiment) to a shorter, measurable lifetime upon transition to elongation.