Editing Transcription (biology) (section)

=== Termination ===
{{main|Terminator (genetics)}}

Bacteria use two different strategies for transcription termination – Rho-independent termination and Rho-dependent termination. In [[Rho-independent transcription termination]], RNA transcription stops when the newly synthesized RNA molecule forms a G-C-rich [[hairpin loop]] followed by a run of Us. When the hairpin forms, the mechanical stress breaks the weak rU-dA bonds, now filling the DNA–RNA hybrid. This pulls the poly-U transcript out of the active site of the RNA polymerase, terminating transcription. In Rho-dependent termination, [[Rho factor|Rho]], a protein factor, destabilizes the interaction between the template and the mRNA, thus releasing the newly synthesized mRNA from the elongation complex.<ref>{{cite journal | vauthors = Richardson JP | title = Rho-dependent termination and ATPases in transcript termination | journal = Biochimica et Biophysica Acta (BBA) - Gene Structure and Expression | volume = 1577 | issue = 2 | pages = 251–260 | date = September 2002 | pmid = 12213656 | doi = 10.1016/S0167-4781(02)00456-6 }}</ref>

Transcription termination in eukaryotes is less well understood than in bacteria, but involves cleavage of the new transcript followed by template-independent addition of adenines at its new 3' end, in a process called [[polyadenylation]].<ref>{{cite journal | vauthors = Lykke-Andersen S, Jensen TH | title = Overlapping pathways dictate termination of RNA polymerase II transcription | journal = Biochimie | volume = 89 | issue = 10 | pages = 1177–82 | date = October 2007 | pmid = 17629387 | doi = 10.1016/j.biochi.2007.05.007 }}</ref>

Beyond termination by a terminator sequences (which is a part of a [[gene]]), transcription may also need to be terminated when it encounters conditions such as DNA damage or an active [[replication fork]]. In bacteria, the [[Mutation Frequency Decline|Mfd]] ATPase can remove a RNA polymerase stalled at a lesion by prying open its clamp. It also recruits [[nucleotide excision repair]] machinery to repair the lesion. Mfd is proposed to also resolve conflicts between DNA replication and transcription.<ref>{{cite journal |last1=Shi |first1=J |last2=Wen |first2=A |last3=Zhao |first3=M |last4=Jin |first4=S |last5=You |first5=L |last6=Shi |first6=Y |last7=Dong |first7=S |last8=Hua |first8=X |last9=Zhang |first9=Y |last10=Feng |first10=Y |title=Structural basis of Mfd-dependent transcription termination. |journal=Nucleic Acids Research |date=18 November 2020 |volume=48 |issue=20 |pages=11762–11772 |doi=10.1093/nar/gkaa904 |pmid=33068413|doi-access=free |pmc=7672476 }}</ref> In eukayrotes, ATPase [[TTF2]] helps to suppress the action of RNAP I and II during [[mitosis]], preventing errors in chromosomal segregation.<ref>{{cite journal |last1=Jiang |first1=Y |last2=Liu |first2=M |last3=Spencer |first3=CA |last4=Price |first4=DH |title=Involvement of transcription termination factor 2 in mitotic repression of transcription elongation. |journal=Molecular Cell |date=7 May 2004 |volume=14 |issue=3 |pages=375–85 |doi=10.1016/s1097-2765(04)00234-5 |pmid=15125840|doi-access=free }}</ref> In archaea, the Eta ATPase is proposed to play a similar role.<ref>{{cite journal |last1=Marshall |first1=CJ |last2=Qayyum |first2=MZ |last3=Walker |first3=JE |last4=Murakami |first4=KS |last5=Santangelo |first5=TJ |title=The structure and activities of the archaeal transcription termination factor Eta detail vulnerabilities of the transcription elongation complex. |journal=Proceedings of the National Academy of Sciences of the United States of America |date=9 August 2022 |volume=119 |issue=32 |pages=e2207581119 |doi=10.1073/pnas.2207581119 |pmid=35917344|doi-access=free |pmc=9371683 |bibcode=2022PNAS..11907581M }}</ref>