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[[R-loop]]s are formed during transcription. An R-loop is a three-stranded nucleic acid structure containing a DNA-RNA hybrid region and an associated non-template single-stranded DNA. Actively transcribed regions of [[DNA]] often form R-loops that are vulnerable to [[DNA damage (naturally occurring)|DNA damage]]. Introns reduce R-loop formation and DNA damage in highly expressed yeast genes.<ref name="pmid28757210">{{cite journal | vauthors = Bonnet A, Grosso AR, Elkaoutari A, Coleno E, Presle A, Sridhara SC, Janbon G, Géli V, de Almeida SF, Palancade B | title = Introns Protect Eukaryotic Genomes from Transcription-Associated Genetic Instability | journal = Molecular Cell | volume = 67 | issue = 4 | pages = 608–621.e6 | date = August 2017 | pmid = 28757210 | doi = 10.1016/j.molcel.2017.07.002 | doi-access = free }}</ref>
===Transcription stress===
[[DNA damage (naturally occurring)|DNA damages]] arise in each cell, every day, with the number of damages in each cell reaching tens to hundreds of thousands, and such DNA damages can impede primary transcription.<ref name = Milano2024>{{cite journal |vauthors=Milano L, Gautam A, Caldecott KW |title=DNA damage and transcription stress |journal=Mol Cell |volume=84 |issue=1 |pages=70–79 |date=January 2024 |pmid=38103560 |doi=10.1016/j.molcel.2023.11.014 |url=}}</ref> The process of of [[gene expression]] itself is a source of endogenous DNA damages resulting from the susceptibility of single-stranded DNA to damage.<ref name = Milano2024/> Other sources of DNA damage are conflicts of the primary transcription machinery with the [[DNA replication]] machinery, and the activity of certain enzymes such as [[topoisomerase]]s and [[base excision repair]] enzymes. Even though these processes are tightly regulated and are usually accurate, occasionally they can make mistakes and leave behind DNA breaks that drive [[chromosomal rearrangement]]s or [[cell death]]. <ref name = Milano2024/>
==RNA processing==
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