How RNA transcripts coordinate DNA recombination and repair

Abstract

Genetic studies in yeast indicate that RNA transcripts facilitate homology-directed DNA repair in a manner that is dependent on RAD52. The molecular basis for so-called RNA−DNA repair, however, remains unknown. Using reconstitution assays, we demonstrate that RAD52 directly cooperates with RNA as a sequence-directed ribonucleoprotein complex to promote two related modes of RNA−DNA repair. In a RNA-bridging mechanism, RAD52 assembles recombinant RNA−DNA hybrids that coordinate synapsis and ligation of homologous DNA breaks. In an RNA-templated mechanism, RAD52-mediated RNA−DNA hybrids enable reverse transcription-dependent RNA-to-DNA sequence transfer at DNA breaks that licenses subsequent DNA recombination. Notably, we show that both mechanisms of RNA−DNA repair are promoted by transcription of a homologous DNA template in trans. In summary, these data elucidate how RNA transcripts cooperate with RAD52 to coordinate homology-directed DNA recombination and repair in the absence of a DNA donor, and demonstrate a direct role for transcription in RNA−DNA repair.

Dipeptide repeat proteins inhibit homology-directed DNA double strand break repair in C9ORF72 ALS/FTD

“…It is increasingly understood that the RNA processing functions of these proteins are capable of destabilizing co-transcriptional structures called R-loops, which are composed of the nascent RNA hybridized with template DNA and the non-template singlestranded DNA, thereby reducing the potential of persistent R-loops to result in DNA DSBs [73,93,94]. In addition to preventing DNA DSBs from occurring during transcription, these proteins may also facilitate transcription-associated homology-directed repair in post-mitotic neurons [41,42,92]. Interestingly, RAD52 plays a key role in RNA-coordinated DNA DSB repair by tethering complementary single strand DNA and RNA to facilitate annealing during homology-directed repair and has been linked to R-loop processing and transcription-associated repair [40,42,43,95,96].…”

“…As a consequence of their inability to utilize homologous recombination (the preferred DNA DSB repair pathway utilized by most replicating cells), high oxygen consumption, high transcription rates and longevity, neurons must utilize elaborate DNA damage response and repair cascades to maintain genomic integrity [36]. Pathways utilized by neurons to repair DNA DSBs include non-homologous end joining (NHEJ) and homology-directed repair pathways; the latter being particularly relevant for the repair of actively transcribed DNA [40][41][42][43].. Notwithstanding this, the elucidation of the specific DNA repair pathways that are disrupted in C9ALS/FTD and the HRE product(s) that are principally involved remains incomplete.…”

RNA-DNA strand exchange by the Drosophila Polycomb complex PRC2

“…A small number of other proteins have been shown to have similar activity, using various types of substrates. These include the repair proteins Rad52/ RecA [45][46][47][48] and PALB2 49 , the human capping enzyme (CE) 50 , the viral protein ICP8 51 and the telomere-inding protein TRF2 52 . Like the activity of PRC2, none of these reactions require ATP hydrolysis (although R-loop formation by RecA is stimulated by ATPγS 45 ), and most use linear DNA substrates 46,47,49,50 or an unpaired or ssDNA region 45,48 .…”

“…RNA-DNA strand exchange has been investigated most closely for Rad52, and its homologue RecA 45,48 . Rad52 has been shown both to carry out "inverse strand exchange" where Rad52 first binds the dsDNA, allowing RNA strand exchange 46 , and to use an RNA-bridging mechanism, in which Rad52 first binds the RNA, and can bridge two dsDNA fragments by forming RNA-DNA hybrids with segments of each of them 47 . Both of these mechanisms are candidates to mediate RNA-mediated repair of DSBs 46,47 .…”

“…Rad52 has been shown both to carry out "inverse strand exchange" where Rad52 first binds the dsDNA, allowing RNA strand exchange 46 , and to use an RNA-bridging mechanism, in which Rad52 first binds the RNA, and can bridge two dsDNA fragments by forming RNA-DNA hybrids with segments of each of them 47 . Both of these mechanisms are candidates to mediate RNA-mediated repair of DSBs 46,47 . PRC2 requires a DNA end for RNA-DNA strand exchange in vitro; for this activity to occur in vivo, either a DNA break would be required, or PRC2 would need to be able to use DNA opened by (an)other factors, or by transcription.…”