Abstract
DNA-RNA hybrid structures have been detected at the vicinity of DNA double-strand breaks (DSBs) occurring within transcriptional active regions of the genome. The induction of DNA-RNA hybrids strongly affects the repair of these DSBs, but the nature of these structures and how they are formed remain poorly understood. Here we provide evidence that R loops, three-stranded structures containing DNA-RNA hybrids and the displaced single-stranded DNA (ssDNA) can form at sub-telomeric DSBs. These R loops are generated independently of DNA resection but are induced alongside two-stranded DNA-RNA hybrids that form on ssDNA generated by DNA resection. We further identified UPF1, an RNA/DNA helicase, as a crucial factor that drives the formation of these R loops and DNA-RNA hybrids to stimulate DNA resection, homologous recombination, microhomology-mediated end joining and DNA damage checkpoint activation. Our data show that R loops and DNA-RNA hybrids are actively generated at DSBs to facilitate DNA repair.
Highlights
DNA-RNA hybrid structures have been detected at the vicinity of DNA double-strand breaks (DSBs) occurring within transcriptional active regions of the genome
The fused 16p telomere was deleted by 59 bp whereas the fused 21q telomere was deleted by 2 bp and there was no microhomology at the fusion junction, implicating classical-non homologous end joining (C-NHEJ) in the fusion (Fig. 1c)
We found that many fusion molecules larger than the unprocessed fusion started to accumulate after 24 h, whereas many fusion molecules smaller than the unprocessed fusion started to appear after 48 h (Supplementary Fig. 1c)
Summary
DNA-RNA hybrid structures have been detected at the vicinity of DNA double-strand breaks (DSBs) occurring within transcriptional active regions of the genome. Dysfunctional telomeres are subjected to fusion by classical-non homologous end-joining (C-NHEJ) driven by ligase. The association of deletion events with microhomology (MH) suggests that A-NHEJ might be involved in mediating telomere fusion[6], the mechanisms that stimulate such extensive deletion remain poorly understood. Extending for up to several hundred bases, R loops are distinct from the transient DNA:RNA hybrids that can occur during transcription; they have been found in various regions in the genome to regulate gene expression, but by exposing ssDNA or causing transcription–replication conflicts, they represent a potential source of genome instability[7,8]
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