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BRCA2 suppresses “head-on” transcription-replication conflicts incurred by dormant origin firing at transcription termination sites [RNA-seq]

ABSTRACT: BRCA2 suppresses “head-on” transcription-replication conflicts incurred by dormant origin firing at transcription termination sites [RNA-seq]

PROVIDER: PRJNA1001277 | ENA |

REPOSITORIES: ENA

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BRCA2 suppresses “head-on” transcription-replication conflicts incurred by dormant origin firing at transcription termination sites [RNA-seq]

Project description:BRCA2 is a tumor suppressor protein responsible for safeguarding the cellular genome from genotoxicity and replication stress, but the mechanism(s) by which this is achieved remains elusive. Here, we provide evidence that BRCA2 acts as a critical suppressor of “head-on” transcription-replication conflicts (HO-TRCs). Using Okazaki-fragment sequencing (Ok-seq) and computational analysis, we identified new origins (dormant origins) that are activated near the transcription termination sites (TTS) of highly expressed, long genes in response to replication stress. Dormant origins are a source for HO-TRCs, and drug treatments that inhibit dormant origin firing led to a reduction in HO-TRCs, R-loop formation, and DNA damage. Using super-resolution microscopy, we showed that HO-TRC events track with elongating RNA polymerase II, but not with transcription initiation. Importantly, RNaseH2 is recruited to sites of HO-TRCs in a BRCA2-dependent manner to help alleviate toxic R-loops associated with HO-TRCs. Collectively, our results identify a new source of genomic instability caused by HO-TRCs in BRCA2-deficient ovarian cancer precursor cells, providing a new strategy in modulating HO-TRCs to enhance genomic instability

2024-03-28 | GSE239857 | GEO

BRCA2 suppresses “head-on” transcription-replication conflicts incurred by dormant origin firing at transcription termination sites [Ok-seq]

2024-03-28 | GSE239856 | GEO

BRCA2 suppresses “head-on” transcription-replication conflicts incurred by dormant origin firing at transcription termination sites

Project description:BRCA2 suppresses “head-on” transcription-replication conflicts incurred by dormant origin firing at transcription termination sites

| PRJNA1001273 | ENA

BRCA2 suppresses “head-on” transcription-replication conflicts incurred by dormant origin firing at transcription termination sites [Ok-seq]

Project description:BRCA2 suppresses “head-on” transcription-replication conflicts incurred by dormant origin firing at transcription termination sites [Ok-seq]

| PRJNA1001276 | ENA

MiDAS in BRCA2-deficient cells originate at early S-phase transcription-replication conflicts

Project description:Multiple replication abnormalities cause cells lacking BRCA2 to enter mitosis with under-replicated DNA and to activate mitotic DNA synthesis (MiDAS). However, the precise position of these MiDAS sites, as well as their origin, remains unknown. Here we labelled mitotic nascent DNA and performed high-throughput sequencing to identify at high-resolution the sites where MiDAS occurs in the absence of BRCA2. This approach revealed 150 genomic loci affected by MiDAS, which map within regions replicating during early S-phase and are therefore distinct from the aphidicolin-induced common fragile sites. Moreover, these sites largely localise near early firing origins and within genes transcribed in early S, suggesting that they stem from transcription-replication conflicts (TCRs). Inhibiting transcription with 5,6-dichloro-1-β-D-ribofuranosylbenzimidazole (DRB) during early S-phase abrogates MiDAS. Strikingly, MiDAS sites co-localise with genomic loci where R-loops form in unchallenged conditions, suggesting that R-loop accumulation caused by BRCA2 inactivation leads to DNA lesion which are repaired by MiDAS. RAD52 is required in this process, as its abrogation in BRCA2-deficient cells reduces the rate of MiDAS and causes DNA damage accumulation in G1. Furthermore, MiDAS sites triggered by BRCA2 inactivation are hotspots for genomic rearrangement in BRCA2-mutated breast tumours. These results indicate that BRCA2 acts in early S-phase to protect TRC- and R-loop-induced DNA lesions, thereby preventing them from becoming a source of genomic instability and tumorigenesis.

2022-08-01 | GSE196163 | GEO

Transcription-Replication Conflicts drive the Synthetic Lethality of PARP Inhibitors with BRCA2-Deficiency

Project description:Transcription-Replication Conflicts drive the Synthetic Lethality of PARP Inhibitors with BRCA2-Deficiency

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MiDAS in BRCA2-deficient cells originate at early S-phase transcription-replication conflicts

Project description:MiDAS in BRCA2-deficient cells originate at early S-phase transcription-replication conflicts

| PRJNA803497 | ENA

BRCA2 suppresses “head-on” transcription-replication conflicts incurred by dormant origin firing at transcription termination sites

Project description:This SuperSeries is composed of the SubSeries listed below.

2024-03-27 | GSE239858 | GEO

Dormant origins and fork protection mechanisms rescue sister forks arrested by transcription

Project description:Yeast Sen1Senataxin is a RNA/DNA helicase that preserves replication forks across RNA Polymerase II-transcribed genes by counteracting RNA:DNA hybrids accumulation. We show that in Sen1-depleted cells early forks clashing head-on with transcription halt, and impair progression of sister forks within the same replicon. Unsolved replication-transcription collisions trigger the local firing of dormant origins that rescue arrested forks. In sen1 mutants the MRX and Mrc1/Ctf4-complexes protect those forks clashing with transcription by preventing genotoxic fork-resection events mediated by the Exo1 nuclease. Hence, sister forks within the same replicon remain coupled when one of the two forks halts. This is different when forks encounter double strand breaks. Moreover, the local firing of dormant origins is not prevented by checkpoint activation but depends on delayed adjacent forks. Furthermore, a productive head-on clash between replication and transcription requires the tuning of origin firing and coordination between Sen1, the MRX and Mrc1/Ctf4-complexes and Exo1.

2017-10-11 | GSE97046 | GEO

CDK12 prevents MYC-induced transcription-replication conflicts

Project description:CDK12 prevents MYC-induced transcription-replication conflicts

| PRJNA991561 | ENA