Dormant origin firing promotes head-on transcription-replication conflicts at transcription termination sites in response to BRCA2 deficiency

Nature Communications, Journal Year: 2024, Volume and Issue: 15(1)

Published: June 3, 2024

Abstract BRCA2 is a tumor suppressor protein responsible for safeguarding the cellular genome from replication stress and genotoxicity, but specific mechanism(s) by which this achieved to prevent early oncogenesis remains unclear. Here, we provide evidence that acts as critical of head-on transcription-replication conflicts (HO-TRCs). Using Okazaki-fragment sequencing (Ok-seq) computational analysis, identified origins (dormant origins) are activated near transcription termination sites (TTS) highly expressed, long genes in response stress. Dormant source HO-TRCs, drug treatments inhibit dormant origin firing led reduction R-loop formation, DNA damage. super-resolution microscopy, showed HO-TRC events track with elongating RNA polymerase II, not initiation. Importantly, RNase H2 recruited HO-TRCs BRCA2-dependent manner help alleviate toxic R-loops associated HO-TRCs. Collectively, our results mechanistic basis how shields against genomic instability preventing through both direct indirect means occurring at predetermined based on pre-cancer transcriptome.

Language: Английский

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Epitranscriptome in action: RNA modifications in the DNA damage response

Molecular Cell, Journal Year: 2024, Volume and Issue: 84(19), P. 3610 - 3626

Published: Oct. 1, 2024

Language: Английский

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RNase H genes cause distinct impacts on RNA:DNA hybrid formation and mutagenesis genome wide

Science Advances, Journal Year: 2023, Volume and Issue: 9(30)

Published: July 26, 2023

RNA:DNA hybrids compromise replication fork progression and genome integrity in all cells. The overall impacts of naturally occurring on integrity, the relative contributions ribonucleases H to mitigating negative effects hybrids, remain unknown. Here, we investigate RNases HII (RnhB) HIII (RnhC) hybrid removal, DNA replication, mutagenesis wide. Deletion either rnhB or rnhC triggers accumulation but with distinct patterns accumulation. Across cells, accumulate strongly noncoding RNAs 5'-UTRs coding sequences. For ΔrnhB, preferentially untranslated regions early We show that is particularly sensitive gene expression ΔrnhC cells disrupted, leading transversions structural variation. Our results resolve outstanding question how native genomic contexts cause shape organization.

Language: Английский

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ADAR1 links R-loop homeostasis to ATR activation in replication stress response

Nucleic Acids Research, Journal Year: 2023, Volume and Issue: 51(21), P. 11668 - 11687

Published: Oct. 13, 2023

Unscheduled R-loops are a major source of replication stress and DNA damage. R-loop-induced defects sensed suppressed by ATR kinase, whereas it is not known whether R-loop itself actively involved in activation and, if so, how this achieved. Here, we report that the nuclear form RNA-editing enzyme ADAR1 promotes resolves genome-wide R-loops, process requires its double-stranded RNA-binding domains. Mechanistically, interacts with TOPBP1 facilitates loading on perturbed forks enhancing association RAD9 9-1-1 complex. When inhibited, DNA-RNA hybrid competes for binding to promote translocation from damaged fork accumulate at region. There, recruits RNA helicases DHX9 DDX21 unwind simultaneously allowing stimulate more efficiently. Collectively, propose tempo-spatially regulated assembly ADAR1-nucleated protein complexes link clearance activation, while crosstalk blocked transposing finetune activity safeguard genome.

Language: Английский

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Direct visualization of replication and R-loop collision using single-molecule imaging

Nucleic Acids Research, Journal Year: 2023, Volume and Issue: 52(1), P. 259 - 273

Published: Nov. 22, 2023

Abstract R-loops are three-stranded nucleic acid structures that can cause replication stress by blocking fork progression. However, the detailed mechanism underlying collision of DNA forks and remains elusive. To investigate how induce stress, we use single-molecule fluorescence imaging to directly visualize replicating Phi29 polymerase (Phi29 DNAp), simplest system, R-loops. We demonstrate a single R-loop block replication, blockage is more pronounced when an RNA–DNA hybrid on non-template strand. show this asymmetry results from secondary structure formation strand, which impedes progression DNAp. also G-quadruplex displaced single-stranded in enhances stalling. Moreover, observe between DNAp RNA transcripts synthesized T7 (T7 RNAp). stalling because presence RNAp. Our work provides insights into impede at resolution.

Language: Английский

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