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Topoisomerase 1 prevents replication stress at R-loop-enriched transcription termination sites

ABSTRACT: Topoisomerase 1 prevents replication stress at R-loop-enriched transcription termination sites

PROVIDER: PRJNA422724 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR11851373.fastq.gz	Fastqsanger.gz
	SRR11851374.fastq.gz	Fastqsanger.gz
	SRR6491520.fastq.gz	Fastqsanger.gz
	SRR6491530.fastq.gz	Fastqsanger.gz
	SRR6491540.fastq.gz	Fastqsanger.gz

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Topoisomerase 1 prevents replication stress at R-loop-enriched transcription termination sites

Project description:R-loops have both positive and negative impacts on chromosome functions. To identify toxic R-loops in the human genome, we have mapped RNA:DNA hybrids, replication stress markers and DNA double strand breaks (DSBs) in cells depleted for Topoisomerase I (Top1), an enzyme that relaxes DNA supercoiling and prevents R-loop formation. RNA:DNA hybrids were found at both promoters (TSS) and terminators (TTS) of highly expressed genes. In contrast, the phosphorylation of RPA by ATR was only detected at TTS, which are preferentially replicated in a head-on orientation relative to the direction of transcription. In Top1-depleted cells, DSBs also cumulated at TTS, leading to persistent checkpoint activation, spreading of -H2AX on chromatin and global replication fork slowdown. These data indicate that fork pausing at the TTS of highly expressed genes containing R-loops prevents head-on conflicts between replication and transcription and maintains genome integrity in a Top1-dependent manner.

2020-06-20 | GSE108172 | GEO

Topoisomerase 1 prevents replication stress at R-loop-enriched transcription termination sites.

Project description:R-loops have both positive and negative impacts on chromosome functions. To identify toxic R-loops in the human genome, here, we map RNA:DNA hybrids, replication stress markers and DNA double-strand breaks (DSBs) in cells depleted for Topoisomerase I (Top1), an enzyme that relaxes DNA supercoiling and prevents R-loop formation. RNA:DNA hybrids are found at both promoters (TSS) and terminators (TTS) of highly expressed genes. In contrast, the phosphorylation of RPA by ATR is only detected at TTS, which are preferentially replicated in a head-on orientation relative to the direction of transcription. In Top1-depleted cells, DSBs also accumulate at TTS, leading to persistent checkpoint activation, spreading of γ-H2AX on chromatin and global replication fork slowdown. These data indicate that fork pausing at the TTS of highly expressed genes containing R-loops prevents head-on conflicts between replication and transcription and maintains genome integrity in a Top1-dependent manner.

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m6A facilitates transcription termination by promoting R-loop formation

Project description:m6A facilitates transcription termination by promoting R-loop formation

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R-loop dependent promoter-proximal termination ensures genome stability

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ZFP281-BRCA2 prevents R-loop accumulation during DNA replication

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DNA Topoisomerase I differentially modulates R loop across long genes and at human replication origins

Project description:Co-transcriptional R-loops are abundant non-B DNA structures in mammalian genomes. DNA Topoisomerase I (Top1) is often thought to regulate R-loop formation owing to its ability to resolve both positive and negative supercoils. How Top1 regulates R-loop structures at a global level is unknown. Here, we performed high-resolution strand-specific R-loop mapping in human cells depleted for Top1 and found that Top1 depletion resulted in both R-loop gains and losses at thousands of transcribed loci, delineating two distinct gene classes. R-loop gains were characteristic for long, highly transcribed, genes located in gene-poor regions anchored to Lamin B1 domains and in proximity to H3K9me3-marked heterochromatic patches. R-loop losses, by contrast, occurred in gene-rich regions overlapping H3K27me3-marked active replication origins. Interestingly, Top1 depletion coincided with a block of the cell cycle in G0/G1 phase and a trend towards global replication delay. Our findings reveal new properties of Top1 in regulating R-loop homeostasis and suggest a potential role for Top1 in controlling replication origin via R-loop formation.

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R-loop dependent promoter-proximal termination ensures genome stability [CUT&Tag]

Project description:R-loop dependent promoter-proximal termination ensures genome stability [CUT&Tag]

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R-loop dependent promoter-proximal termination ensures genome stability [PRO-seq]

Project description:R-loop dependent promoter-proximal termination ensures genome stability [PRO-seq]

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R-loop dependent promoter-proximal termination ensures genome stability [ATAC-seq]

Project description:R-loop dependent promoter-proximal termination ensures genome stability [ATAC-seq]

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R-loop dependent promoter-proximal termination ensures genome stability [ChIP-seq]

Project description:R-loop dependent promoter-proximal termination ensures genome stability [ChIP-seq]