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The fork protection complex generates DNA topological stress-induced DNA damage while ensuring full and faithful genome duplication [TrAEL-seq]

ABSTRACT: The fork protection complex generates DNA topological stress-induced DNA damage while ensuring full and faithful genome duplication [TrAEL-seq]

PROVIDER: PRJNA1001842 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR25503014.fastq.gz	Fastqsanger.gz
	SRR25503015.fastq.gz	Fastqsanger.gz
	SRR25503016.fastq.gz	Fastqsanger.gz
	SRR25503017.fastq.gz	Fastqsanger.gz

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The fork protection complex generates DNA topological stress-induced DNA damage while ensuring full and faithful genome duplication [TrAEL-seq]

Project description:The fork protection complex (FPC), composed of Mrc1, Tof1, and Csm3, supports rapid and stable DNA replication. Here, we show that FPC activity also introduces DNA damage by increasing DNA topological stress during replication. Mrc1 action increases DNA topological stress during plasmid replication, while Mrc1 or Tof1 activity causes replication stress and DNA damage within topologically constrained regions. We show that the recruitment of Top1 to the fork by Tof1 suppresses the DNA damage generated in these loci. While FPC activity introduces some DNA damage due to increased topological stress, the FPC is also necessary to prevent DNA damage in long replicons across the genome, indicating that the FPC is required for complete and faithful genome duplication. We conclude that FPC regulation must balance ensuring full genome duplication through rapid replication with minimizing the consequential DNA topological stress-induced DNA damage caused by rapid replication through constrained regions.

2024-10-21 | GSE239966 | GEO

The fork protection complex generates DNA topological stress-induced DNA damage while ensuring full and faithful genome duplication [ChIP-seq]

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The Fork Protection Complex generates DNA topological stress induced DNA damage while ensuring full and faithful genome duplication

Project description:The Fork Protection Complex generates DNA topological stress induced DNA damage while ensuring full and faithful genome duplication

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The fork protection complex generates DNA topological stress-induced DNA damage while ensuring full and faithful genome duplication [ChIP-seq]

Project description:The fork protection complex generates DNA topological stress-induced DNA damage while ensuring full and faithful genome duplication [ChIP-seq]

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The fork protection complex generates DNA topological stress-induced DNA damage while ensuring full and faithful genome duplication.

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TrAEL-seq captures DNA replication

Project description:TrAEL-seq captures DNA replication

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The Fork Protection Complex generates DNA topological stress induced DNA damage while ensuring full and faithful genome duplication

Project description:This SuperSeries is composed of the SubSeries listed below (GSE239965, GSE239966).

2024-10-21 | GSE239967 | GEO

TrAEL-seq captures DNA replication dynamics in mammalian cells

Project description:Precise DNA replication is critical to the maintenance of genome stability, and the DNA replication machinery is a focal point of many current and upcoming chemotherapeutics. TrAEL-seq is a robust method for profiling DNA replication genome-wide that works in unsynchronised cells and does not require treatment with drugs or nucleotide analogues. Here, we provide an updated method for TrAEL-seq including multiplexing of up to 6 samples that dramatically improves sample quality and throughput, and we validate TrAEL-seq in multiple mammalian cell lines. The updated protocol is straightforward and robust yet provides excellent resolution comparable to OK-seq in mammalian cell samples, and does not require cell synchronisation, drug treatment, labelling or sorting. High resolution replication profiles can be obtained across large panels of samples and in dynamic systems, for example during the progressive onset of oncogene induced senescence. In addition to mapping zones where replication initiates and terminates, TrAEL-seq is sensitive to replication fork speed, revealing effects of both transcription and proximity to replication initiation zones on fork progression. Although forks move more slowly through transcribed regions, this does not have a significant impact on the broader dynamics of replication fork progression, which is dominated by rapid fork movement in long replication regions (>1Mb). Short and long replication regions are not intrinsically different, and instead replication forks accelerate across the first ~1 Mb of travel such that forks progress faster in the middle of regions lying between widely spaced initiation zones. We propose that this is a natural consequence of fewer replication forks being active later in S phase when these distal regions are replicated and there being less competition for replication factors.

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Genome-wide analysis of DNA replication by TrAEL-seq in mouse embryonic stem cells

Project description:We have applied the TrAEL-seq method to profile DNA replication in wild type and Snf2h knockoutmouse embryonic stem cells.

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