Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Tight CDK1 inhibition elicits domain-specific pre-RC setting in S-phase, suppressing CFS instability

ABSTRACT: Genome integrity requires replication to be completed before chromosome segregation. This coordination essentially relies on replication-dependent activation of a dedicated checkpoint that inhibits CDK1, delaying mitotic onset. Under-replication of Common Fragile Sites (CFSs), however, escapes surveillance, which generates mitotic chromosome breaks. Using human cells, we asked whether this leakage results from insufficient CDK1 inhibition under modest stresses used to destabilize CFSs. We found that tight CDK1 inhibition does suppress CFS instability in so-stressed cells. Molecular combing and Repli-Seq analyses consistently showed a burst of replication initiations in mid S-phase across large origin-poor domains shaped by transcription, including CFSs. CFS rescue and extra-initiations strikingly require availability of essential pre-Replication Complex (pre-RC) proteins during the S-phase, showing that CDK1 inhibition promotes targeted and mistimed pre-RC reloading. In addition to delay mitotic onset, tight checkpoint activation therefore advances replication completion of origin-poor domains at risk of under-replication, two complementary roles preserving genome stability.

ORGANISM(S): Homo sapiens

PROVIDER: GSE185282 | GEO | 2022/12/31

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Similar Datasets

Tight CDK1 inhibition elicits domain-specific pre-RC setting in S-phase, suppressing CFS instability

Project description:Tight CDK1 inhibition elicits domain-specific pre-RC setting in S-phase, suppressing CFS instability

| PRJNA768449 | ENA

Genome-wide replication dynamics quantification reveals stress-induced delayed/under-replication as a hallmark of CFSs

Project description:We report Repli-Seq analysis of the replication program in human lymphoblasts grown in the absence or in the presence of aphidicolin, an inhibitor of replicative DNA polymerases used in vitro to destabilize CFSs. We identified regions displaying specific replication delay upon aphidicolin treatment, resulting in under-replication. We then further study the mechanisms leading to such specific delayed/under-replication within CFSs and show that transcription-dependent segregation of initiation events out of the gene body generates long-traveling forks in large transcribed domains, which elicits the replication timing delay responsible for CFS instability upon replication stress.

2019-12-29 | GSE134709 | GEO

3D genome organization, transcription and aberrant DNA replication contribute to genome instability at fragile sites

Project description:Common fragile sites (CFSs) are regions susceptible to replication stress and are hotspots for chromosomal instability in cancer. Several features characterizing CFSs have been associated with their instability, however, these features are prevalent across the genome and do not account for all known CFSs. Here we explored the DNA replication timing (RT) and transcriptional profile under mild replication stress in the context of the 3D genome organization. We report the analysis of DNA replication timing profiling of human fibroblasts (BJ-hTERT), grown with or without aphidicolin, a DNA polymerase inhibitor used to induce CFS expression. We find that aphidicolin treatment affects the RT of a small portion of the genome. However, CFSs are enriched for delayed RT regions under stress. We further study the mechanism leading to recurrent chromosomal instability at CFSs and find that the 3D genome organization underlies fragility at RT delayed large expressed genes. We report a fragility signature at the core of CFSs comprised of delayed replication of large expressed gene spanning over a TAD-boundary. The fragility signature allows for mapping of the core fragile site and the identification of novel fragile sites in BJ cells.

2020-06-09 | GSE150543 | GEO

3D genome organization, transcription and aberrant DNA replication contribute to genome instability at fragile sites

Project description:Common fragile sites (CFSs) are regions susceptible to replication stress and are hotspots for chromosomal instability in cancer. Several features characterizing CFSs have been associated with their instability, however, these features are prevalent across the genome and do not account for all known CFSs. Here we explored the transcriptional profile and DNA replication timing under mild replication stress in the context of the 3D genome organization. We report the analysis of nascent RNA-seq for high-throughput profiling of gene expression in human fibroblasts (BJ-hTERT), grown with or without aphidicolin, a DNA polymerase inhibitor used to induce CFS expression. We find that aphidicolin treatment does not affect the transcriptional program. However, large expressed genes are susceptible to replication timing delay under stress. We further study the mechanism leading to recurrent chromosomal instability at CFSs and find that the 3D genome organization underlies fragility at large expressed genes. We report a fragility signature at the core of CFSs comprised of a large expressed gene spanning over a TAD-boundary with delayed DNA replication. The fragility signature allows for mapping of the core fragile site and the identification of novel fragile sites in BJ cells.

2020-06-08 | GSE150354 | GEO

TDP1 phosphorylation at S61 promotes Top1cc repair via the MUS81-dependent pathway during mitosis

Project description:Topoisomerase 1 (Top1) removes supercoils from DNA during replication and transcription, is critical for mitotic progression to the G1 phase, and ensures DNA topology. Tyrosyl-DNA phosphodiesterase 1 (TDP1) mediates the removal of trapped Top1-DNA covalent complexes (Top1ccs). Here, we identify CDK1-dependent phosphorylation of TDP1 at S61 residue during mitosis. TDP1 defective for S61 phosphorylation (TDP1S61A) is trapped on the mitotic chromosomes, triggering DNA damage and mitotic defects. Moreover, we show that Top1cc repair in mitosis occurs via MUS81-dependent mitotic DNA repair mechanism. Replication stress (RS) induced by Camptothecin (CPT) or Aphidicolin (APH) leads to TDP1S61A enrichment at common fragile sites (CFSs), which over-stimulates MUS81-dependent chromatid breaks, anaphase bridges, and micronuclei, ultimately culminating in 53BP1 nuclear bodies in the G1-phase. Our findings provide a new insight into the cell cycle-dependent regulation of TDP1 dynamics forthe repair of trapped Top1ccs during mitosis that prevents genomic instability following RS.

2024-06-26 | PXD053309 | Pride

Coupling of Cdc20 inhibition and activation by BubR1

Project description:Tight regulation of the APC/C-Cdc20 ubiquitin ligase that targets Cyclin B1 for degradation is important for mitotic fidelity. The spindle assembly checkpoint (SAC) inhibits Cdc20 through the mitotic checkpoint complex (MCC). In addition, phosphorylation of Cdc20 by Cyclin B1-Cdk1 independently inhibits APC/C-Cdc20 activation. This creates a conundrum for how Cdc20 gets activated prior to Cyclin B1 degradation. Here we show that the MCC component BubR1 harbours both Cdc20 inhibition and activation activities, allowing for cross-talk between the two Cdc20 inhibition pathways. Specifically BubR1 acts as a substrate specifier for PP2A-B56 to enable efficient Cdc20 dephosphorylation in the MCC. A mutant Cdc20 mimicking the dephosphorylated state escapes a mitotic checkpoint arrest arguing that restricting Cdc20 dephosphorylation to the MCC is important. Collectively our work reveals how Cdc20 can be dephosphorylated in the presence of Cyclin B1-Cdk1 activity without causing premature anaphase onset.

2021-02-18 | MSV000086910 | MassIVE

Genome-wide Analysis of Re-replication Reveals Inhibitory Controls that Target Multiple Stages of Replication Initiation

Project description:DNA replication must be tightly controlled during each cell cycle to prevent unscheduled replication and ensure proper genome maintenance. The currently known controls that prevent re-replication act redundantly to inhibit pre-Replicative Complex (pre-RC) assembly outside of the G1 phase of the cell cycle. We have analyzed the effects of re-replication on the S. cerevisiae genome using a combination of Comparitive Genomic Hybridization (CGH) of re-replicating strains and Genome-Wide Location Analysis of pre-RC components. These data indicate which sites in the genome assemble pre-RCs under re-replication conditions, which sites undergo re-initiation and the extent of re-replication. Keywords: comparative genomic hybridization, ChIP-chip, re-replication, DNA replication, pre-RC

2006-03-20 | GSE4487 | GEO

Genome-wide map of DNA replication origin in Schizosaccharomyces pombe

Project description:DNA replication origins, or DNA sites pre-RC is bound to, were identified by ChIP-seq of pre-RC components, Orc4 and Mcm2. DNA copy number analysis revealed that ~40% of the detected sites were efficient and early-firing origins.

2019-01-19 | GSE125335 | GEO

Genome-wide High Resolution Mapping of Mitotic DNA Synthesis Sites and Common Fragile Sites by Direct Sequencing [WGS]

Project description:Common fragile sites (CFSs) are genomic loci prone to the formation of breaks or gaps on metaphase chromosomes. Here, we seek to map human CFSs with high resolution on a genome-wide scale by sequencing the sites of mitotic DNA synthesis (MiDASeq) that are specific for CFSs. We generated a nucleotide-resolution atlas of MiDAS sites (MDSs) that covered most of know CFSs, and comprehensively analyzed their sequence characteristics and genomic features.

2020-05-01 | GSE149375 | GEO