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Homo sapiens

ABSTRACT: PREP1 down-regulation changes the DNA replication timing of Lamin-associated DNA and induces DNA damage [Repli-Seq]

PROVIDER: PRJNA395425 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR5860270.fastq.gz	Fastqsanger.gz
	SRR5860271.fastq.gz	Fastqsanger.gz
	SRR5860272.fastq.gz	Fastqsanger.gz
	SRR5860273.fastq.gz	Fastqsanger.gz
	SRR5860264.fastq.gz	Fastqsanger.gz

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PREP1 down-regulation changes the DNA replication timing of Lamin-associated DNA and induces DNA damage [RNA-Seq]

Project description:Down-regulation (DR) of PREP1 (aka PKNOX1) tumor suppressor induces H2Ax foci in human fibroblasts. Here we have analyzed the effect of PREP1 DR on DNA replication using cell cycle analysis, Repliseq, DNA combing, ChIP-seq, RNA-seq and immunofluorescence (IF). In human cells, PREP1 DR similarly affects both the rate of DNA replication and the progression of cells through the S phase. Genome wide, PREP1 DR induces late to early DNA replication shifts in normally late-replicated genomic regions amounting to 25% of the genome, in addition to unscheduled origins firing. A concomitant strong increase of unidirectional replication forks explains the appearance of DNA damage foci. The DNA target of PREP1 DR is the Lamin Associated DNA, in agreement with the simultaneous decrease of Lamin B1. Therefore PREP1 is a novel regulator of replication timing and Lamin B1 level, which ChIP-seq and RNA-seq data indicate as independent from its transcriptional activity. This activity must constitute the basis for its tumor suppression function.

2018-02-28 | GSE101774 | GEO

PREP1 down-regulation changes the DNA replication timing of Lamin-associated DNA and induces DNA damage [ChIP-Seq]

2018-02-28 | GSE101773 | GEO

PREP1 down-regulation changes the DNA replication timing of Lamin-associated DNA and induces DNA damage [Repli-Seq]

2018-02-28 | GSE101775 | GEO

PREP1 down-regulation changes the DNA replication timing of Lamin-associated DNA and induces DNA damage

Project description:PREP1 down-regulation changes the DNA replication timing of Lamin-associated DNA and induces DNA damage

| PRJNA395422 | ENA

Homo sapiens

Project description:PREP1 down-regulation changes the DNA replication timing of Lamin-associated DNA and induces DNA damage [ChIP-Seq]

| PRJNA395427 | ENA

Homo sapiens

Project description:PREP1 down-regulation changes the DNA replication timing of Lamin-associated DNA and induces DNA damage [RNA-Seq]

| PRJNA395426 | ENA

Camptothecin-Induced Replication Stress Affects DNA Replication Profiling by E/L Repli-Seq

Project description:E/L Repli-seq is a powerful tool for detecting cell type-specific replication landscapes in mammalian cells, but its potential to monitor DNA replication under replication stress awaits better understanding. Here, we used E/L Repli-seq to examine the temporal order of DNA replication in human retinal pigment epithelium cells treated with the topoisomerase I inhibitor camptothecin. We found that the replication profiles by E/L Repli-seq exhibits characteristic patterns after replication-stress induction, including the loss of specific initiation zones within individual early replicating timing domains. We also observed global disappearance of the replication timing domain structures in the profiles, which can be explained by checkpoint-dependent suppression of replication initiation. Thus, our results demonstrate the effectiveness of E/L Repli-seq at identifying cells with replication-stress-induced altered DNA replication programs.

2021-09-30 | GSE167045 | GEO

Cohesin maintains replication timing to suppress DNA damage on cancer genes [MYC-repli-stress]

Project description:Cohesin maintains replication timing to suppress DNA damage on cancer genes [MYC-repli-stress]

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Genome-wide analysis of replication timing in preimplantation mouse embryos

Project description:Replication timing is cell type specific, is tightly linked to the 3D nuclear organisation of the genome and is considered an epigenetic fingerprint. In spite of its importance in maintaining the epigenome the developmental regulation of replication timing in mammals in vivo has not been explored. Here, using single cell Repli-seq, we generated the genome-wide replication timing maps of mouse embryos from the zygote until the blastocyst stage.

2023-10-16 | GSE218365 | GEO

The establishment of a DNA replication timing program in the early embryo.

Project description:Single Embryo Repli-Seq was utilized to investigate the replication timing in zygotes and 2-cell cleavage stage embryos. The aim was to understand the temporal progression of DNA replication during the early stages of embryonic development in mammals.

2024-05-23 | GSE237400 | GEO

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