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Reorganization of the DNA replication landscape during mitotic clonal expansion is closely linked with adipogenic gene expression [E/L Repli-seq (BrdUIP), scRepli-seq]

ABSTRACT: Reorganization of the DNA replication landscape during mitotic clonal expansion is closely linked with adipogenic gene expression [E/L Repli-seq (BrdUIP), scRepli-seq]

PROVIDER: PRJNA895359 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR22077800.fastq.gz	Fastqsanger.gz
	SRR22077801.fastq.gz	Fastqsanger.gz
	SRR22077802.fastq.gz	Fastqsanger.gz
	SRR22077803.fastq.gz	Fastqsanger.gz
	SRR22077804.fastq.gz	Fastqsanger.gz

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Reorganization of the DNA replication landscape during mitotic clonal expansion is closely linked with adipogenic gene expression [E/L Repli-seq (BrdUIP), scRepli-seq]

Project description:The temporal order of DNA replication along chromosomes is reorganized in the context of cell differentiation and disease states and is thought to reflect transcriptional competence of the genome. During differentiation of mouse 3T3-L1 cells into adipocytes, cells undergo one or two rounds of cell division called mitotic clonal expansion (MCE). MCE is an essential step for adipogenesis; however, little is known about the regulation of DNA replication during this period. Here, we performed genome-wide mapping of replication timing (RT) in mouse 3T3-L1 cells before and during MCE and identified a number of chromosomal regions shifting toward either earlier or later replication through two rounds of replication. These RT changes were confirmed in individual cells by single-cell DNA replication sequencing. Coordinate changes between a shift toward earlier replication and transcriptional activation of adipogenesis-associated genes were observed. RT changes occur before full expression of these genes, indicating that RT reorganization may contribute to the mature adipocyte phenotype. To support this, cells undergoing two rounds of DNA replication during MCE have higher potential to differentiate into lipid droplet-accumulating adipocytes, compared with cells undergoing a single round of DNA replication and non-replicating cells.

2022-12-22 | GSE216767 | GEO

Reorganization of the DNA replication landscape during mitotic clonal expansion is closely linked with adipogenic gene expression

Project description:Reorganization of the DNA replication landscape during mitotic clonal expansion is closely linked with adipogenic gene expression

| PRJNA895357 | ENA

Reorganization of the DNA replication landscape during mitotic clonal expansion is closely linked with adipogenic gene expression [RNA-seq]

Project description:Reorganization of the DNA replication landscape during mitotic clonal expansion is closely linked with adipogenic gene expression [RNA-seq]

| PRJNA895350 | ENA

scRepli-seq analysis of aphidicolin treated embryos

Project description:To analyze chromosome abnormalities of 8-cell embryos with/without aphidicolin treatment, we performed single cell replication sequencing (scRepli-seq). This submission is similar to our submission GSE226309.

2024-06-24 | GSE255456 | GEO

scRepli-seq analysis of SCNT 4-cell and 8-cell embryos

Project description:To analyze replication timing of SCNT 4-cell and 8-cell embryos, we performed single cell replication sequencing (scRepli-seq). This submission is similar to our submission GSE226309.

2024-06-24 | GSE255457 | GEO

Reorganization of the DNA replication landscape during mitotic clonal expansion is closely linked with adipogenic gene expression [RNA-seq]

2022-12-22 | GSE216765 | GEO

Mouse ESC 46C replication analysis by repli-chip

Project description:Mouse ESC 46C replication timing has been assessed by repli-chip.

2017-07-28 | GSE95090 | GEO

scRepli-seq analysis of aphidicolin treated embryos

Project description:scRepli-seq analysis of aphidicolin treated embryos

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genome-wide analysis of replication timing by repli-chip and repli-seq

Project description:genome-wide analysis of replication timing by repli-chip and repli-seq

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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

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