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Homo sapiens

ABSTRACT: Genome-wide mapping of CTCF binding in asynchronous and mitotic cells

PROVIDER: PRJNA396218 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR7647830_1.fastq.gz	Fastqsanger.gz
	SRR7647830_2.fastq.gz	Fastqsanger.gz
	SRR7647827_1.fastq.gz	Fastqsanger.gz
	SRR7647827_2.fastq.gz	Fastqsanger.gz
	SRR7647828_1.fastq.gz	Fastqsanger.gz

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Homo sapiens

Project description:FoxA1 binding in asynchronous and mitotic HUH7 cells

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Mapping of CTCF occupancy in interphase and mitosis cells

Project description:To address whether CTCF is involved in the transcription of early G1 genes immediately after mitotic exit, we carried out ChIP sequencing (ChIP-seq) experiments to evaluate CTCF binding to genomic DNA in asynchronous cells and nocodazole-arrested mitotic cells. Of the 62,996 peaks identified in the asynchronous cells, 41,397 peaks (65.71%) were lost in the mitotic cells. However, the 21,599 peaks (34.29%) were identified in the both conditions, indicating that the enrichment level of CTCF is decreased in the mitotic cells. It has been reported that expression profiles of the first 2 hours of G1 phase in HeLa cells. A scatter plot comparison of the genes expressed in the early G1 phase indicated the reduced CTCF binding level in the mitotic phase. These results indicate that CTCF was dissociated or CTCF bound to chromosomes was reduced in the mitotic chromatin and then may be re-associated to chromatin in the early G1 phase.

2019-06-18 | GSE83579 | GEO

Genome-wide analysis of mitosis, early G1, late G1 and G2 in mouse pluripotent cells

Project description:We provide the genome-wide map of Esrrb binding in mitotic and asynchronous ES cells together with the Esrrb-induced transcriptomic changes in early G1, late G1 and G2.

2016-08-29 | GSE75066 | GEO

Mus musculus

Project description:Genome-wide analysis of SOX2 binding in asynchronous and mitotic mouse embryonic stem cells.

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Brn2 (POU3F2) ChIP-seq data obtained from asynchronous or mitotically arrested mouse neural stem/progenitor cells

Project description:dataset contains 8 samples: 2 asynchronous and 2 mitotically synchronized populations (one with 90% and another with 95% mitotic purity) and 4 corresponding inputs. Cells were synchonized for 10h with colchicine at 330nM. asyncronous samples (interphase) were sonicated and prepared in parallel with same cell number as the corresponding mitotic samples. Fetal neural stem/progenitor cells were obtained from mouse telencephalon (ventral region) at E13.5. This data generated 4 genome-wide binding profiles corresponding to Brn2 (POU3f2) binding sites, aligned to MM9 mus musculus dataset.

2021-02-13 | E-MTAB-9758 | biostudies-arrayexpress

Homo sapiens

Project description:Genome-wide mapping of MYCN binding in neuroblastoma cells

| PRJNA294529 | ENA

Genome-wide analysis of SOX2 binding in asynchronous and mitotic mouse embryonic stem cells.

Project description:SOX2 is part of the core network of transcription factors regulating embryonic stem cell pluripotency. We found that SOX2 has the ability to remain bound to mitotic chromosomes, in contrast to most transcription factors that are excluded from mitotic chromatin as transcription shuts down. We obtained a highly purified population of mitotic mouse embryonic stem cells and compared the genome-wide binding profile of SOX2 to that in asynchronous cells by Chromatin Immunoprecipitation followed by high throughput sequencing (ChIP-seq), and show that SOX2 remains bound to a small set of genes during mitosis.

2016-11-07 | GSE89599 | GEO

Expression and FoxA1 binding in asynchronous and mitotic HUH7 cells

Project description:Expression and FoxA1 binding in asynchronous and mitotic HUH7 cells

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Homo sapiens

Project description:Genome-wide mapping of OCT4, NANOG and CTCF in human embryonic stem cells

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Exploring the interaction between the SWI/SNF chromatin remodeling complex and the zinc finger factor CTCF

Project description:The transcription factor CCCTC-binding factor (CTCF) modulates pleiotropic functions mostly related to gene expression regulation. The role of CTCF in large scale genome organization is also well established. A unifying model to explain relationships between many CTCF-mediated activities involve direct or indirect interactions with numerous protein cofactors recruited to specific binding sites. The co-association of CTCF with other architectural proteins such as cohesin, chromodomain helicases and BRG1 further support the interplay between master regulators of mammalian genome folding. Here we report a comprehensive LC-MS/MS mapping of the components of the SWI/SNF chromatin remodeling complex co-associated with CTCF including subunits belonging to the core, signature and ATPase modules. We further show that the localization patterns of representative SWI/SNF members significantly overlap with CTCF sites on transcriptionally active chromatin regions. Moreover, we provide evidence of a direct binding of the BRK-BRG1 domain to the zinc finger motifs 4-8 of CTCF, thus suggesting that these domains mediate the interaction of CTCF with the SWI/SNF complex. These findings provide an updated view of the cooperative nature between CTCF and the SWI/SNF ATP-dependent chromatin-remodeling complexes, an important step for understanding how these architectural proteins collaborate to shape the genome.

2021-09-09 | PXD022037 | Pride

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