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The study of SWI/SNF subunits and other transcription factors deposition in asynchronous and mitotic mESCs and cells released from mitosis

ABSTRACT: The study of SWI/SNF subunits and other transcription factors deposition in asynchronous and mitotic mESCs and cells released from mitosis

PROVIDER: PRJNA783615 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR17038400_1.fastq.gz	Fastqsanger.gz
	SRR17038400_2.fastq.gz	Fastqsanger.gz
	SRR17038401_1.fastq.gz	Fastqsanger.gz
	SRR17038401_2.fastq.gz	Fastqsanger.gz
	SRR17038402_1.fastq.gz	Fastqsanger.gz

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The study of SWI/SNF subunits and other transcription factors deposition in asynchronous and mitotic mESCs and cells released from mitosis

Project description:We executed CUT&RUN-seq for SWI/SNF components ARID1A, BRD9, SMARCA4, SMARCB1, SMARCE1, as well as ESRRB, SOX2, and EZH2 in asynchronous and mitotic cells and reported that, in asynchronous cells, ARID1A localized primarily at enhancer regions and EZH2 preferentially deposited at bivalent promoters and silent enhancer domains. The remaining factors were enriched at both TSS/promoters and to varying degrees at active enhancers. Unexpectedly, in mitosis, the chromatin regulatory factors almost all tethered at proximal gene regions with very little binding at enhancers. While the SWI/SNF subunits were bound principally at promoters, EZH2, the catalytic subunit of Polycomb Repressive Complex 2 was bound at both promoters and silent enhancers in mitotic cells. Moreover, we reported that upon the degradation of SMARCE1 in mitosis, the occupancy of SOX2, ESRRB, and EZH2 on mitotic chromatin was disrupted.

2023-03-19 | GSE189560 | GEO

The study of SWI/SNF subunits and other transcription factors deposition in asynchronous and mitotic mESCs and cells released from mitosis II

Project description:The study of SWI/SNF subunits and other transcription factors deposition in asynchronous and mitotic mESCs and cells released from mitosis II

| PRJNA894697 | ENA

The study of ESRRB occupancy in asynchronous and mitotic mESCs.

Project description:The study of ESRRB occupancy in asynchronous and mitotic mESCs.

| PRJNA1020083 | ENA

The study of ESRRB occupancy in asynchronous and mitotic mESCs.

Project description:We performed ChIP-seq for ESRRB and investigated its deposition in asynchronous and mitotic cells.

2023-09-22 | GSE243808 | GEO

The study of SWI/SNF subunits and other transcription factors deposition in asynchronous and mitotic mESCs and cells released from mitosis II

Project description:We conduct ATAC-seq in SMARCE1 MD/MD(R42A) after mitotic release 90 min in either DMSO treated or BRG1 inhibitor BRM014 treated conditions

2023-03-19 | GSE216655 | GEO

The study of histone modifications and SOX2 occupancy in asynchronous and mitotic mESCs.

Project description:We performed ChIP-seq for H3K4me3, H3K27ac, H3K4me1, H3K27me3, H3K36me3, H3K9me3, and H4K20me3 to characterize chromatin states and investigated SOX2 deposition in asynchronous and mitotic cells.

2023-03-19 | GSE189561 | GEO

The study of histone modifications and SOX2 occupancy in asynchronous and mitotic mESCs.

Project description:The study of histone modifications and SOX2 occupancy in asynchronous and mitotic mESCs.

| PRJNA783614 | ENA

SERBP1 iCLIP in mitotic and asynchronous cells with Blu577 treatment

Project description:In the associated paper, SERBP1 is shown to form granules in mitotic cells in a PKCɛ-dependent manner (M-bodies). We performed SERBP1 iCLIP in DLD1 cells that were either asynchronous or enriched for mitotic cells and after treatment with 2 hours of 500nM Blu577 or equivalent DMSO. We found that SERBP1 alters its positioning on rRNA in mitosis in a Blu577-dependent manner, identifying an alternative binding position that coincides with the formation of M-bodies. Mitotic enrichment was performed by single thymidine block, release in to G2 block with RO3306, and release and mitotic shake-off. The fastq files provided are demultiplexed, with adapters and barcodes trimmed and UMI sequences are found in the fastq headers.

2021-10-05 | E-MTAB-10830 | biostudies-arrayexpress

Mitotic bookmarking by SWI/SNF subunits

Project description:For cells to initiate and sustain a differentiated state, it is necessary that a “memory” of this state is transmitted through mitosis to the daughter cells. Mammalian SWItch/ Sucrose Non- Fermentable (SWI/SNF) complexes, also called Brg1/ Brg- associated factors (BAF), control cell identity by modulating chromatin architecture to regulate gene expression, but whether they participate in cell fate memory is unclear. Here, we provide evidence that subunits of SWI/SNF act as mitotic bookmarks to safeguard cell identity during cell division. The SWI/SNF core subunits SMARCE1 and SMARCB1 are displaced from enhancers but bound on promoters during mitosis and we show that this binding is required for appropriate reactivation of bound genes after mitotic exit. Ablation of SMARCE1 during a single mitosis in mouse embryonic stem cells is sufficient to disrupt gene expression, impair the occupancy of several established bookmarks at a subset of their targets, and cause aberrant neural differentiation. Thus, SWI/SNF subunit SMARCE1 plays a mitotic bookmarking role and is essential for heritable epigenetic fidelity during transcriptional reprogramming.

2023-03-18 | GSE189563 | GEO

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

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