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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 II

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

ORGANISM(S): Mus musculus

PROVIDER: GSE216655 | GEO | 2023/03/19

REPOSITORIES: GEO

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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 SMARCE1 and SOX2 deposition in DMSO or BRM014 treated Smarce1-MD(R42A) and Smarce1-MD cells at 90 min after releasing from mitosis.

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The study of nascent RNA transcripts in asynchronous cells and cells released from mitosis at the indicated timepoints between Smarce1- MD (R42A) and Smarce1- MD mESCs.

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Transcription profiling of Smarce1- MD (R42A) and Smarce1- MD mESCs with BMP4 rescue.

Project description:To evaluate the effects of mitotic degradation of SMARCE1 upon gene expression, we performed RNA-sequencing (RNA-seq) of cultures of four independent subclones each of Smarce1-MD and control Smarce1-MD (R42A) mESCs. We found that transcription of the core pluripotency regulatory network was not disrupted. In contrast, GO analysis showed that neural differentiation-associated terms were enriched among genes upregulated in Smarce1-MD mESCs. To better understand the difference in neural fates in the neural induction experiments, we performed differential gene expression analysis and gene set enrichment analysis (GSEA) studies. Mitotic degradation of SMARCE1 resulted in higher expression of GABA receptors and hyper-activation of synaptic signaling on neural induction, indicating the aberrant neural cell fate commitment compared to SMARCE1-MD (R42A) cultures. And then we add back BMP4 to partically rescue the phenotype and very small amount of BMP4 will rescue the phenotype.

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