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ChIP-seq of pro-B cells to test the role of phase separation in EBF1 pioneering function

ABSTRACT: ChIP-seq of pro-B cells to test the role of phase separation in EBF1 pioneering function

PROVIDER: PRJNA945914 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR23901478_1.fastq.gz	Fastqsanger.gz
	SRR23901478_2.fastq.gz	Fastqsanger.gz
	SRR23901479_1.fastq.gz	Fastqsanger.gz
	SRR23901479_2.fastq.gz	Fastqsanger.gz
	SRR23901480_1.fastq.gz	Fastqsanger.gz

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RNA-seq of pro-B cells to test the role of phase separation in EBF1 pioneering function

Project description:EBF1 is a transcription factor crucial for early B cell development. The phase separation ability of the EBF1 C-terminal domain (CTD) is essential for the transcription activation and pioneering function of EBF1. We identified the specific tyrosine residues in the CTD required for phase separation. We transduced pro-B cells with EBF1 wt, deletion of the entire CTD (dC), or mutation of these tyrosines (YmA). We performed ChIP-seq, ATAC-seq, and RNA-seq to see the effect of disrupting phase separation ability on DNA binding, chromatin opening, and target gene expression. Our findings confirm that phase separation is important for the EBF1 function.

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ChIP-seq of pro-B cells to test the role of phase separation in EBF1 pioneering function

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ATAC-seq of pro-B cells to test the role of phase separation in EBF1 pioneering function

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The role of phase separation in EBF1 pioneering function

Project description:The role of phase separation in EBF1 pioneering function

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RNA-seq of pro-B cells to test the role of phase separation in EBF1 pioneering function

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ATAC-seq of pro-B cells to test the role of phase separation in EBF1 pioneering function

Project description:ATAC-seq of pro-B cells to test the role of phase separation in EBF1 pioneering function

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The CTD of EBF1 enhances Brg1 recruitment to chromatin

Project description:EBF1 binds lymphoid progenitor chromatin prior to the detection of chromatin accessibility, whereby a C-terminal domain (CTD) enables “pioneering” independently of cooperating transcription factors. The CTD of EBF1 includes a short prion-like domain (PLD) with an ability of liquid-liquid phase separation in vitro and in vivo. The PLD of EBF1 mediates the recruitment of the chromatin remodeler Brg1 (a subunit of SWI/SNF remodeling complex).

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The role of phase separation in EBF1 pioneering function

Project description:This SuperSeries is composed of the SubSeries listed below.

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A comprehensive Proteomic Investigation of Ebf1 Heterozygosity in pro-B lymphocytes utilizing Data Independent Acquisition

Project description:Early B cell factor 1 (EBF1) is one of the key transcription factors required for orchestrating B-cell lineage development. Although studies have shown that Ebf1 haploinsufficiency is involved in the development of leukemia, no study has been conducted that characterizes the global effect of Ebf1 heterozygosity on the proteome of pro-B lymphocytes. Here, we employ both DIA (Data Independent Acquisition) and shotgun DDA (Data Dependent Acquisition) workflows for profiling proteins that are differently expressed between Ebf1+/+ and Ebf1+/- cells. Both DDA and DIA were able to reveal the downregulation of the EBF1 transcription factor in Ebf1+/- pro-B lymphocytes. Further examination of differentially expressed proteins by DIA revealed that, similar to EBF1, the expression of other B-cell lineage regulators, such as TCF3 and Pax5, is also down-regulated in Ebf1 heterozygous cells. Functional DIA analysis of differentially expressed proteins showed that EBF1 heterozygosity resulted in the deregulation of at least 8 transcription factors involved in lymphopoiesis, and to the deregulation of key proteins playing crucial roles in survival, development and differentiation of pro-B lymphocytes.

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Dynamic EBF1 occupancy directs sequential epigenetic and transcriptional events in B cell programming [EBF1-ChIP-Seq-Cre]

Project description:EBF1 is essential for B cell specification and commitment. To explore the dynamics of EBF1 initiated B cell programming, we performed EBF1 ChIP-seq, ATAC-seq, bisulfite-seq, RNA-seq and several histone ChIP-seq analyses at different stages of the transition from Ebf1-/- pre-pro-B to pro-B triggered by EBF1 restoration. We also performed Pax5 ChIP-seq in Ebf1-/- pre-pro-B cell and EBF1-restored pro-B cell to study the pioneering function of EBF1 that allows other transcription factors to access certain chromatin sites.

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