Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

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

ABSTRACT: 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.

ORGANISM(S): Mus musculus

PROVIDER: GSE227615 | GEO | 2024/01/18

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Similar Datasets

ChIP-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.

2024-01-18 | GSE227614 | GEO

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

2024-01-18 | GSE227613 | GEO

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).

2020-11-08 | GSE145991 | GEO

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.

2017-12-20 | PXD008396 | Pride

Gene expression profile of EBF1-wt & EBF1-H240A

Project description:To study the function of EBF1-H240 residue, a gain-of function microarray analysis was performed by transducing Empty, Ebf1-wt and Ebf1-H240A expressing vectors into Ebf1-/- progenitor cells.

2016-11-21 | GSE87634 | GEO

The CTD of EBF1 enhances Brg1 recruitment to chromatin

Project description:The CTD of EBF1 enhances Brg1 recruitment to chromatin

| PRJNA608933 | ENA

Ebf1 ChIP

Project description:Ebf1 is a key determinant of B-lymphocyte specification. In order to identify unknown transcriptional targets, endogenous Ebf1 was isolated by chromatin-IP from primary pro-B cells and the copurified DNA was hybridized to promoter tiling arrays. Ebf1 was ChIPed using a polyclonal antibody directed against an N-terminal peptide from primary pro-B cells grown in the presence of Il7. The resulting DNA was analyzed by tiling array hybridization.

2010-06-24 | E-GEOD-21469 | biostudies-arrayexpress

Gene expression analysis after reconstitution of Ebf1-deficient pre-pro-B cells with Ebf1

Project description:Ebf1 deficient pre-pro B-cells (Fraction A) can be cultured in the presence of stromal feeders and cytokines. The retroviral transduction of these cells with Ebf1 was used as gain-of-function experiment for the analysis of direct and functional target genes of Ebf1. Ebf1 deficient pre-pro B-cells were retrovirally transduced with an Ebf1-expressing or control retrovirus. 24h after transduction the infected cells were isolated and their gene expression profile was compared.

2010-07-29 | E-GEOD-21455 | biostudies-arrayexpress

Transcription factor Ebf1 regulates differentiation stage-specific signaling, proliferative expansion and survival of B cells [EBF1]

Project description:Transcription factor Ebf1 is an important determinant of early B lymphopoiesis. To gain insight into differentiation stage-specific functions of Ebf1, we conditionally inactivated Ebf1. We found that Ebf1 is required for proliferation, survival and signaling of pro-B cells and peripheral B cell subsets. The proliferation defect of Ebf1-deficient pro-B cells, including the impaired expression of IL-7Ra and several cell cycle regulators, is overcome by transformation with v-Abl. The survival defect of transformed Ebf1fl/fl pro-B cells can be rescued by the forced expression of the Ebf1 targets c-Myb or Bcl-xL. In mature B cells, Ebf1 deficiency interferes with the BAFF-R and BCR-dependent Akt signaling pathways, as well as with germinal center formation and class switch recombination. Genome-wide analyses of Ebf1 binding and Ebf1-mediated gene expression in mature B cells and comparison with reported data sets in pro-B cells provide insight into the basis for lineage- and stage-specific functions of Ebf1. EBF1 binding in splenic B cells in mice

2012-04-02 | E-GEOD-35910 | biostudies-arrayexpress

Genome-wide occupancy of EBF1-wt & EBF1-H240A

Project description:To study the function of EBF1-H240 residue, genome-wide EBF1 ChIP was performed in A-MuLV transformed pro-B (Ebf1fl/fl;RERTCre) cells transduced with Ebf1wt and Ebf1H240A expressing vectors.

2016-11-21 | GSE87636 | GEO

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data