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Series GSE104045 Query DataSets for GSE104045
Status Public on Jul 19, 2018
Title System-wide Dissection of the Transcriptional Response to RUNX1 During Hematopoietic Specification [ChIP-seq]
Organism Mus musculus
Experiment type Genome binding/occupancy profiling by high throughput sequencing
Summary The specification of hematopoietic cells in the developing embryo occurs in specific stages and is regulated by the successive establishment of specific transcriptional networks. However, the molecular mechanisms of how the different stages switch from one to another are still not well understood. Hematopoietic cells arise from endothelial cells within the dorsal aorta which transit into hematopoietic cells by a process called the endothelial-hematopoietic transition (EHT) which does not involve DNA replication. The transcription factor RUNX1 is essential for this process. Using the differentiation of mouse embryonic stem cells carrying an inducible version of RUNX1, we have previously shown that hematopoietic genes are primed prior to the EHT by the binding of transcription factors required to form both endothelial and hematopoietic cells (FLI-1 and SCL/TAL1). We demonstrated that after induction RUNX1 reshapes the transcription factor binding landscape by causing a relocation of these factors and pulling them towards its binding sites. In the study presented here, we employed the same system to globally dissect the transcriptional processes that underlay the EHT. We demonstrate that the RUNX1-mediated movement of FLI-1 involves the recruitment of the basal transcription components CDK9 and BRD4 to promoters. The looping factor LDB1 to binds to distal elements and after induction relocates towards RUNX1/FLI-1 to form a co-localizing complex in chromatin. This entire process is blocked by treatment with the BRD4 inhibitor JQ1. Our study constitutes a paradigm for transcriptional processes driving transitions in cellular shape and function which are widely observed in development and disease.
 
Overall design ChIP-seq expreiments have been used to study RUNX1 transcription factor during Hematopoietic specification
 
Contributor(s) Gilmour J, Assi SA, Noailles L, Lichtinger M, Obier N, Bonifer C
Citation(s) 29991720
Submission date Sep 20, 2017
Last update date Jul 25, 2021
Contact name Salam Adli Assi
E-mail(s) s.a.assi@bham.ac.uk
Organization name University of Birmingham
Department Institute for Cancer and Genomic Sciences
Street address IBR
City Birmingham
ZIP/Postal code B15 2TT
Country United Kingdom
 
Platforms (1)
GPL17021 Illumina HiSeq 2500 (Mus musculus)
Samples (19)
GSM2788296 iRx_BRD4_noDox_ChIPseq
GSM2788297 iRx_BRD4_plusDox_ChIPseq
GSM2788298 iRx_CDK9_noDox_ChIPseq
This SubSeries is part of SuperSeries:
GSE104046 The Co-operation of RUNX1 with LDB1, CDK9 and BRD4 Drives Transcription Factor Complex Relocation During Haematopoietic Specification
Relations
BioProject PRJNA408096
SRA SRP118297

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE104045_RAW.tar 5.6 Gb (http)(custom) TAR (of BW)
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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