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Series GSE123502 Query DataSets for GSE123502
Status Public on Apr 30, 2019
Title CHD4 is essential for transcriptional repression and lineage progression in B lymphopoiesis [RNA-seq]
Organism Mus musculus
Experiment type Expression profiling by high throughput sequencing
Summary Cell-lineage specification is a tightly regulated process that is dependent on appropriate expression of lineage- and developmental stage-specific transcriptional programs. Accessibility and inaccessibility of gene loci are controlled dynamically during cellular development. Here, we show that Chromodomain Helicase DNA-binding protein 4 (CHD4), a major ATPase/helicase subunit of Nucleosome Remodeling and Deacetylase Complexes (NuRD) in lymphocytes, is essential for specification of the early B cell lineage transcriptional program. In the absence of CHD4 in early B cell progenitors in vivo, B cell progenitors are arrested at an early pro-B-like stage of development, unresponsive to IL-7 receptor signaling and complete V(D)J rearrangements at Igh loci inefficiently. Importantly, CHD4-deficient B cells express a significant number of non-B cell lineage genes, including genes involved in the development of other hematopoietic lineages and neuronal cells. The absence of CHD4 increased chromatin accessibility at hundreds of these gene loci, suggesting that its ability to repress transcription by mobilizing nucleosomes and compacting chromatin is a barrier against inappropriate transcription. Together, our data demonstrate the importance of CHD4 in establishing and maintaining an appropriate transcriptome in early B lymphopoiesis via chromatin accessibility.
 
Overall design RNA-seq transcriptome analysis of three independent RNA samples each from wild type or Chd4 conditional knockout pro-B cells.
 
Contributor(s) Arends T, Dege C, Bortnick A, Danhorn T, Knapp JR, Jia H, Harmacek L, Fleenor CJ, Straign D, Walton K, Leach SM, Feeney AJ, Murre C, O'Connor BP, Hagman J
Citation(s) 31085655
Submission date Dec 07, 2018
Last update date Jul 30, 2019
Contact name James R Hagman
E-mail(s) hagmanj@njhealth.org
Phone 3033981398
Organization name National Jewish Health
Department Biomedical Research
Lab Hagman
Street address 1400 Jackson St
City Denver
State/province Colorado
ZIP/Postal code 80206
Country USA
 
Platforms (1)
GPL17021 Illumina HiSeq 2500 (Mus musculus)
Samples (6)
GSM3505725 CHD4_cKO_1 [Chd4_rep1237]
GSM3505726 CHD4_WT_1 [Ctrl_rep1238]
GSM3505727 CHD4_WT_2 [Ctrl_rep1240]
This SubSeries is part of SuperSeries:
GSE123504 CHD4 is essential for transcriptional repression and lineage progression in B lymphopoiesis
Relations
BioProject PRJNA508956
SRA SRP173193

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
GSE123502_subread_genecounts.txt.gz 3.1 Mb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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