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| Status |
Public on May 22, 2019 |
| Title |
Chromodomain Helicase DNA-binding 4 (CHD4) is required for B cell identity and lineage progression |
| Organism |
Mus musculus |
| Experiment type |
Expression profiling by high throughput sequencing
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| Summary |
B cell specification and identity are controlled by transcription factors and cytokine receptors that drive the expression of stage-specific transcriptomes during lineage progression. A key feature of these mechanisms is the repression of inappropriate transcription. Here, we utilized RNA-seq to demonstrate that chromodomain helicase DNA-binding protein 4 (CHD4), an ATPase/helicase subunit of Mi-2/NuRD chromatin remodeling complexes, is essential for B cell identity. In mice that lack CHD4 selectively in the B lineage, defects include developmental arrest at the early pro-B cell stage. While many pro-B-specific genes are expressed in the mutant cells, transcripts that are normally restricted to other tissues including pancreas and bone are expressed out of context. Moreover, CHD4-deficient pro-B cells do not proliferate in response to IL-7, exhibit greatly decreased utilization of distal VH segments and accumulate DNA damage. Together, our data confirm the importance of CHD4 and NuRD complexes for the generation of functional B cells.
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| Overall design |
RNA-seq transcriptome analysis of three independent RNA samples each from wild type or Chd4 conditional knockout pro-B cells sorted as B220+CD43+CD24+BP1-IgM- bone marrow cells. Following analysis of RNA-seq, the mutant cell population was found to have increased enrichment of plasmacytoid dendritic cells. The data was not used in the publication, 'Arends, T, C Dege, A Bortnick, et al. CHD4 is essential for transcriptional repression and lineage progression in B lymphopoiesis. PNAS USA [Epub ahead of print]. (PMID: 31085655)'.
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| Contributor(s) |
Dege C, Arends T, Bortnick A, Jia H, Straign D, Harmacek L, Walton K, Leach SM, Danhorn T, Feeney AJ, Murre C, O'Connor B, Hagman J |
| Citation missing |
Has this study been published? Please login to update or notify GEO. |
| Submission date |
Jul 25, 2016 |
| Last update date |
May 22, 2019 |
| Contact name |
James R Hagman |
| E-mail(s) |
hagmanj@njhealth.org
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| Phone |
3033981398
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| Organization name |
National Jewish Health
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| Department |
Biomedical Research
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| Lab |
Hagman
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| Street address |
1400 Jackson St
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| City |
Denver |
| State/province |
Colorado |
| ZIP/Postal code |
80206 |
| Country |
USA |
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| Platforms (1) |
| GPL18635 |
Ion Torrent Proton (Mus musculus) |
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| Samples (6)
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| Relations |
| BioProject |
PRJNA331171 |
| SRA |
SRP079694 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE84806_genecounts.tar.gz |
302.3 Kb |
(ftp)(http) |
TAR |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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