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| Status |
Public on Oct 31, 2023 |
| Title |
BRD9 determines the cell fate of hematopoietic stem cells by regulating chromatin state [human_Brd9_CTCF-ChIP-seq] |
| Organism |
Homo sapiens |
| Experiment type |
Genome binding/occupancy profiling by high throughput sequencing
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| Summary |
Switch/sucrose nonfermentable (SWI/SNF) complexes are ATP-dependent chromatin remodeler complexes that play critical roles in timely and appropriate gene regulation by modulating chromatin architecture and DNA accessibility. SWI/SNF complexes can be grouped into three subcomplexes of differing sizes, canonical BAF (cBAF), polybromo BAF (PBAF), and newly identified noncanonical BAF (ncBAF). The most recently characterized ncBAF lacks the core BAF subunits ARID, BAF47, and BAF57, but includes unique subunits GLTSCR1/1L and BRD9, one of the bromodomain-containing proteins.We recently demonstrated the novel mechanism for the ncBAF disruption caused by mutations in a spiceosomal protein, SF3B1, especially in 65–83% for myelodysplastic syndromes (MDS) with ring sideroblasts as well as in >20% of mucosal/uveal melanomas, suggesting that the disturbed ncBAF may have some roles in the malignant hematopoiesis.Mechanistically, SF3B1 mutant recognizes an aberrant, deep intronic branchpoint within BRD9 and thereby induces the inclusion of an aberrant exon and subsequently profound degradation of BRD9 mRNA by triggering nonsense-mediated RNA decay (NMD). However, compared to the roles of cBAF, the functions of BRD9/ncBAF in normal and malignant hematopoiesis in vivo have been totally uncharacterized.
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| Overall design |
The K562 cell lines were cultured in RPMI with 10% FCS and 1% P/S to the logarithmic growth phase, treated K562 cells with DMSO and 100nM dBRD9 for 4 days, then compare CTCF binding in K562 cells after different treatment.
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| Contributor(s) |
Nomura M, Zang W, Nishimura K, Xiao M |
| Citation(s) |
38102116 |
| |
| Submission date |
Jul 03, 2023 |
| Last update date |
Jan 02, 2024 |
| Contact name |
Masaki Nomura |
| E-mail(s) |
[email protected]
|
| Organization name |
Foundation for Biomedical Research and Innovation at Kobe
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| Street address |
6-3-7 Minatojima Minamimachi, Chuo Ward
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| City |
Kobe |
| State/province |
Hyogo |
| ZIP/Postal code |
650-0047 |
| Country |
Japan |
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| Platforms (1) |
| GPL24676 |
Illumina NovaSeq 6000 (Homo sapiens) |
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| Samples (4)
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| This SubSeries is part of SuperSeries: |
| GSE203322 |
BRD9 determines the cell fate of hematopoietic stem cells by regulating chromatin state |
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| Relations |
| BioProject |
PRJNA990572 |
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