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Series GSE236330 Query DataSets for GSE236330
Status Public on Oct 31, 2023
Title BRD9 determines the cell fate of hematopoietic stem cells by regulating chromatin state [mouse_Brd9_H3K27Ac-ChIP-seq]
Organism Mus musculus
Experiment type Genome binding/occupancy profiling by high throughput sequencing
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.
 
Overall design 2.0 x 10E6 total BM cells of Mx1-Cre control, Mx1-Cre Brd9fl/fl mice transplanted via tail vein injection into lethally irradiated (two times 450 cGy) CD45.1+ recipient mice. Four weeks after BMT, the recipient mice received 20 mg/kg pIpC injection every other day for a total of 3 doses. Five months after pIpC injection, the recipient mice were sacrificed for sample preparation.
 
Contributor(s) Nomura M, Inoue D, 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) masaki.nomura.fbri@gmail.com
Organization name Foundation for Biomedical Research and Innovation at Kobe
Street address 6-3-7 Minatojima Minamimachi, Chuo Ward
City Kobe
State/province Hyogo
ZIP/Postal code 650-0047
Country Japan
 
Platforms (1)
GPL24247 Illumina NovaSeq 6000 (Mus musculus)
Samples (4)
GSM7528029 Input_WT_S [mouse_Brd9_H3K27Ac-ChIP-seq]
GSM7528030 H3K27Ac_WT2 [mouse_Brd9_H3K27Ac-ChIP-seq]
GSM7528031 Input_KO_S [mouse_Brd9_H3K27Ac-ChIP-seq]
This SubSeries is part of SuperSeries:
GSE203322 BRD9 determines the cell fate of hematopoietic stem cells by regulating chromatin state
Relations
BioProject PRJNA990574

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Supplementary file Size Download File type/resource
GSE236330_RAW.tar 342.0 Mb (http)(custom) TAR (of BIGWIG)
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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