|
| Status |
Public on Aug 31, 2023 |
| Title |
BRWD1 orchestrates chromatin topology by converting static to dynamic cohesin complexes (ChIP-Seq) |
| Organism |
Mus musculus |
| Experiment type |
Genome binding/occupancy profiling by high throughput sequencing
|
| Summary |
Lymphocyte development consists of sequential and mutually exclusive cell states of proliferative selection and antigen receptor gene recombination. Transitions between each state require large, coordinated changes in epigenetic landscapes and transcriptional programs. How this occurs remains unclear. Herein, we demonstrate that in small pre-B cells, the lineage and stage-specific epigenetic reader BRWD1 reorders three-dimensional chromatin topology to affect transition between proliferative and gene recombination molecular programs. BRWD1 regulated the switch between poised and active enhancers interacting with promoters and coordinated this with Igk locus contraction. BRWD1 did so by converting chromatin-bound static cohesin to dynamic complexes competent to mediate long-range looping. Remarkably, ATP depletion recapitulated cohesin distributions observed in Brwd1-/- cells. Therefore, in small pre-B cells, cohesin conversion appears to be the main energetic mechanism dictating where dynamic looping occurs in the genome. Our findings provide a new mechanism of cohesin regulation and reveal how cohesin function can be regulated by lineage contextual mechanisms to facilitate specific cell fate transitions.
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| |
|
| Overall design |
ChIP-seq of CTCF, H3K27Ac, H3M4me1, NIPBL, RAD21, SMC3, and WAPL in small pre-B cells isolated from mice, with WT, BRWD1KO genotypes , and WT small pre-B cells treated with oligomycin (ATPneg). Two biological replicates were collected for each ChIP sample. Input samples were collected in duplicate, or were used as previously released (GSM2753125).
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| |
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| Contributor(s) |
Mandal M, Maienschein-Cline M, Hu Y, Mohsin A, Veselits ML, Wright NE, Okoreeh MK, Yoon YM, Veselits J, Georgopoulos K, Clark MR |
| Citation(s) |
37985858 |
| |
| Submission date |
Dec 21, 2022 |
| Last update date |
Nov 30, 2023 |
| Contact name |
Mark Maienschein-Cline |
| E-mail(s) |
mmaiensc@uic.edu
|
| Organization name |
University of Illinois at Chicago
|
| Department |
Research Resources Center
|
| Lab |
Center for Research Informatics
|
| Street address |
1819 W Polk Ave, Rm 336 M/C 789
|
| City |
Chicago |
| State/province |
IL |
| ZIP/Postal code |
60612 |
| Country |
USA |
| |
|
| Platforms (1) |
| GPL24247 |
Illumina NovaSeq 6000 (Mus musculus) |
|
| Samples (40)
|
|
| This SubSeries is part of SuperSeries: |
| GSE221519 |
BRWD1 orchestrates chromatin topology by converting static to dynamic cohesin complexes |
|
| Relations |
| BioProject |
PRJNA914724 |
| SRA |
SRP414316 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE221518_CTCF_merged.bed.gz |
857.9 Kb |
(ftp)(http) |
BED |
| GSE221518_CTCF_raw_counts.txt.gz |
779.0 Kb |
(ftp)(http) |
TXT |
| GSE221518_CTCF_subtracted_counts.txt.gz |
525.9 Kb |
(ftp)(http) |
TXT |
| GSE221518_CTCF_subtracted_norm.txt.gz |
4.5 Mb |
(ftp)(http) |
TXT |
| GSE221518_NIPBL_merged.bed.gz |
651.5 Kb |
(ftp)(http) |
BED |
| GSE221518_NIPBL_raw_counts.txt.gz |
618.0 Kb |
(ftp)(http) |
TXT |
| GSE221518_NIPBL_subtracted_counts.txt.gz |
442.8 Kb |
(ftp)(http) |
TXT |
| GSE221518_NIPBL_subtracted_norm.txt.gz |
3.1 Mb |
(ftp)(http) |
TXT |
| GSE221518_RAD21_merged.bed.gz |
929.1 Kb |
(ftp)(http) |
BED |
| GSE221518_RAD21_raw_counts.txt.gz |
866.4 Kb |
(ftp)(http) |
TXT |
| GSE221518_RAD21_subtracted_counts.txt.gz |
631.0 Kb |
(ftp)(http) |
TXT |
| GSE221518_RAD21_subtracted_norm.txt.gz |
4.5 Mb |
(ftp)(http) |
TXT |
| GSE221518_RAW.tar |
9.3 Gb |
(http)(custom) |
TAR (of BED, BW) |
| GSE221518_SMC3_merged.bed.gz |
873.7 Kb |
(ftp)(http) |
BED |
| GSE221518_SMC3_raw_counts.txt.gz |
770.1 Kb |
(ftp)(http) |
TXT |
| GSE221518_SMC3_subtracted_counts.txt.gz |
566.2 Kb |
(ftp)(http) |
TXT |
| GSE221518_SMC3_subtracted_norm.txt.gz |
4.2 Mb |
(ftp)(http) |
TXT |
| GSE221518_WAPL_merged.bed.gz |
1.3 Mb |
(ftp)(http) |
BED |
| GSE221518_WAPL_raw_counts.txt.gz |
1.3 Mb |
(ftp)(http) |
TXT |
| GSE221518_WAPL_subtracted_counts.txt.gz |
967.0 Kb |
(ftp)(http) |
TXT |
| GSE221518_WAPL_subtracted_norm.txt.gz |
6.5 Mb |
(ftp)(http) |
TXT |
| GSE221518_h3k27ac_merged.bed.gz |
2.4 Mb |
(ftp)(http) |
BED |
| GSE221518_h3k27ac_raw_counts.txt.gz |
1.9 Mb |
(ftp)(http) |
TXT |
| GSE221518_h3k27ac_subtracted_counts.txt.gz |
1.7 Mb |
(ftp)(http) |
TXT |
| GSE221518_h3k27ac_subtracted_norm.txt.gz |
12.6 Mb |
(ftp)(http) |
TXT |
| GSE221518_h3k4me1_merged.bed.gz |
1.8 Mb |
(ftp)(http) |
BED |
| GSE221518_h3k4me1_raw_counts.txt.gz |
1.4 Mb |
(ftp)(http) |
TXT |
| GSE221518_h3k4me1_subtracted_counts.txt.gz |
1.3 Mb |
(ftp)(http) |
TXT |
| GSE221518_h3k4me1_subtracted_norm.txt.gz |
10.0 Mb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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