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GEO help: Mouse over screen elements for information. |
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Status |
Public on Oct 20, 2020 |
Title |
BAZ2A safeguards genome architecture of ground-state pluripotent stem cells |
Organism |
Mus musculus |
Experiment type |
Expression profiling by high throughput sequencing Genome binding/occupancy profiling by high throughput sequencing Other
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Summary |
Chromosomes have an intrinsic tendency to segregate into compartments, forming long-distance contacts between loci of similar chromatin states. How genome compartmentalization is regulated remains elusive. Here, comparison of mouse ground-state embryonic stem cells (ESCs) characterized by open and active chromatin, and advanced serum ESCs with a more closed and repressed genome, reveals distinct regulation of their genome organization due to differential dependency on BAZ2A/TIP5, a component of the chromatin remodeling complex NoRC. On ESC chromatin, BAZ2A interacts with SNF2H, DNA topoisomerase 2A (TOP2A) and cohesin. BAZ2A associates with chromatin subdomains within the active A compartment, which intersect through long-range contacts. We found that ground-state chromatin selectively requires BAZ2A to limit the invasion of active domains into repressive compartments. BAZ2A depletion increases chromatin accessibility at B compartments. Furthermore, BAZ2A regulates H3K27me3 genome occupancy in a TOP2A-dependent manner. Finally, ground-state ESCs require BAZ2A for growth, differentiation, and correct expression of developmental genes. Our results uncover the propensity of open chromatin domains to invade repressive domains, which is counteracted by chromatin remodeling to establish genome partitioning and preserve cell identity.
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Overall design |
RNAseq, ChIPseq, ATACseq and HiC in mouse ESCs
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Web link |
https://www.embopress.org/doi/full/10.15252/embj.2020105606
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Contributor(s) |
Dalcher D, Tan JY, Bersaglieri C, Peña-Hernández R, Vollenweider E, Zeyen S, Schmid MW, Bianchi V, Butz SC, Roganowicz M, Kuzyakiv R, Baubec T, Marques AC, Santoro R |
Citation(s) |
33433018 |
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Submission date |
Mar 22, 2018 |
Last update date |
Jan 19, 2021 |
Contact name |
Raffaella Santoro |
E-mail(s) |
raffaella.santoro@dmmd.uzh.ch
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Phone |
+41 44 635 54 75
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Organization name |
University of Zurich
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Department |
Dep. of Molecular Mechanisms of Disease
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Street address |
Winterthurerstrasse 190
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City |
Zurich |
ZIP/Postal code |
8057 |
Country |
Switzerland |
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Platforms (3) |
GPL17021 |
Illumina HiSeq 2500 (Mus musculus) |
GPL19057 |
Illumina NextSeq 500 (Mus musculus) |
GPL21103 |
Illumina HiSeq 4000 (Mus musculus) |
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Samples (49)
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Relations |
BioProject |
PRJNA445292 |
SRA |
SRP136267 |
Supplementary file |
Size |
Download |
File type/resource |
GSE112222_CTRL-merged.hic |
437.8 Mb |
(ftp)(http) |
HIC |
GSE112222_DEG_2i_siTIP5_vs_siCTRL.csv.gz |
166.8 Kb |
(ftp)(http) |
CSV |
GSE112222_DEG_2i_vs_serum.csv.gz |
192.9 Kb |
(ftp)(http) |
CSV |
GSE112222_DEG_serum_siTIP5_vs_siCTRL.csv.gz |
155.0 Kb |
(ftp)(http) |
CSV |
GSE112222_EdgeR_2i_siTIP5_vs_siCTRL_mm10.csv.gz |
8.6 Mb |
(ftp)(http) |
CSV |
GSE112222_EdgeR_2i_vs_serum_mm10.csv.gz |
8.4 Mb |
(ftp)(http) |
CSV |
GSE112222_EdgeR_Serum_siTIP5_vs_siCTRL_mm10.csv.gz |
8.3 Mb |
(ftp)(http) |
CSV |
GSE112222_RAW.tar |
9.4 Gb |
(http)(custom) |
TAR (of BED, BW, HIC) |
GSE112222_Tip5-merged.hic |
478.4 Mb |
(ftp)(http) |
HIC |
GSE112222_raw_counts.csv.gz |
492.3 Kb |
(ftp)(http) |
CSV |
SRA Run Selector |
Raw data are available in SRA |
Processed data provided as supplementary file |
Processed data are available on Series record |
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