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Series GSE112222 Query DataSets for GSE112222
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
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.
 
Overall design RNAseq, ChIPseq, ATACseq and HiC in mouse ESCs
Web link https://www.embopress.org/doi/full/10.15252/embj.2020105606
 
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
Submission date Mar 22, 2018
Last update date Jan 19, 2021
Contact name Raffaella Santoro
E-mail(s) raffaella.santoro@dmmd.uzh.ch
Phone +41 44 635 54 75
Organization name University of Zurich
Department Dep. of Molecular Mechanisms of Disease
Street address Winterthurerstrasse 190
City Zurich
ZIP/Postal code 8057
Country Switzerland
 
Platforms (3)
GPL17021 Illumina HiSeq 2500 (Mus musculus)
GPL19057 Illumina NextSeq 500 (Mus musculus)
GPL21103 Illumina HiSeq 4000 (Mus musculus)
Samples (49)
GSM3061144 RNAseq_2i_siCTRL_rep1
GSM3061145 RNAseq_2i_siCTRL_rep2
GSM3061146 RNAseq_2i_siCTRL_rep3
Relations
BioProject PRJNA445292
SRA SRP136267

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

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 SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file
Processed data are available on Series record

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