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Series GSE234292 Query DataSets for GSE234292
Status Public on Mar 11, 2024
Title Systematic assessment of ISWI subunits reveals that NURF creates local accessibility for CTCF [Hi-C]
Organism Mus musculus
Experiment type Other
Summary Catalytic activity of the ISWI family of remodelers is critical for nucleosomal organization and transcription factor binding, including the insulator protein CTCF. To define which subcomplex mediate these diverse functions we phenotyped a panel of isogenic mouse stem cell lines each lacking one of six ISWI accessory subunits. Individual deletions of either CERF, RSF1, ACF, WICH or NoRC subcomplexes cause only moderate effects on the chromatin landscape, while removal of the NURF specific subunit BPTF leads to drastic reduction in chromatin accessibility and Snf2h ATPase localization around CTCF sites. While this reduces distances to the adjacent nucleosomes it only modestly impacts CTCF binding itself. In absence of accessibility bound CTCF is nevertheless impaired in function resulting in lower occupancy of cohesin and cohesin-loading factors, and reduced insulation at these sites, highlighting the need of NURF-mediated remodeling for open chromatin and proper CTCF function. Our comprehensive analysis reveals a specific role for NURF in mediating Snf2h localization and chromatin opening at bound CTCF sites showing that local accessibility is critical for cohesin binding and insulator function.
 
Overall design Hi-C in mouse Embryonic Stem Cells, in wild-type and Bptf knock-out (duplicates).
 
Contributor(s) Iurlaro M, Masoni F, Fliamer I, Burger L, Giorgetti L, Schübeler D
Citation(s) 38816647
Submission date Jun 06, 2023
Last update date Jun 10, 2024
Contact name Dirk Schuebeler
Organization name Friedrich Miescher Institute for Biomedical Research
Street address Maulbeerstrasse 66
City Basel
ZIP/Postal code 4058
Country Switzerland
 
Platforms (1)
GPL19057 Illumina NextSeq 500 (Mus musculus)
Samples (4)
GSM7461656 HiC_ESC_wt_rep1
GSM7461657 HiC_ESC_wt_rep2
GSM7461658 HiC_ESC_BPTFko_rep1
This SubSeries is part of SuperSeries:
GSE234295 Systematic assessment of ISWI subunits reveals that NURF creates local accessibility for CTCF
Relations
BioProject PRJNA980695

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
GSE234292_HiC_BPTFko_repmerged.mcool 1.2 Gb (ftp)(http) MCOOL
GSE234292_HiC_wt_repmerged.mcool 1.3 Gb (ftp)(http) MCOOL
GSE234292_RAW.tar 2.9 Gb (http)(custom) TAR (of MCOOL)
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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