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Series GSE250225 Query DataSets for GSE250225
Status Public on Mar 11, 2024
Title Systematic assessment of ISWI subunits reveals that NURF creates local accessibility for CTCF (ATAC-Seq)
Organism Mus musculus
Experiment type Genome binding/occupancy profiling by high throughput sequencing
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 ATACseq in mouse Embryonic Stem Cells, in wild-type and Snf2l (Smarca1) knock-out (duplicates). All samples processed in the same batch.
 
Contributor(s) Iurlaro M, Masoni F, Burger L, Schübeler D
Citation(s) 38816647
Submission date Dec 14, 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)
GPL24247 Illumina NovaSeq 6000 (Mus musculus)
Samples (4)
GSM7975855 ATACseq_ESC_wt_E_rep1
GSM7975856 ATACseq_ESC_wt_E_rep2
GSM7975857 ATACseq_ESC_snf2l_ko_E_rep1
This SubSeries is part of SuperSeries:
GSE250229 Systematic assessment of ISWI subunits reveals that NURF creates local accessibility for CTCF
Relations
BioProject PRJNA1052704

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Supplementary file Size Download File type/resource
GSE250225_RAW.tar 34.6 Mb (http)(custom) TAR (of WIG)
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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