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Series GSE234293 Query DataSets for GSE234293
Status Public on Mar 11, 2024
Title Systematic assessment of ISWI subunits reveals that NURF creates local accessibility for CTCF [SMF]
Organism Mus musculus
Experiment type Methylation 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 Amplicon-based Single Molecule Footprinting (SMF) in mouse Embryonic Stem Cells, in wild-type and Bptf knock-out (triplicates).
 
Contributor(s) Iurlaro M, Masoni F, Burger L, Schübeler D
Citation missing Has this study been published? Please login to update or notify GEO.
Submission date Jun 06, 2023
Last update date Mar 11, 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)
GPL16417 Illumina MiSeq (Mus musculus)
Samples (6)
GSM7461660 SMF_ESC_wt_rep1
GSM7461661 SMF_ESC_wt_rep2
GSM7461662 SMF_ESC_wt_rep3
This SubSeries is part of SuperSeries:
GSE234295 Systematic assessment of ISWI subunits reveals that NURF creates local accessibility for CTCF
Relations
BioProject PRJNA980701

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Supplementary file Size Download File type/resource
GSE234293_SMF_Meth_calls.txt.gz 9.5 Kb (ftp)(http) TXT
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Raw data are available in SRA
Processed data are available on Series record

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