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| Status |
Public on Mar 11, 2024 |
| Title |
Systematic assessment of ISWI subunits reveals that NURF creates local accessibility for CTCF [RNA-seq] |
| Organism |
Mus musculus |
| Experiment type |
Expression profiling by high throughput sequencing
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| 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.
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| Overall design |
RNAseq in mouse Embryonic Stem Cells, in wild-type and Rsf1, Wstf, Cecr2, Tip5, Acf1 and Bptf knock-out (duplicates or triplicates). Wild-type processed in five different batches.
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| Contributor(s) |
Iurlaro M, Masoni F, Burger 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
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| Street address |
Maulbeerstrasse 66
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| City |
Basel |
| ZIP/Postal code |
4058 |
| Country |
Switzerland |
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| Platforms (2) |
| GPL17021 |
Illumina HiSeq 2500 (Mus musculus) |
| GPL24247 |
Illumina NovaSeq 6000 (Mus musculus) |
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| Samples (24)
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| This SubSeries is part of SuperSeries: |
| GSE234295 |
Systematic assessment of ISWI subunits reveals that NURF creates local accessibility for CTCF |
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| Relations |
| BioProject |
PRJNA980622 |
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