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Series GSE112132 Query DataSets for GSE112132
Status Public on Apr 18, 2019
Title Mammalian ISWI and SWI/SNF selectively mediate binding of distinct groups of transcription factors (ChIP-seq data sets)
Organism Mus musculus
Experiment type Genome binding/occupancy profiling by high throughput sequencing
Summary Remodelers define nucleosome composition, presence and position. Mammalian imitation-switch-type (ISWI) comprise one class, mostly relying on the ATPase Snf2h for activity. We show that embryonic stem cells are viable without Snf2h, enabling to study its function and contrast it to Brg1, the ATPase of SWI/SNF. Loss of Snf2h specifically affects nucleosomal positioning and increases linker lengths genome-wide providing in vivo evidence for ISWI function in ruling nucleosomal spacing. Systematic analysis of transcription factor binding reveals selective requirement on either remodeling activity. One group, containing the transcriptional repressor REST depend on BRG1, while a non-overlapping set including the insulator protein CTCF, relies on Snf2h. Importantly localized reduction in CTCF binding decreases long-range interactions. Collectively, this links mammalian ISWI to nuclear organization, demonstrates its cellular role for nucleosomal periodicity and reveals that transcription factors rely on specific remodeling pathways for proper genomic binding.
 
Overall design ATAC-seq (14, 2 or 3 replicates per condition), Bis-seq (4, single replicate per condition), ChIP-seq (18 CTCF and 20 REST, 1 or 2 replicates per condition), HiC-seq (8, two replicates per condition), MNase-seq (8, 2 replicates per condition) and RNA-seq (18, 2 to 5 replicates per condition) profiling of mouse embryonic stem cells of wildtype, Snf2h ko, Snf2h ko/add-back (wildtype and mutant) and Brg1 ko genotypes.
 
Contributor(s) Barisic D, Stadler MB, Iurlaro M, Schübeler D
Citation(s) 30996347
Submission date Mar 21, 2018
Last update date Apr 23, 2019
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)
GPL17021 Illumina HiSeq 2500 (Mus musculus)
Samples (38)
GSM3058327 ChIP_wt_CTCF-IP_1
GSM3058328 ChIP_Snf2hko_CTCF-IP_1
GSM3058329 ChIP_wt_CTCF-input_1
This SubSeries is part of SuperSeries:
GSE112136 Mammalian ISWI and SWI/SNF selectively mediate binding of distinct groups of transcription factors
Relations
BioProject PRJNA445200
SRA SRP136258

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Supplementary file Size Download File type/resource
GSE112132_RAW.tar 331.6 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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