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Series GSE195906 Query DataSets for GSE195906
Status Public on Feb 04, 2022
Title Transcriptional regulation and chromatin architecture maintenance are decoupled functions at the Sox2 locus.
Organism Mus musculus musculus x Mus musculus castaneus
Experiment type Other
Summary How distal regulatory elements regulate gene transcription and chromatin topology is not clearly defined, yet these processes are intimately linked to cell lineage specification during development. Through allele-specific genome editing and chromatin interaction analysis of the Sox2 locus in mouse embryonic stem cells, we found a striking decoupling of transcriptional control and chromatin architecture. We trace nearly all Sox2 transcriptional activation to a small number of key transcription factor binding sites, whose deletion has no effect on promoter-enhancer interaction frequencies or topological domain organization. Local chromatin architecture maintenance, including at the topologically associating domain (TAD) boundary downstream of the Sox2 enhancer, is conversely widely distributed over multiple transcription factor bound regions and maintained in a CTCF independent manner. Furthermore, disruption of promoter-enhancer interactions via induced ectopic chromatin loop formation has no effect on Sox2 expression. These findings indicate many transcription factors are involved in modulating chromatin architecture independently from CTCF.
Overall design Allele-specific 4C-seq interrogation of the mouse Sox2 locus in ESCs with different deletions of regulatory regions. Overall: 4 baits; 14 different genotypes; 1-4 replicates
Contributor(s) Sexton T, Sikorska N
Citation(s) 35710138
Submission date Feb 01, 2022
Last update date Jun 22, 2022
Contact name Tom Sexton
Organization name IGBMC (Institute of Genetics and Molecular and Cellular Biology)
Street address 1 rue Laurent Fries
City Illkirch
ZIP/Postal code 67404
Country France
Platforms (1)
GPL31871 Illumina HiSeq 4000 (Mus musculus musculus x Mus musculus castaneus)
Samples (69)
GSM5856193 nearSCR F1 ns rep1
GSM5856194 nearSCR F1 ns rep2
GSM5856195 nearSCR F1 mus rep3
BioProject PRJNA802654

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Supplementary file Size Download File type/resource
GSE195906_RAW.tar 93.0 Mb (http)(custom) TAR (of CIS)
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Raw data are available in SRA
Processed data provided as supplementary file

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