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Series GSE123386 Query DataSets for GSE123386
Status Public on May 13, 2019
Title A Preformed Chromatin Architecture Ensures Robust Shh Transcription during Limb Development [ChIP-Seq]
Organism Mus musculus
Experiment type Genome binding/occupancy profiling by high throughput sequencing
Summary During embryogenesis, enhancer-promoter interactions control gene transcriptional activation. These interactions can be tissue-specific or tissue-invariant and occur mostly within larger insulated regulatory domains called Topologically Associating Domains (TADs). Boundary elements, which delineate the extent of TADs, frequently interact with each other and have been associated with constitutive transcription and CTCF/Cohesin binding. In this work, we set out to investigate the regulatory role of a tissue-invariant, preformed interaction between two boundaries that involve the Shh gene and its unique limb enhancer, the ZRS, located one megabase away. Using CRISPR/Cas9 we specifically perturb CTCF binding sites or constitutive transcription at the ZRS-containing boundary, without altering the enhancer sequence. Using capture-HiC (cHiC) we show that both types of perturbation result in altered preformed chromatin interactions and lead to a reduction of Shh expression in developing limb buds. Finally, we demonstrate that the disruption of the chromatin structure in combination with a hypomorphic ZRS allele results in a dramatic Shh loss- of- function and digit agenesis. We thus propose that preformed chromatin structures can ensure stable enhancer promoter communication during development and robustness of gene transcriptional activation.
Overall design We used ChIP-seq in E10.5 Wildtype and mutant limb buds to assess the binding of transcription factors CTCF and Rad21, but also of the histone marks H3K27ac and H3K36me3
Contributor(s) Paliou C, Andrey G
Citation(s) 31147463
Submission date Dec 06, 2018
Last update date Aug 13, 2019
Contact name Christina Paliou
Organization name Max Planck Institute for Molecular Genetics
Street address Ihnestrasse 63-73
City Berlin
ZIP/Postal code 14195
Country Germany
Platforms (3)
GPL17021 Illumina HiSeq 2500 (Mus musculus)
GPL19057 Illumina NextSeq 500 (Mus musculus)
GPL21103 Illumina HiSeq 4000 (Mus musculus)
Samples (21)
GSM3502471 CTCF-FLHL-E105-i4-Mm-Rep1-L10936
GSM3502472 CTCF-FLHL-E105-i4i5-Mm-Rep1-L10938
GSM3502473 CTCF-FLHL-E105-i4i5-Mm-Rep2-L14966
This SubSeries is part of SuperSeries:
GSE123388 A Preformed Chromatin Architecture Ensures Robust Shh Transcription during Limb Development
BioProject PRJNA508611
SRA SRP172678

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Supplementary file Size Download File type/resource 339.1 Mb (ftp)(http) BW 615.0 Mb (ftp)(http) BW 422.1 Mb (ftp)(http) BW 492.1 Mb (ftp)(http) BW
GSE123386_RAW.tar 3.8 Gb (http)(custom) TAR (of BW)
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Raw data are available in SRA
Processed data provided as supplementary file
Processed data are available on Series record

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