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Series GSE92591 Query DataSets for GSE92591
Status Public on Mar 24, 2017
Title Functional analysis of CTCF sites associated with cytokine-sensing mammary-specific enhancers in the complex casein locus [ChIP-seq]
Organism Mus musculus
Experiment type Genome binding/occupancy profiling by high throughput sequencing
Summary The zinc finger protein CTCF has been invoked in establishing functional boundaries between genes and thereby controlling enhancer activities. However, there is limited genetic evidence to support such a concept. We have now addressed this question in a locus containing five mammary-specific genes controlled by enhancers. We have identified four CTCF binding sites in the casein locus, two at the outside boundaries and two associated with a super-enhancer. Individual deletions of these sites from the mouse genome did not alter expression of the five casein genes and Odam. However, deletion of the border CTCF site separating the Csn1s1 enhancer from non-mammary genes resulted in the activation of Sult1d1 at a distance of more than 95 kb but not the more proximal Sult1e1 gene. Loss of this CTCF site led to de novo interactions between the Csn1s1 enhancer and the Sult1d1 promoter but not with the silent Sult1e1 gene. Our study suggests that most CTCF sites associated with cell-specific enhancers and super-enhancers have no measurable in vivo activity. Only the loss of one CTCF site led to the induction of a juxtaposed active non-target promoter. Our study also demonstrated that cell-specific enhancers are unable to activate juxtaposed silent non-target promoters.
Overall design ChIP-seq for mutant mice ΔA were done for CTCF, GR, H3K27ac, Pol2, SMC1 and STAT5A in mammary tissue at lactation day 1 (L1). ChIP-seq for ΔC was done for CTCF in mammary tissue at L1.
Contributor(s) Lee H, Willi M, Wang C, Yang C, Liu C, Hennighausen L
Citation(s) 28334928
Submission date Dec 19, 2016
Last update date May 15, 2019
Contact name Michaela Willi
Organization name NIH
Department NIDDK
Street address 9000 Rockville Pike
City Bethesda
ZIP/Postal code 20814
Country USA
Platforms (1)
GPL17021 Illumina HiSeq 2500 (Mus musculus)
Samples (29)
GSM2433085 ChIP-Seq-delA-L1-CTCF-rep1
GSM2433086 ChIP-Seq-delA-L1-CTCF-rep2
GSM2433087 ChIP-Seq-delA-L1-GR-rep1
This SubSeries is part of SuperSeries:
GSE95758 Functional analysis of CTCF sites associated with cytokine-sensing mammary-specific enhancers in the complex casein locus
BioProject PRJNA358082
SRA SRP095360

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Supplementary file Size Download File type/resource
GSE92591_RAW.tar 1.7 Gb (http)(custom) TAR (of BEDGRAPH)
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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