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Series GSE60014 Query DataSets for GSE60014
Status Public on Jul 28, 2015
Title Identification of Hnf6 binding sites in male and female mouse liver
Organism Mus musculus
Experiment type Genome binding/occupancy profiling by high throughput sequencing
Summary ∼40,000 HNF6 binding sites were identified in mouse liver chromatin, including several thousand sites showing significant differences in level of HNF6 binding between male and female mouse liver. These sex-biased HNF6 binding sites showed strong enrichment for sex-biased DNase hypersensitive sites and for proximity to genes showing local sex-biased chromatin marks and a corresponding sex-biased expression. ~90% of genome-wide CUX2 binding sites identified previously in female mouse liver (Conforto TL, Zhang Y, Sherman J, Waxman DJ., Mol Cell Biol. 2012;32(22):4611-4627) were also bound by HNF6, giving evidence for genome-wide competition between HNF6 and CUX2 for chromatin binding in female mouse liver. These HNF6/CUX2 common binding sites were enriched for genomic regions more accessible in male than in female mouse liver chromatin, and showed strongest enrichment for male-biased genes, suggesting HNF6 displacement by CUX2 as a mechanism to explain the observed CUX2 repression of male-biased genes in female liver. However, HNF6 binding was sex-independent at a majority of its binding sites, and peak regions of HNF6 binding were frequently associated with co-binding by multiple other liver transcription factors, consistent with HNF6 playing a global regulatory role in both male and female liver.
Overall design Livers were excised from individual male and female mice, cross-linked and sonicated, then used to identify HNF6 binding sites by ChIP-Seq using antibody specific to HNF6 (sc-13050; Santa Cruz Biotechnology, Inc).
Contributor(s) Conforto TL, Steinhardt IV GF, Waxman DJ
Citation(s) 26218442
Submission date Aug 01, 2014
Last update date May 15, 2019
Contact name David J. Waxman
Organization name Boston University
Department Department of Biology and Bioinformatics Program
Street address 5 Cummington Mall
City Boston
State/province MA
ZIP/Postal code 02215
Country USA
Platforms (1)
GPL11002 Illumina Genome Analyzer IIx (Mus musculus)
Samples (8)
GSM1463852 F_Hnf6_ChIPSeq_G73_M1
GSM1463853 F_Hnf6_ChIPSeq_G73_M2
GSM1463854 F_Hnf6_ChIPSeq_G76_M10
BioProject PRJNA257278
SRA SRP045180

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Supplementary file Size Download File type/resource
GSE60014_RAW.tar 441.1 Mb (http)(custom) TAR (of BED)
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Raw data are available in SRA
Processed data provided as supplementary file

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