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Series GSE115286 Query DataSets for GSE115286
Status Public on Jun 27, 2019
Title Genome-wide maps of chromatin state and KAP1 occupancy in KRAB zinc finger protein (KRAB-ZFP) gene cluster KO ES cells and testis
Organism Mus musculus
Experiment type Genome binding/occupancy profiling by high throughput sequencing
Summary We have shown that many mouse KRAB-ZFPs target retrotransposons which are generally marked by H3K9me3 and KAP1 in ES cells. To test whether these KRAB-ZFPs are require to establish and maintain repressive chromatin marks at these elements, we performed ChIP-seq with antibodies against KAP1 (2 KRAB-ZFP cluster KOs) and H3K9me3 (5 KRAB-ZFP cluster KOs). We show that KRAB-ZFP targeted retrotransposons show reduced KAP1 binding and H3K9me3 in these KO ES cells. Furthermore, we performed ChIP-seq with antibodies against histone modifications typical for promoters and enhancers in Chr4-cl KO ES cells and testis. We show that, in ES cells, ETn retrotransposons gain signatures of active enhancers which acts on earby gene expression. In testis, a handful of different retrotransposons gain enhancer marks, although to a lesser degree. In conclusion, our data shows that KRAB-ZFPs are required to maintain H3K9me3 at retrotransposons in ES cells and to prevent some retrotransposons of becoming enhancers that affect gene expression patterns.
Overall design Native or cross-linked chromatin was prepared from ES cells or testis and immunoprecipitated with antibodies against KAP1 or various histone modifications
Contributor(s) Wolf G, De Iaco A, Tinkham M, Macfarlan TS, Trono D
Citation(s) 32479262
Submission date Jun 04, 2018
Last update date Jun 15, 2020
Contact name Gernot Wolf
Organization name NIH
Department NICHD
Lab Macfarlan lab
Street address 6 Center Drive
City Bethesda
State/province Maryland
ZIP/Postal code 20892
Country USA
Platforms (2)
GPL17021 Illumina HiSeq 2500 (Mus musculus)
GPL21493 Illumina HiSeq 3000 (Mus musculus)
Samples (54)
GSM3173641 H3K9me3 Chr4-cl WT B6/129 ES cells #26
GSM3173642 H3K9me3 Chr4-cl WT B6/129 ES cells #49
GSM3173643 H3K9me3 Chr4-cl KO B6/129 ES cells #6
This SubSeries is part of SuperSeries:
GSE115291 Retrotransposon reactivation and mobilization upon deletions of megabase-scale KRAB zinc finger gene clusters in mice
BioProject PRJNA474489
SRA SRP149698

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Supplementary file Size Download File type/resource
GSE115286_RAW.tar 4.4 Gb (http)(custom) TAR (of BIGWIG)
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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