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Series GSE115287 Query DataSets for GSE115287
Status Public on Jun 27, 2019
Title Genome-wide binding patterns of murine KRAB zinc finger proteins
Organism Mus musculus
Experiment type Genome binding/occupancy profiling by high throughput sequencing
Summary Mammalian genomes encode several hundred Kr├╝ppel-associated box zinc finger proteins (KRAB-ZFPs) that bind DNA in a sequence-specific manner through tandem arrays of C2H2-type zinc fingers and repress transcription via KRAB-dependent recruitment of the silencing cofactor KAP1. The KRAB-ZFP family rapidly amplified and diversified in mammals by segmental gene duplications, mutations, and zinc finger rearrangements likely in response to continued transposable element invasions, but the biological functions and in vivo requirement of these proteins has gone largely unexplored. Here we report the identification of the genome-wide binding profiles of 61 mouse KRAB-ZFPs by overexpression of epitope-tagged transgenes. We found that 51 of these KRAB-ZFPs target at least one retrotransposon group. Interestingly, evolutionary young and still active retrotransposons such as IAP and ETn elements are targeted by several KRAB-ZFPs which are mainly encoded within two gene clusters that are not conserved in any other sequenced species. This indicated that an evolutionary arms race drives the rapid expansion of KRAB-ZFP genes in order to restrict active retrotransposons.
 
Overall design Epitope tagged KRAB zinc finger proteins were overexpressed in F9 EC or B6 ES cells and ChIP-seq was performed to identify their genomic binding sites
 
Contributor(s) Wolf G, De Iaco A, 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 (74)
GSM3173695 2610305D13Rik
GSM3173696 AW146154
GSM3173697 EtOHi1
This SubSeries is part of SuperSeries:
GSE115291 Retrotransposon reactivation and mobilization upon deletions of megabase-scale KRAB zinc finger gene clusters in mice
Relations
BioProject PRJNA474488
SRA SRP149699

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE115287_KRAB-ZFP_MACS14_peaks.txt.gz 1.1 Mb (ftp)(http) TXT
GSE115287_RAW.tar 13.0 Gb (http)(custom) TAR (of BIGWIG)
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file
Processed data are available on Series record

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