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Series GSE77440 Query DataSets for GSE77440
Status Public on Jun 04, 2016
Title ZFP57 maintains the parent-of-origin-specific expression of the imprinted genes and differentially affects non-imprinted targets in mouse embryonic stem cells (ChIP-seq)
Organism Mus musculus
Experiment type Genome binding/occupancy profiling by high throughput sequencing
Summary ZFP57 is necessary for maintaining repressive epigenetic modifications at Imprinting control regions (ICRs). In mouse embryonic stem cells (ESCs), ZFP57 binds ICRs (ICRBS) and many other loci (non-ICRBS). To address the role of ZFP57 on all its target sites, we performed high-throughput and multi-locus analyses of inbred and hybrid mouse ESC lines carrying different gene knockouts. By using an allele-specific RNA-seq approach, we demonstrate that ZFP57 loss results in derepression of the imprinted allele of multiple genes in the imprinted clusters. We also find marked epigenetic differences between ICRBS and non-ICRBS suggesting that different cis-acting regulatory functions are repressed by ZFP57 at these two classes of target loci. Overall, these data demonstrate that ZFP57 is pivotal to maintain the allele-specific epigenetic modifications of ICRs that in turn are necessary for maintaining the imprinted expression over long distances. At non-ICRBS, ZFP57 inactivation results in acquisition of epigenetic features that are characteristic of poised enhancers, suggesting that another function of ZFP57 in early embryogenesis is to repress cis-acting regulatory elements whose activity is not yet required.
 
Overall design Examination of ZFP57, KAP1 and H3K9me3 occupancy in Zfp57-/- mouse ESCs compared to the wild-type.
Web link http://genome.ucsc.edu/cgi-bin/hgTracks?hgS_doOtherUser=submit&hgS_otherUserName=bioinformatico&hgS_otherUserSessionName=Riso_et_al_2016
 
Contributor(s) Riso V, Cammisa M, Kukreja H, Anvar Z, Verde G, Sparago A, Acurzio B, Lad S, Lonardo V, Sankar A, Helin K, Feil R, Fico A, Angelini C, Grimaldi G, Riccio A
Citation(s) 27257070
Submission date Feb 01, 2016
Last update date May 15, 2019
Contact name Marco Cammisa
E-mail(s) cammisamarco.py@gmail.com
Organization name Institute of Genetics and Biophysics "A. Buzzati Traverso" (IGB-ABT)
Street address Via Castellino Pietro, 111
City Naples
State/province Naples
ZIP/Postal code 80131
Country Italy
 
Platforms (1)
GPL17021 Illumina HiSeq 2500 (Mus musculus)
Samples (12)
GSM2051866 A3 Input ChIP-seq
GSM2051867 A3 ZFP57 ChIP-seq
GSM2051868 A3 KAP1 ChIP-seq
This SubSeries is part of SuperSeries:
GSE77444 ZFP57 maintains the parent-of-origin-specific expression of the imprinted genes and differentially affects non-imprinted targets in mouse embryonic stem cells
Relations
BioProject PRJNA310341
SRA SRP069149

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
GSE77440_RAW.tar 3.0 Gb (http)(custom) TAR (of BED, BEDGRAPH)
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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