GEO Accession viewer

Status Public on Oct 08, 2016

Title ZMYND8 co-localizes with NuRD on target genes and regulates recruitment of GATAD2A/NuRD to sites of DNA damage [ChIP-seq]

Organism Homo sapiens

Experiment type Genome binding/occupancy profiling by high throughput sequencing

Summary The NuRD complex is generally thought to repress transcription at both hyper- and hypomethylated regions in the genome. In addition, the complex is involved in the DNA damage response. Here, we show that ZMYND8 bridges NuRD to a number of putative DNA-binding zinc finger proteins. The ZMYND8 MYND domain directly interacts with PPPL? motifs in the NuRD subunit GATAD2A. Furthermore, GATAD2A and GATAD2B exclusively form homodimers and they thus define mutually exclusive NuRD subcomplexes. ZMYND8 and MBD3 share a large number of genome-wide binding sites, mostly active promoters and enhancers. Depletion of ZMYND8 does not affect NuRD occupancy genome-wide and expression of NuRD/ZMYND8 target genes in steady-state asynchronous cells. However, ZMYND8 facilitates immediate recruitment of GATAD2A/NuRD to induced sites of DNA damage. These results thus show that a specific substoichiometric interaction with a NuRD subunit paralogue provides unique functionality to a distinct NuRD subcomplex.

Overall design ChIP-seq samples for endogenous ZMYND8 (2 replicates), MBD3 (2 replicates), ZMYND8 in ZMYND8-KO cells, MBD3 in ZMYND8-KO cells, input of wild-type HeLa cells, GFP ChIP on WT HeLa cells, GFP ChIP on ZMYND8-GFP, GFP ChIP on GFP-GATAD2A and GFP ChIP on GFP-GATAD2B

Contributor(s) Spruijt CG

Citation(s) 27732854

Submission date Apr 01, 2016

Last update date May 15, 2019

Contact name Cornelia Gijsbertha Spruijt

E-mail(s) nellekespruijt@hotmail.com

Organization name Radboud University

Department RIMLS

Lab Proteomics and Chromatin Biology

Street address Geert Grooteplein 26-28

City Nijmegen

ZIP/Postal code 6525 GA

Country Netherlands

Platforms (3)

Samples (11)

This SubSeries is part of SuperSeries:

Relations

BioProject PRJNA317161

SRA SRP072758

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Supplementary file Size Download File type/resource

GSE79834_RAW.tar 3.7 Gb (http) (custom) TAR (of BED)

SRA Run Selector

Raw data are available in SRA

Processed data provided as supplementary file