GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
Series GSE70920 Query DataSets for GSE70920
Status Public on Apr 05, 2016
Title The chromatin remodeler ATRX binds to atypical chromatin domains at the 3’ exons of ZNF genes to preserve H3K9me3 enrichment
Organism Homo sapiens
Experiment type Genome binding/occupancy profiling by high throughput sequencing
Summary Here, we report that ATRX co-localizes with the H3K9-methyl transferase SETDB1 (also known as ESET), the co-repressor TRIM28 (also known as KAP1), and the transcription factor ZNF274 at 3’ exons of Zinc Finger Genes (ZNFs) containing an atypical H3K9me3/H3K36me3 chromatin signature. Disruption of ATRX and ZNF274 leads to a significant reduction of H3K9me3, particularly at the 3’ ZNF exons and other atypical chromatin regions, higher percentages of DNA damage, and defects in cell cycle. Taken together, our studies suggest that ATRX binds the 3’ exons of ZNFs to maintain genomic stability through the regulation of their H3K9me3 levels
Overall design XL-MNase ChIP-seq of ATRX was performed in the erythroleukemic cell line K562 and the Neuroblastoma cell line LAN6. Two independent replicates using different ATRX antibodies were performed in K562. Additionally, Native ChIP-seq of H3K9me3 in LAN6, ATRX WT and ATRX KO K562 cells was performed. Input samples were sequenced as control.
Contributor(s) Bernstein E, Valle-Garcia D, Qadeer ZA
Citation(s) 27029610
Submission date Jul 14, 2015
Last update date May 15, 2019
Contact name Emily Bernstein
Phone (212) 824-9335
Organization name Mount Sinai School of Medicine
Department Oncological Sciences
Lab Bernstein Lab
Street address 1470 Madison Avenue, 6th floor Rm 302
City New York
State/province NY
ZIP/Postal code 10029
Country USA
Platforms (2)
GPL16791 Illumina HiSeq 2500 (Homo sapiens)
GPL18573 Illumina NextSeq 500 (Homo sapiens)
Samples (10)
GSM1821903 K562-Input_control-XL-MNase_ChIP
GSM1821904 K562-ATRX_SC-XL-MNase_ChIP
GSM1821905 K562-ATRX_Abcam-XL-MNase_ChIP
BioProject PRJNA289924
SRA SRP061171

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
GSE70920_RAW.tar 5.3 Gb (http)(custom) TAR (of BED, BIGWIG)
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap