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Series GSE193310 Query DataSets for GSE193310
Status Public on Apr 24, 2022
Title Two steps cross-linking LCL ChIP-seq
Organism Homo sapiens
Experiment type Genome binding/occupancy profiling by high throughput sequencing
Summary The chromatin remodeller ATRX interacts with the histone chaperone DAXX, to deposit the histone variant H3.3 at sites of nucleosome turnover. ATRX is known to bind repetitive, heterochromatic regions of the genome including telomeres, ribosomal DNA and pericentric repeats many of which are putative G-quadruplex forming sequences (PQS). At these sites ATRX plays an ancillary role in a wide range of nuclear processes facilitating replication, chromatin modification and transcription. Here, using an improved protocol for chromatin immunoprecipitation, we show that ATRX also binds active regulatory elements in euchromatin. Mutations in ATRX lead to perturbation of gene expression associated with a reduction in chromatin accessibility, histone modification, transcription factor binding and deposition of H3.3 at the sequences to which it normally binds. In erythroid cells where down regulation of a-globin expression is a hallmark of ATR-X syndrome, perturbation of chromatin accessibility and gene expression occurs in only a subset of cells. The stochastic nature of this process suggests that ATRX acts as a general facilitator of cell specific transcriptional and epigenetic programmes, both in heterochromatin and euchromatin.
 
Overall design To identify the binding sites of ATRX and runx3, ChIP-seq was carried out on lymphoblastoid cell lines.
 
Contributor(s) Truch J
Citation(s) 35710802
Submission date Jan 09, 2022
Last update date Jun 22, 2022
Contact name Julia Truch
Organization name University of Oxford
Department RDM - WIMM
Lab GIBBONS/HIGGS
Street address John Radcliffe Hospital, Headley Way, Headington
City Oxford
ZIP/Postal code Oxford OX3 9DS
Country United Kingdom
 
Platforms (1)
GPL18573 Illumina NextSeq 500 (Homo sapiens)
Samples (16)
GSM5788896 Ctr1_LCL_ATRX_H300
GSM5788897 Ctr2_LCL_ATRX_H300
GSM5788898 Ctr3_LCL_ATRX_H300
Relations
BioProject PRJNA795780

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
GSE193310_LCL_ATRX_peaks.bed.gz 73.9 Kb (ftp)(http) BED
GSE193310_LCL_runx3_peaks.bed.gz 219.1 Kb (ftp)(http) BED
GSE193310_RAW.tar 5.5 Gb (http)(custom) TAR (of BW)
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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