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Series GSE97866 Query DataSets for GSE97866
Status Public on Jun 14, 2017
Title Tissue-specific CTCF/Cohesin-mediated chromatin architecture delimits enhancer interactions and function in vivo (ATAC-Seq)
Organism Mus musculus
Experiment type Genome binding/occupancy profiling by high throughput sequencing
Summary The genome is organized via CTCF/cohesin binding sites, which partition chromosomes into 1-5Mb topologically associated domains (TADs), and further into smaller contact sub-domains within TADs (sub-TADs; 40-1000kb). Here we examined in vivo an ~80kb sub-TAD, containing the mouse α-globin gene cluster, lying within a ~1Mb TAD. We find that the sub-TAD is flanked by predominantly convergent CTCF/cohesin sites which are ubiquitously bound by CTCF but only interact during erythropoiesis, defining a self-interacting erythroid compartment. Whereas the α-globin regulatory elements normally act solely on promoters downstream of the enhancers, removal of a conserved upstream CTCF/cohesin boundary extends the sub-TAD to the adjacent upstream CTCF/cohesin binding site. The α-globin enhancers now interact with the flanking chromatin, upregulating expression of genes within this extended sub-TAD. Rather than acting solely as a barrier to chromatin modification, CTCF/cohesin boundaries in this sub-TAD regulate both directionality and specificity of enhancer interactions with surrounding promoters.
 
Overall design ATAC-seq on chromatin isolated from primary erythroid ter119+ cells obtained from the spleens of acetylphenylhydrazine treated mice. Wild-type C57BL/6 mice were comparied with mice containing deletions for HS-29 (D29) or HS-38 and/or HS-39 (D38, D39,D3839) CTCF binding sites. Experiments are performed in duplicate in mutant and WT mice.
 
Contributor(s) Hanssen LP, Telenius JM, Higgs DR
Citation(s) 28737770
Submission date Apr 17, 2017
Last update date May 15, 2019
Contact name Jelena M Telenius
E-mail(s) jelena.telenius@ndcls.ox.ac.uk
Organization name Oxford University
Department Weatherall Institute of Molecular Medicine (WIMM)
Lab Genome Biology Research Group
Street address MRC Weatherall Institute of Molecular Medicine University of Oxford John Radcliffe Hospital Headington
City Oxford
ZIP/Postal code OX3 9DS
Country United Kingdom
 
Platforms (2)
GPL16417 Illumina MiSeq (Mus musculus)
GPL19057 Illumina NextSeq 500 (Mus musculus)
Samples (10)
GSM2579373 Mouse D29 mutant erythroid cells ATAC-seq biological replicate 1
GSM2579374 Mouse D29 mutant erythroid cells ATAC-seq biological replicate 2
GSM2579375 Mouse D3839 mutant erythroid cells ATAC-seq biological replicate 1
This SubSeries is part of SuperSeries:
GSE97871 Tissue-specific CTCF/Cohesin-mediated chromatin architecture delimits enhancer interactions and function in vivo
Relations
BioProject PRJNA383114
SRA SRP104126

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

Supplementary file Size Download File type/resource
GSE97866_RAW.tar 1.1 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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