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| 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.
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| 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.
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| 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)
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| 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 |
| |
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| Platforms (2) |
| GPL16417 |
Illumina MiSeq (Mus musculus) |
| GPL19057 |
Illumina NextSeq 500 (Mus musculus) |
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| 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 |
| GSM2579376 |
Mouse D3839 mutant erythroid cells ATAC-seq biological replicate 2 |
| GSM2579377 |
Mouse D38 mutant erythroid cells ATAC-seq biological replicate 1 |
| GSM2579378 |
Mouse D38 mutant erythroid cells ATAC-seq biological replicate 2 |
| GSM2579379 |
Mouse D39 mutant erythroid cells ATAC-seq biological replicate 1 |
| GSM2579380 |
Mouse D39 mutant erythroid cells ATAC-seq biological replicate 2 |
| GSM2579381 |
Mouse wild-type erythroid cells ATAC-seq biological replicate 1 |
| GSM2579382 |
Mouse wild-type erythroid cells ATAC-seq biological replicate 2 |
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| This SubSeries is part of SuperSeries: |
| GSE97871 |
Tissue-specific CTCF/Cohesin-mediated chromatin architecture delimits enhancer interactions and function in vivo |
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| Relations |
| BioProject |
PRJNA383114 |
| SRA |
SRP104126 |
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