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Series GSE107753 Query DataSets for GSE107753
Status Public on Aug 17, 2018
Title Single-allele chromatin interactions identify regulatory hubs in dynamic compartmentalized domains [Capture-C]
Organism Mus musculus
Experiment type Other
Summary The genome is organized into self-interacting chromatin domains containing genes and the cis-regulatory elements controlling their expression. How these domains form and how elements within them interact is not fully understood. We have developed Tri-C, a sensitive, high-resolution Chromosome Conformation Capture (3C) approach to identify concurrent chromatin interactions in single cells. Combining Tri-C with conventional 3C and polymer modeling, we show that, rather than folding into stable pre-formed loops, self-interacting domains form dynamic compartmentalized chromatin structures, delimited by CTCF/Cohesin boundaries. Within these tissue-specific domains, all regions of chromatin contact each other, but preferential structures are formed in which multiple enhancers and promoters interact simultaneously. Flanking CTCF/Cohesin-bound elements are excluded from these interactions and form distinct structures. These observations are best explained by a dynamic loop extrusion mechanism and subsequent stabilization of enhancer-promoter interactions, rather than the current view of long-range interactions occurring via the formation of discrete pre-formed chromatin loops.
 
Overall design Capture-C combines 3C library preparation with oligonucleotide capture for the desired viewpoint restriction fragments. Experiments were performed in biological triplicates of primary erythroid and ES cells.
 
Contributor(s) Oudelaar AM, Hughes JR
Citation(s) 30374068
Submission date Dec 06, 2017
Last update date May 15, 2019
Contact name A Marieke Oudelaar
E-mail(s) marieke.oudelaar@imm.ox.ac.uk
Organization name University of Oxford
Department MRC Weatherall Institute of Molecular Medicine
Street address John Radcliffe Hospital
City Oxford
ZIP/Postal code OX3 9DS
Country United Kingdom
 
Platforms (2)
GPL16417 Illumina MiSeq (Mus musculus)
GPL19057 Illumina NextSeq 500 (Mus musculus)
Samples (42)
GSM2878022 Mouse erythroid cells biological replicate 1; Capture-C, viewpoints #1
GSM2878023 Mouse erythroid cells biological replicate 2; Capture-C, viewpoints #1
GSM2878024 Mouse erythroid cells biological replicate 3; Capture-C, viewpoints #1
This SubSeries is part of SuperSeries:
GSE107940 Single-allele chromatin interactions identify regulatory hubs in dynamic compartmentalized domains
Relations
BioProject PRJNA421280
SRA SRP126223

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Supplementary file Size Download File type/resource
GSE107753_All_gfc_files.tar.gz 84.4 Mb (ftp)(http) TAR
GSE107753_README_Samples_and_processedfiles.txt 19.0 Kb (ftp)(http) TXT
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Raw data are available in SRA
Processed data are available on Series record
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