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Series GSE59027 Query DataSets for GSE59027
Status Public on Dec 30, 2015
Title Hierarchical folding and reorganization of chromosomes are linked to transcriptional changes in cellular differentiation
Organism Mus musculus
Experiment type Other
Summary Mammalian chromosomes fold into arrays of megabase‐sized topologically associating domains (TADs), which are arranged into compartments spanning multiple megabases of genomic DNA. TADs have internal substructures that are often cell type specific, but their higher‐order organization remains elusive. Here, we investigate TAD higher‐order interactions with Hi‐C through neuronal differentiation and show that they form a hierarchy of domains‐within‐domains (metaTADs) extending across genomic scales up to the range of entire chromosomes. We find that TAD interactions are well captured by tree‐like, hierarchical structures irrespective of cell type. metaTAD tree structures correlate with genetic, epigenomic and expression features, and structural tree rearrangements during differentiation are linked to transcriptional state changes. Using polymer modelling, we demonstrate that hierarchical folding promotes efficient chromatin packaging without the loss of contact specificity, highlighting a role far beyond the simple need for packing efficiency.
 
Overall design Hi-C was performed in mouse embryonic stem cells (ESC), neural progenitor cells (NPC), and midbrain-like neurons (Neurons) using both HindIII and NcoI restriction enzymes
 
Contributor(s) Fraser J, Ferrai C, Pombo A, Dostie J
Citation(s) 26700852
Submission date Jul 02, 2014
Last update date May 15, 2019
Contact name Josee Dostie
E-mail(s) josee.dostie@mcgill.ca
Organization name McGill University
Department Biochemistry
Street address 3655 Prom. Sir-William-Osler
City Montreal
State/province Quebec
ZIP/Postal code H3G 1Y6
Country Canada
 
Platforms (1)
GPL13112 Illumina HiSeq 2000 (Mus musculus)
Samples (6)
GSM1424556 Hi-C ESC-HindIII
GSM1424557 Hi-C ESC-NcoI
GSM1424558 Hi-C NPC-HindIII
Relations
BioProject PRJNA254154
SRA SRP044017

Download family Format
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Supplementary file Size Download File type/resource
GSE59027_RAW.tar 743.4 Mb (http)(custom) TAR (of TAR)
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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