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Series GSE89244 Query DataSets for GSE89244
Status Public on Aug 14, 2017
Title Evolutionary Principles Predict 3D Chromatin Organization
Organism Drosophila melanogaster
Experiment type Genome binding/occupancy profiling by high throughput sequencing
Summary TADs, CTCF loop domains, and A/B compartments have been identified as important structural and functional components of 3D chromatin organization, yet the relationship between these features is not well understood. Using high-resolution Hi-C and HiChIP we show that Drosophila chromatin is organized into domains we term compartmental domains that correspond precisely with A/B compartments at high resolution. We find that transcriptional state is a major predictor of Hi-C contact maps in several eukaryotes tested, including C. elegans and A. thaliana. Architectural proteins insulate compartmental domains by reducing interaction frequencies between neighboring regions in Drosophila, but CTCF loops do not play a distinct role in this organism. In mammals, compartmental domains exist alongside CTCF loop domains to form topological domains. The results suggest that compartmental domains are responsible for domain structure in all eukaryotes, with CTCF playing an important role in domain formation in mammals.
Overall design ChIP-seq, HiChIP, and ChIAPET, ATAC-seq
Contributor(s) Rowley J, Nichols M, Lyu X, Ando-Kuri M, Rivera SM, Hermetz K, Wang P, Ruan Y, Corces VG
Citation(s) 28826674
Submission date Oct 27, 2016
Last update date May 15, 2019
Contact name M Jordan Rowley
Phone 7343580454
Organization name Univ of Nebraska Medical Center
Department GCBA
Lab Rowley
Street address 601 S Saddle Creek Rd
City Omaha
State/province NE
ZIP/Postal code 68106
Country USA
Platforms (1)
GPL13304 Illumina HiSeq 2000 (Drosophila melanogaster)
Samples (18)
GSM2362844 CP190_HiChIP
GSM2362845 Pol2Ser2_HiChIP
GSM2362846 PolII_ChIAPET
BioProject PRJNA350820
SRA SRP092185

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
GSE89244_RAW.tar 2.1 Gb (http)(custom) TAR (of BW, HIC)
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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