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| 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
Other
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| 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.
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| Overall design |
ChIP-seq, HiChIP, and ChIAPET, ATAC-seq
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| Contributor(s) |
Rowley J, Nichols M, Lyu X, Ando-Kuri M, Rivera SM, Hermetz K, Wang P, Ruan Y, Corces VG |
| Citation(s) |
28826674 |
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| Submission date |
Oct 27, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
M Jordan Rowley |
| E-mail(s) |
jordan.rowley@unmc.edu, jordrow@gmail.com
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| Phone |
7343580454
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| Organization name |
Univ of Nebraska Medical Center
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| Department |
GCBA
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| Lab |
Rowley
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| Street address |
601 S Saddle Creek Rd
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| City |
Omaha |
| State/province |
NE |
| ZIP/Postal code |
68106 |
| Country |
USA |
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| Platforms (1) |
| GPL13304 |
Illumina HiSeq 2000 (Drosophila melanogaster) |
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| Samples (18)
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| Relations |
| BioProject |
PRJNA350820 |
| SRA |
SRP092185 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE89244_RAW.tar |
2.1 Gb |
(http)(custom) |
TAR (of BW, HIC) |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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