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| Status |
Public on Jan 03, 2018 |
| Title |
TADs are 3D structural units of higher-order chromosome organization in Drosophila [ph] |
| Organism |
Drosophila melanogaster |
| Experiment type |
Other
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| Summary |
Deciphering the rules of genome folding in the cell nucleus is essential in order to understand its functions. Recent Hi-C studies have revealed that the genome is partitioned into topologically associating domains (TADs), which demarcate functional epigenetic domains defined by combinations of specific chromatin marks. However, whether TADs are true physical units in each cell nucleus, or whether they reflect statistical frequencies of measured interactions within cell populations is unclear. Here, using a combination of Hi-C, 3D-Fluorescent In Situ Hybridization (3D-FISH), super-resolution microscopy and polymer modeling, we provide an integrative view of chromatin folding in Drosophila. We observed that repressed TADs form a succession of discrete nano-compartments, interspersed by less condensed active regions. Single-cell analysis revealed a consistent TAD-based physical compartmentalization of the chromatin fiber, with some degree of heterogeneity in intra-TAD conformations and in cis and trans inter-TAD contact events. These results indicate that TADs are fundamental 3D genome units that engage in dynamic higher-order inter-TAD connections. This domain-based architecture is likely to play a major role in regulatory transactions during DNA-dependent processes.
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| Overall design |
HiC experiments in ph mutant drosophila embryos
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| Contributor(s) |
Szabo Q, Jost D, Chang J, Cattoni D, Papadopoulos GL, Bonev B, Sexton T, Gurgo J, Jacquier C, Nollmann M, Bantignies F, Cavalli G |
| Citation(s) |
29503869 |
| Submission date |
May 19, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Jia-Ming Chang |
| E-mail(s) |
chang.jiaming@gmail.com
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| Organization name |
National Chengchi University
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| Department |
Department of Computer Science
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| Street address |
NO.64, Sec. 2, ZhiNan Rd., Wenshan District
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| City |
Taipei |
| ZIP/Postal code |
11605 |
| Country |
Taiwan |
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| Platforms (1) |
| GPL13304 |
Illumina HiSeq 2000 (Drosophila melanogaster) |
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| Samples (2) |
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| This SubSeries is part of SuperSeries: |
| GSE99107 |
TADs are 3D structural units of higher-order chromosome organization in Drosophila |
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| Relations |
| BioProject |
PRJNA387323 |
| SRA |
SRP107636 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE99106_nm_none_10000.bins.txt.gz |
92.7 Kb |
(ftp)(http) |
TXT |
| GSE99106_nm_none_10000.n_contact.txt.gz |
115.6 Mb |
(ftp)(http) |
TXT |
| GSE99106_nm_none_160000.bins.txt.gz |
6.0 Kb |
(ftp)(http) |
TXT |
| GSE99106_nm_none_160000.n_contact.txt.gz |
4.9 Mb |
(ftp)(http) |
TXT |
| GSE99106_nm_none_20000.bins.txt.gz |
46.6 Kb |
(ftp)(http) |
TXT |
| GSE99106_nm_none_20000.n_contact.txt.gz |
46.4 Mb |
(ftp)(http) |
TXT |
| GSE99106_nm_none_40000.bins.txt.gz |
23.3 Kb |
(ftp)(http) |
TXT |
| GSE99106_nm_none_40000.n_contact.txt.gz |
65.4 Mb |
(ftp)(http) |
TXT |
| GSE99106_nm_none_5000.bins.txt.gz |
174.7 Kb |
(ftp)(http) |
TXT |
| GSE99106_nm_none_5000.n_contact.txt.gz |
233.9 Mb |
(ftp)(http) |
TXT |
| GSE99106_nm_none_80000.bins.txt.gz |
12.0 Kb |
(ftp)(http) |
TXT |
| GSE99106_nm_none_80000.n_contact.txt.gz |
17.9 Mb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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