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| Status |
Public on Apr 10, 2012 |
| Title |
Conserved Topological Domains in Mammalian Genomes Identified by High-resolution Analysis of Chromatin Interactions |
| Organisms |
Homo sapiens; Mus musculus |
| Experiment type |
Other
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| Summary |
The spatial organization of the genome is intimately linked to its biological function, yet our understanding of higher order genomic structure is limited. Here we present high-resolution analyses of chromosomal organization in pluripotent and differentiated human and murine cell types determined using the Hi-C technique. We find that the mammalian genome is composed of over 1000 topological domains, which are stable among different cell types and highly conserved across species. These megabase-long genomic structures, defined by prominent local chromatin interactions and separated by narrow boundary regions, likely function to restrict regulatory interactions between cis-acting elements and limit the spreading of heterochromatin during cellular differentiation. Interestingly, the boundaries are enriched not only for binding sites of the insulator protein CTCF, but also for promoters of house keeping genes, supporting a role for both CTCF and housekeeping genes in the establishment or maintenance of the topological domains.
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| Overall design |
Hi-C experiment were conducted in mESC, hESC and IMR90 cells
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| Contributor(s) |
Dixon J, Ren B |
| Citation(s) |
22495300 |
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| Submission date |
Jan 17, 2012 |
| Last update date |
Feb 22, 2021 |
| Contact name |
Feng Yue |
| E-mail(s) |
fyue@ucsd.edu
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| Organization name |
Ludwig Institue for Cancer Research
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| Street address |
9500 Gilman Dr.
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| City |
La Jolla |
| State/province |
CA |
| ZIP/Postal code |
92093 |
| Country |
USA |
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| Platforms (2) |
| GPL11154 |
Illumina HiSeq 2000 (Homo sapiens) |
| GPL13112 |
Illumina HiSeq 2000 (Mus musculus) |
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| Samples (9)
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| Relations |
| SRA |
SRP010370 |
| BioProject |
PRJNA150781 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE35156_GSM862720_J1_mESC_HindIII_ori_HiC.nodup.hic.summary.txt.gz |
8.5 Gb |
(ftp)(http) |
TXT |
| GSE35156_GSM862721_J1_mESC_HindIII_rep_HiC.nodup.summary.txt.gz |
5.7 Gb |
(ftp)(http) |
TXT |
| GSE35156_GSM862722_J1_mESC_NcoI_HiC.nodup.hic.summary.txt.gz |
7.0 Gb |
(ftp)(http) |
TXT |
| GSE35156_GSM862723_hESC_HindIII_HiC.nodup.summary.txt.gz |
1.6 Gb |
(ftp)(http) |
TXT |
| GSE35156_GSM862724_IMR90_HindIII_HiC.nodup.summary.txt.gz |
6.0 Gb |
(ftp)(http) |
TXT |
| GSE35156_GSM892304_cortex_HindIII_ori_HiC.nodup.hic.summary.txt.gz |
6.4 Gb |
(ftp)(http) |
TXT |
| GSE35156_GSM892305_cortex_HindIII_replicate_Hic.nodup.hic.summary.txt.gz |
5.1 Gb |
(ftp)(http) |
TXT |
| GSE35156_GSM892306_hESC_HindIII_HiC_replicate.nodup.hic.summary.txt.gz |
7.7 Gb |
(ftp)(http) |
TXT |
| GSE35156_GSM892307_IMR90_HindIII_HiC_replicate.nodup.hic.summary.txt.gz |
4.9 Gb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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