A 3D map of the human genome at kilobase resolution reveals principles of chromatin looping.

Cell
Authors
Keywords
Abstract

We use in situ Hi-C to probe the 3D architecture of genomes, constructing haploid and diploid maps of nine cell types. The densest, in human lymphoblastoid cells, contains 4.9 billion contacts, achieving 1 kb resolution. We find that genomes are partitioned into contact domains (median length, 185 kb), which are associated with distinct patterns of histone marks and segregate into six subcompartments. We identify ∼10,000 loops. These loops frequently link promoters and enhancers, correlate with gene activation, and show conservation across cell types and species. Loop anchors typically occur at domain boundaries and bind CTCF. CTCF sites at loop anchors occur predominantly (>90%) in a convergent orientation, with the asymmetric motifs "facing" one another. The inactive X chromosome splits into two massive domains and contains large loops anchored at CTCF-binding repeats.

Year of Publication
2014
Journal
Cell
Volume
159
Issue
7
Pages
1665-80
Date Published
2014 Dec 18
ISSN
1097-4172
URL
DOI
10.1016/j.cell.2014.11.021
PubMed ID
25497547
Links
Grant list
DP2 OD008540 / OD / NIH HHS / United States
HG003067 / HG / NHGRI NIH HHS / United States
HG006193 / HG / NHGRI NIH HHS / United States
OD008540-01 / OD / NIH HHS / United States