A 3D Map of the Human Genome at Kilobase Resolution Reveals Principles of Chromatin Looping

Overview

Journal Cell

Publisher Cell Press

Specialty Cell Biology

Date 2014 Dec 16

PMID 25497547

Citations 4280

Authors

Suhas S P Rao

Miriam H Huntley

Neva C Durand

Elena K Stamenova

Ivan D Bochkov

James T Robinson

Adrian L Sanborn

Ido Machol

Arina D Omer

Eric S Lander

Erez Lieberman Aiden

Affiliations

Soon will be listed here.

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.

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