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

Abstract

Summary We use in situ Hi-C to probe the three-dimensional 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-kilobase resolution. We find that genomes are partitioned into local domains, 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.

Two independent modes of chromatin organization revealed by cohesin removal

“…Rao et al also identified intriguing emergent “loop” cliques enriched in super-enhancers upon cohesin depletion 37 . We also observed such features in our primary hepatocytes using a new Hi-C browser 38 , though we note that in both cases these patterns do not resemble the sharp cis -only focal patterns of CTCF-associated Hi-C peaks commonly referred to as loops 12 . Rather, these larger patches appear to be enhanced compartmental interactions between very active regions that line up well with actively transcribed genes 38 .…”

“…The co-existence of two processes with different modes and scales of action can help explain the difficulties in the field in delineating and unambiguously classifying the different features of Hi-C maps, leading to a confusing plethora of denominations and definitions 7,8,12,40–42 . Our data demonstrates clearly the existence of local, cohesin-dependent, self-interacting domains identifiable as TADs.…”

“…TADs are thought to contribute to gene expression, notably by promoting or preventing interactions between promoters and distant regulatory elements 9–11 . Finally, peaks (often termed loops 12 ) are visible as focal enrichments in contact frequency between pairs of loci, often at the corner of TAD squares. Despite a lack of supporting mechanistic experiments, compartments, TADs and peaks are typically assumed to constitute hierarchical levels of chromosome folding.…”

“…Cohesin and CTCF co-localize at TAD boundaries and the bases of Hi-C peaks 7,12 , but their roles are not fully defined. The recently proposed loop extrusion model 14,15 yields predictions that are consistent with experiments.…”

Unravelling the molecular basis for regulatory T‐cell plasticity and loss of function in disease

“…Hence, DNA looping facilitates gene network formation as a single enhancer may interact with more than one promoter, and a single promoter may be contacted by more than one enhancer. Many of these interactions occur in a tissue‐specific manner and appear to be the major determinants of cell type‐specific responses 111, 113, 114, 115. Critically, many enhancers do not interact with the nearest active gene but contact gene promoters many hundreds to thousands of kilobases away through long‐range DNA looping (modelled for T cells in Figure 8).…”