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Review
. 2016 Jun:40:8-14.
doi: 10.1016/j.ceb.2016.01.009. Epub 2016 Feb 4.

The three-dimensional genome: principles and roles of long-distance interactions

M Jordan Rowley  1 , Victor G Corces  2
Affiliations
Review

The three-dimensional genome: principles and roles of long-distance interactions

M Jordan Rowley et al. Curr Opin Cell Biol. 2016 Jun.

Abstract

The linear sequence of eukaryotic genomes is arranged in a specific manner within the three-dimensional nuclear space. Interactions between distant sites partition the genome into domains of highly associating chromatin. Interaction domains are found in many organisms, but their properties and the principles governing their establishment vary between different species. Topologically associating domains (TADs) extending over large genomic regions are found in mammals and Drosophila melanogaster, whereas other types of contact domains exist in lower eukaryotes. Here we review recent studies that explore the mechanisms by which long distance chromatin interactions determine the 3D organization of the genome and the relationship between this organization and the establishment of specific patterns of gene expression.

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Figures

Figure 1
Figure 1. Chromosome Organization in Eukaryotes
Chromatin interactions detected by Hi-C displayed as heatmaps for human [47] (A); D. melanogaster [4] (B); C. elegans [12] (C); A. thaliana [9] (D); S. pombe [14] (E); and S. cerevisiae [15] (F). A) Large TADs in mammals occur with CTCF in reverse – forward orientation at domain borders. Arrows indicate CTCF motif orientation connected by chromatin interactions (red arcs). B) Clustering of architectural proteins at domain borders. High occupancy architectural binding sites (APBS) correlate with domain borders in D. melanogaster. C) The Dosage Compensation Complex (DCC) binds domain borders in C. elegans hermaphrodites. Interaction domains are stronger on the X chromosome in C. elegans and correlate with condensin-containing DCC binding sites. D) Architectural proteins in A. thaliana are unknown. A. thaliana has distinct chromatin interaction structures (indicated by arrow). E) Globule domains in S. pombe. Cohesin (displayed as rings) sites correlate with edges of globule domains. F) Small domains in S. cerevisiae. Micro-C allows high resolution contact maps and identification of short chromatin interaction domains. Cohesin (displayed as rings) loader Scc2 correlates with domain borders.
Figure 2
Figure 2. Changes to Domain Organization
A) Hi-C of human embryonic stem cells (H1 ESC – bottom right) compared to lung fibroblast cells (IMR90 – top left) [47]. Arrows indicate TAD structure changes. B) Hi-C of D. melanogaster under heat shock (bottom right) compared to normal temperature (top left) [4].
See this image and copyright information in PMC

References

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