Principles of Chromosome Architecture Revealed by Hi-C

Abstract

Chromosomes are folded and compacted in interphase nuclei, but the molecular basis of this folding is poorly understood. Chromosome conformation capture methods, such as Hi-C, combine chemical crosslinking of chromatin with fragmentation, DNA ligation, and high-throughput DNA sequencing to detect neighboring loci genome-wide. Hi-C has revealed the segregation of chromatin into active and inactive compartments and the folding of DNA into self-associating domains and loops. Depletion of CTCF, cohesin, or cohesin-associated proteins was recently shown to affect the majority of domains and loops in a manner that is consistent with a model of DNA folding through extrusion of chromatin loops. Compartmentation was not dependent on CTCF or cohesin. Hi-C contact maps represent the superimposition of CTCF/cohesin-dependent and -independent folding states.

Keywords: DNA loops; Hi-C; chromosome conformation capture; chromosome structure; nuclear compartments; topologically associating domains.

Figure 1. Hi-C–Detected Chromatin Folding Paradigms

Left: Cartoon representation of Hi-C data, represented as a heatmap or Hi-C contact map. The strength of each pixel indicates the relative, pair-wise contact probability of two loci. TADs are on-diagonal boxes of contact enrichment. Loops are radially symmetric peaks of contact intensity, often located at the corners of TADs in mammalian cells. Off-diagonal boxes indicate interactions due to compartmentation. Right: Cartoon representation of DNA folding. TADs are more tightly folded than regions between them. TADs and loops may be either mostly transcriptionally active (grey) or inactive (black). Loops may also be more tightly folded, but additionally have an increased likelihood of contact between their boundaries or anchors. Compartmentation is indicated by homotypic (active-active or inactive-inactive) TAD-TAD interactions. The bona fide pattern of chromatin folding is unknown and only indicated schematically.

Figure 2. Cohesin-dependent Loop Extrusion Hypothesis

A loop extrusion complex containing cohesin (yellow ring) is loaded onto DNA and begins extruding a small loop of chromatin. Extrusion continues until cohesin dissociates from DNA or until it reaches CTCF protein bound to its motif in an orientation that points towards the complex. At this point, the complex stalls or stops on that side of the loop, but can continue extruding on the opposite side. If CTCF bound to an improperly oriented motif is encountered, the complex is likely to bypass that site. Once a second, properly oriented CTCF site is encountered, the complex stalls or stops at this second site. Stopping or stalling is likely transient, in which case loops are not stable structures. The continuous breaking and forming of loops may be apparent as loop TADs in Hi-C contact maps from populations of cells. The actual pattern of chromatin folding is unknown and only indicated schematically.