The 3D Genome as Moderator of Chromosomal Communication

Abstract

Proper expression of genes requires communication with their regulatory elements that can be located elsewhere along the chromosome. The physics of chromatin fibers imposes a range of constraints on such communication. The molecular and biophysical mechanisms by which chromosomal communication is established, or prevented, have become a topic of intense study, and important roles for the spatial organization of chromosomes are being discovered. Here we present a view of the interphase 3D genome characterized by extensive physical compartmentalization and insulation on the one hand and facilitated long-range interactions on the other. We propose the existence of topological machines dedicated to set up and to exploit a 3D genome organization to both promote and censor communication along and between chromosomes.

Keywords: CTCF; Hi-C; biophysics; cohesin; condensin; domains; enhancer; gene expression; gene regulation; polymers; promoter; simulations.

Figure 1. Chromosomal communication

Top: communication between genomic loci by 3D looping interactions. For large loops, e.g. tens to hundreds of Kb, such interactions are not sensitive to locus orientation. Also, 3D interactions do not readily distinguish interactions with loci located on the same chromosome (in cis) or on different chromosomes (in trans). Middle: Singles emanating from one locus (e.g. RNA transcribed at that locus, a protein complexes recruited at that site) can spread in cis along the chromatin fiber till a target locus is reached. This mode of communications can be sensitive to relative orientation of the target locus, and is strictly in cis. Bottom: Communication by 3D diffusion of factors such as RNA or proteins released from one locus till they reach target loci. This mode of communication is not sensitive to target orientation and cannot distinguish cis from trans.

Figure 2. Physical aspects of chromosomal communication

A. Short-range character of molecular interactions: molecular affinity is limited to 1-10nm range, and long-range attraction between chromosomal loci are impossible. B. Polymeric nature of chromatin made interactions even between relatively close loci infrequent, leading to large cell-to-cell variation. C. Localized dynamics of chromatin leads to mostly local exploration limited to 1-2um swept during a cell cycle. D. Chromosomal territories make cis interactions are much more likely and showing less cell-to-cell variation, while trans being highly variable. E. Individual proteins are much small (~3nm) than sizes of even modest (100-150Kb) chromatin region that has ~300nm in diameter and ~1-3um in length, making it difficult to insulate 3D interactions between chromosomal loci.

Figure 3. Loop extrusion as a moderator of chromosomal communications

A. The mechanism of loop extrusion. B. Blocking of loop extrusion by boundary element (e.g. CTCF) that can halt cohesin only if properly oriented, as determined by orientation of its binding site. Fudenberg et al. assumed that interactions with CTCF would halt loop-extruding activity of only one of two cohesin motors, while the unobstructed motor can continue extruding a loop. C. In this picture, loop extrusion is a universal mechanism that provides both formation of TADs and cis communication during interphase and chromosome compaction during mitosis, both by about 100Kb loops but with different spacing between the loops. During interphase loop extrusion is performed by cohesin and blocking at TAD boundaries can be performed by several factors, including binding by CTCF. Blocking of loop extrusion allows small insulating factors to insulate interactions between distal elements (Fig 2E). D. We propose that loop extrusion can also facilitate close-range contacts between functional elements, by bringing them in direct molecular contact. Such interactions are possibly only within a TAD and are completely insulated by extruding-blocking boundary elements. E. During mitosis, loop extrusion is performed by condensins that should be more abundant on DNA making each loop reinforced by multiple condensins (Goloborodko et al., 2015, 2016).