Mechanisms and Functions of Chromosome Compartmentalization

Abstract

Active and inactive chromatin are spatially separated in the nucleus. In Hi-C data, this is reflected by the formation of compartments, whose interactions form a characteristic checkerboard pattern in chromatin interaction maps. Only recently have the mechanisms that drive this separation come into view. Here, we discuss new insights into these mechanisms and possible functions in genome regulation. Compartmentalization can be understood as a microphase-segregated block co-polymer. Microphase separation can be facilitated by chromatin factors that associate with compartment domains, and that can engage in liquid-liquid phase separation to form subnuclear bodies, as well as by acting as bridging factors between polymer sections. We then discuss how a spatially segregated state of the genome can contribute to gene regulation, and highlight experimental challenges for testing these structure-function relationships.

Keywords: HP1; compartment; euchromatin; heterochromatin; microphase separation.

Figure 1:

Active and inactive genomic regions form microphase separated compartments in the eukaryotic nucleus. A. Schematic of a eukaryotic cell nucleus showing different chromosomes in different colors to illustrate chromosome territories. B. Each chromosome is made up of both euchromatin or active (A, red) and heterochromatin or inactive (B, blue) chromatin which spatially cluster to form separate compartments within the nucleus. C. Schematic of subnuclear localization of A and B compartments. B compartments (blue) are spatially localized to the nuclear periphery and surrounding the nucleoli, while A compartments (red) are more interior. D. A and B compartments are visible in Hi-C matrices by a characteristic ‘checkerboard’ pattern (bottom left triangle), which, when subject to eigenvector decomposition, consist of alternating A and B compartments (top right triangle).

Figure 2:

Mechanisms of compartmentalization. A. The chromatin fiber is a block co-polymer consisting of alternating active (A, red) and inactive (B, blue) blocks (domains). B. Each type of domain recruits separate multivalent binding factors, as depicted by fuzzy interactions. C. Chromatin domains with similar marks and binding proteins localize together; this is proposed to be through a microphase separation mechanism. The binding factors may act as bridging factors mediating PPPS or participate in LLPS, depending on the context. D. Euchromatic regions consist of the A1 (dark red) and A2 (lighter red) sub-compartments [18], have low chromatin density, and are bound by Pol II (red major sectors) and binding factors such as Bromodomain containing proteins (orange circles). A1 domains differ from A2 domains in that A1 domains are in close proximity to Nuclear Speckles (large red circle), while A2 is active chromatin more distant from Nuclear Speckles. Heterochromatin is split into the B1 (light blue), B2 (medium blue), and B3 (dark blue) sub-compartments, and has a higher DNA density than the A compartment. The B1 sub-compartment is bound by the Polycomb complex (light blue rounded triangle) while the B2 and B3 sub-compartments contain HP1 (dark blue bean shape). B2 is often near the nucleoli (orange semicircle), consisting of nucleolar associating domains (NADs), while B3 is frequently close to the nuclear lamina (green lines), and consists of lamina associating domains (LADs).

Figure 3:

Experimental perturbations to compartmentalization to elucidate function A. Tethering of HP1 (dark blue bean) to an A compartment (light red line) using LacO/LacI results in gene silencing and new interactions forming between the ectopic HP1 site and heterochromatic regions (dark blue lines), this forms an ectopic B2 or B3 sub-compartment [67]. B. Knockout of the Lamin B receptor in mouse thymocytes results in loss of heterochromatin tethering to the nuclear periphery; however, compartmentalization per se is preserved [66]. The B3 sub-compartment is disrupted in its nuclear localization, but not in its long-range interactions. By microscopy, the A compartment (red) is now observed to be closest to the nuclear periphery, while the B compartment (blue) is within the nuclear interior. C. Knockdown of Srrm2, a structural component of nuclear speckles (NS), results in loss of NS foci (see Figure 2D), and dispersion of the NS components (small dark red circles) throughout the nucleus. A compartment strength is decreased, while B compartment strength is increased [47]. This is specifically affecting the A1 subcompartment that is usually close to NS foci. D. Ectopic induction of phase separated droplets using Intrinsically Disordered Region (IDR) containing proteins related to active transcription such as TAF15, FUS, or BRD4 using the CasDrop system results in droplets (fuzzy cluster of orange circles) that exclude heterochromatin, form in regions of the nucleus with low chromatin density, and can function to pull two distal active regions together by fusion of separate CasDrops, forming an ectopic A1 or A2 compartment [27].