Biology and Physics of Heterochromatin-Like Domains/Complexes

Abstract

The hallmarks of constitutive heterochromatin, HP1 and H3K9me2/3, assemble heterochromatin-like domains/complexes outside canonical constitutively heterochromatic territories where they regulate chromatin template-dependent processes. Domains are more than 100 kb in size; complexes less than 100 kb. They are present in the genomes of organisms ranging from fission yeast to human, with an expansion in size and number in mammals. Some of the likely functions of domains/complexes include silencing of the donor mating type region in fission yeast, preservation of DNA methylation at imprinted germline differentially methylated regions (gDMRs) and regulation of the phylotypic progression during vertebrate development. Far cis- and trans-contacts between micro-phase separated domains/complexes in mammalian nuclei contribute to the emergence of epigenetic compartmental domains (ECDs) detected in Hi-C maps. A thermodynamic description of micro-phase separation of heterochromatin-like domains/complexes may require a gestalt shift away from the monomer as the “unit of incompatibility” that determines the sign and magnitude of the Flory–Huggins parameter, χ. Instead, a more dynamic structure, the oligo-nucleosomal “clutch”, consisting of between 2 and 10 nucleosomes is both the long sought-after secondary structure of chromatin and its unit of incompatibility. Based on this assumption we present a simple theoretical framework that enables an estimation of χ for domains/complexes flanked by euchromatin and thereby an indication of their tendency to phase separate. The degree of phase separation is specified by χN, where N is the number of “clutches” in a domain/complex. Our approach could provide an additional tool for understanding the biophysics of the 3D genome.

Heterochromatin diversity modulates genome compartmentalization and loop extrusion barriers

“…A/B ratio) and (ii) the lengths and distribution of homotypic blocks (e.g. AAAABBBB vs ABABABAB) and (iii) the nature of their multivalent biomolecular interactions and incompatibilities (Erdel & Rippe, 2018; Gavrilov et al, 2011; Halperin, 1991; Singh et al, 2020). Importantly, compartmentalization patterns in population Hi-C maps will not only be influenced by these intrinsic biomolecular properties but also by cell-cell or allelic heterogeneity in chromatin state, and potentially by tethering of different regions to the lamina and nuclear bodies.…”

HP1-Driven Micro-Phase Separation of Heterochromatin-Like Domains/Complexes

“… 18 The reduced heterochromatic B-B type contacts in the HP1a KD is due to reduced HP1a levels within the chromosome arms outside constitutive heterochromatin; HP1a localises to 2213 sites in the arms that can be up to several kilobases in size with the median being 730 bp 18 ; these are smaller than the HLD/Cs observed in mammals. 2 A generalised block co-polymer model consisting of A- and B-type repeating units that assemble euchromatic A- and heterochromatic B-type chromatin respectively, can be used to explain the effects of the HP1a KD if the HP1a bound to H3K9me3 in the B-type compartments causes preferential interactions between heterochromatic B-type chromatin. 18 Regulation of the 3-D organisation of the Drosophila genome during ZGA by HP1a does not extend to differentiated cells where B-type compartmentalisation is unaffected by HP1a KD.…”

“… 1 Outside constitutive heterochromatin, heterochromatin-like domains (HLD, >.1 Mb) and complexes (HLC, <.1 Mb) are found along the chromosome arms. 2 HLD/Cs are present in eukaryotic genomes as divergent as fission yeast and human, with expansions in size and number in mammals. In human, there are ~163 to 859 HLDs and ~18 853 to 32 292 HLCs, depending on cell type.…”

“…In human, there are ~163 to 859 HLDs and ~18 853 to 32 292 HLCs, depending on cell type. 2 Some of the largest HLDs are the KRAB-ZNF HLDs on chromosome 19. Notably, contacts among these large HLDs emerge as the heterochromatic B4 sub-compartment in Hi-C maps.…”

Inter-nucleosomal potentials from nucleosomal positioning data

“…To reveal the thermodynamic properties and hence give indication on the mechanical code, we move to a larger global scale and ask for nucleosomal distribution patterns along a single chromosome as well as universal pattern between all chromosomes of a given genome. For this, we need to eliminate some of the smaller structures to reveal structure on a coarser level which is also more in line with the local phase separation picture [ 13 ].…”