BIOLOGY AND PHYSICS OF HETEROCHROMATIN-LIKE DOMAINS/COMPLEXESA DETAILED ASSESSMENT OF GROUNDWATER QUALITY IN THE KABUL BASIN, AFGHANISTAN, AND SUITABILITY FOR FUTURE DEVELOPMENT
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Date
2020-08-11
Authors
Singh, Prim B.
Belyakin, Stepan N.
Laktionov, Petr P.
Journal Title
Journal ISSN
Volume Title
Publisher
MDPI
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.
Description
Keywords
HP1, H3K9me2/3, epigenetic compartmental domains, block copolymers, Flory–Huggins parameter χ, unit of incompatibility, Type of access: Open Access
Citation
Singh, P. B., Belyakin, S. N., & Laktionov, P. P. (2020). Biology and Physics of Heterochromatin-Like Domains/Complexes. Cells, 9(8), 1881. https://doi.org/10.3390/cells9081881