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      Biology and Physics of Heterochromatin- Like Domains/Complexes

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          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.

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          Theory of Microphase Separation in Block Copolymers

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            Block copolymer thermodynamics: theory and experiment.

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              Role for DNA methylation in genomic imprinting.

              The paternal and maternal genomes are not equivalent and both are required for mammalian development. The difference between the parental genomes is believed to be due to gamete-specific differential modification, a process known as genomic imprinting. The study of transgene methylation has shown that methylation patterns can be inherited in a parent-of-origin-specific manner, suggesting that DNA methylation may play a role in genomic imprinting. The functional significance of DNA methylation in genomic imprinting was strengthened by the recent finding that CpG islands (or sites) in three imprinted genes, H19, insulin-like growth factor 2 (Igf-2), and Igf-2 receptor (Igf-2r), are differentially methylated depending on their parental origin. We have examined the expression of these three imprinted genes in mutant mice that are deficient in DNA methyltransferase activity. We report here that expression of all three genes was affected in mutant embryos: the normally silent paternal allele of the H19 gene was activated, whereas the normally active paternal allele of the Igf-2 gene and the active maternal allele of the Igf-2r gene were repressed. Our results demonstrate that a normal level of DNA methylation is required for controlling differential expression of the paternal and maternal alleles of imprinted genes.
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                Author and article information

                Journal
                Cells
                Cells
                cells
                Cells
                MDPI
                2073-4409
                11 August 2020
                August 2020
                : 9
                : 8
                : 1881
                Affiliations
                [1 ]Nazarbayev University School of Medicine, Nur-Sultan City 010000, Kazakhstan
                [2 ]Epigenetics Laboratory, Department of Natural Sciences, Novosibirsk State University, 2 Pirogova St., 630090 Novosibirsk, Russia
                [3 ]Genomics laboratory, Institute of molecular and cellular biology SD RAS, Lavrentyev ave, 8/2, 630090 Novosibirsk, Russia; belyakin@ 123456mcb.nsc.ru (S.N.B.); laktionov@ 123456mcb.nsc.ru (P.P.L.)
                Author notes
                [* ]Correspondence: prim.singh@ 123456nu.edu.kz ; Tel.: +7-7172-694706
                Author information
                https://orcid.org/0000-0002-9571-0974
                https://orcid.org/0000-0002-2315-4382
                Article
                cells-09-01881
                10.3390/cells9081881
                7465696
                32796726
                4cff8b53-5a64-4049-81a7-633f3280a0ff
                © 2020 by the authors.

                Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license ( http://creativecommons.org/licenses/by/4.0/).

                History
                : 09 July 2020
                : 04 August 2020
                Categories
                Review

                hp1,h3k9me2/3,epigenetic compartmental domains,block copolymers,flory–huggins parameter χ,unit of incompatibility

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