On the relations of phase separation and Hi-C maps to epigenetics

Prim B. Singh, Andrew G. Newman

Research output: Contribution to journalReview articlepeer-review

1 Citation (Scopus)

Abstract

The relationship between compartmentalization of the genome and epigenetics is long and hoary. In 1928, Heitz defined heterochromatin as the largest differentiated chromatin compartment in eukaryotic nuclei. Müller’s discovery of position-effect variegation in 1930 went on to show that heterochromatin is a cytologically visible state of heritable (epigenetic) gene repression. Current insights into compartmentalization have come from a high-throughput top-down approach where contact frequency (Hi-C) maps revealed the presence of compartmental domains that segregate the genome into heterochromatin and euchromatin. It has been argued that the compartmentalization seen in Hi-C maps is owing to the physiochemical process of phase separation. Oddly, the insights provided by these experimental and conceptual advances have remained largely silent on how Hi-C maps and phase separation relate to epigenetics. Addressing this issue directly in mammals, we have made use of a bottom-up approach starting with the hallmarks of constitutive heterochromatin, heterochromatin protein 1 (HP1) and its binding partner the H3K9me2/3 determinant of the histone code. They are key epigenetic regulators in eukaryotes. Both hallmarks are also found outside mammalian constitutive heterochromatin as constituents of larger (0.1–5 Mb) heterochromatin-like domains and smaller (less than 100 kb) complexes. The well-documented ability of HP1 proteins to function as bridges between H3K9me2/3-marked nucleosomes contributes to polymer–polymer phase separation that packages epigenetically heritable chromatin states during interphase. Contacts mediated by HP1 ‘bridging’ are likely to have been detected in Hi-C maps, as evidenced by the B4 heterochromatic subcompartment that emerges from contacts

Original languageEnglish
Article number191976
Number of pages26
JournalRoyal Society Open Science
Volume7
Issue number3
DOIs
Publication statusPublished - 1 Mar 2020

Keywords

  • Block copolymers
  • Epigenetics
  • H3K9me2/3
  • Hi-C maps
  • HP1
  • Polymer–polymer phase separation
  • block copolymers
  • DNA METHYLATION
  • polymer-polymer phase separation
  • DROSOPHILA HETEROCHROMATIN PROTEIN
  • PERICENTRIC HETEROCHROMATIN
  • epigenetics
  • HP1 PROTEINS
  • 3
  • POSITION-EFFECT VARIEGATION
  • HISTONE H3
  • CELL-CYCLE
  • ZINC FINGER PROTEINS
  • LYSINE 9
  • RECEPTOR GENES

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