Phase separation drives heterochromatin domain formation

Amy R. Strom, Alexander Emelyanov, Mustafa Mir, Dmitry Fyodorov, Xavier Darzacq, Gary H. Karpen

Research output: Contribution to journalArticle

235 Citations (Scopus)

Abstract

Constitutive heterochromatin is an important component of eukaryotic genomes that has essential roles in nuclear architecture, DNA repair and genome stability, and silencing of transposon and gene expression. Heterochromatin is highly enriched for repetitive sequences, and is defined epigenetically by methylation of histone H3 at lysine 9 and recruitment of its binding partner heterochromatin protein 1 (HP1). A prevalent view of heterochromatic silencing is that these and associated factors lead to chromatin compaction, resulting in steric exclusion of regulatory proteins such as RNA polymerase from the underlying DNA. However, compaction alone does not account for the formation of distinct, multi-chromosomal, membrane-less heterochromatin domains within the nucleus, fast diffusion of proteins inside the domain, and other dynamic features of heterochromatin. Here we present data that support an alternative hypothesis: That the formation of heterochromatin domains is mediated by phase separation, a phenomenon that gives rise to diverse non-membrane-bound nuclear, cytoplasmic and extracellular compartments. We show that Drosophila HP1a protein undergoes liquid-liquid demixing in vitro, and nucleates into foci that display liquid properties during the first stages of heterochromatin domain formation in early Drosophila embryos. Furthermore, in both Drosophila and mammalian cells, heterochromatin domains exhibit dynamics that are characteristic of liquid phase-separation, including sensitivity to the disruption of weak hydrophobic interactions, and reduced diffusion, increased coordinated movement and inert probe exclusion at the domain boundary. We conclude that heterochromatic domains form via phase separation, and mature into a structure that includes liquid and stable compartments. We propose that emergent biophysical properties associated with phase-separated systems are critical to understanding the unusual behaviours of heterochromatin, and how chromatin domains in general regulate essential nuclear functions.

Original languageEnglish (US)
Pages (from-to)241-245
Number of pages5
JournalNature
Volume547
Issue number7662
DOIs
StatePublished - Jul 13 2017

Fingerprint

Heterochromatin
Drosophila
Chromatin
Genome Components
Drosophila Proteins
Genomic Instability
Nucleic Acid Repetitive Sequences
DNA-Directed RNA Polymerases
Hydrophobic and Hydrophilic Interactions
DNA Repair
Histones
Methylation
Lysine
Embryonic Structures
Gene Expression
Membranes
DNA

ASJC Scopus subject areas

  • Medicine(all)
  • General

Cite this

Strom, A. R., Emelyanov, A., Mir, M., Fyodorov, D., Darzacq, X., & Karpen, G. H. (2017). Phase separation drives heterochromatin domain formation. Nature, 547(7662), 241-245. https://doi.org/10.1038/nature22989

Phase separation drives heterochromatin domain formation. / Strom, Amy R.; Emelyanov, Alexander; Mir, Mustafa; Fyodorov, Dmitry; Darzacq, Xavier; Karpen, Gary H.

In: Nature, Vol. 547, No. 7662, 13.07.2017, p. 241-245.

Research output: Contribution to journalArticle

Strom, AR, Emelyanov, A, Mir, M, Fyodorov, D, Darzacq, X & Karpen, GH 2017, 'Phase separation drives heterochromatin domain formation', Nature, vol. 547, no. 7662, pp. 241-245. https://doi.org/10.1038/nature22989
Strom, Amy R. ; Emelyanov, Alexander ; Mir, Mustafa ; Fyodorov, Dmitry ; Darzacq, Xavier ; Karpen, Gary H. / Phase separation drives heterochromatin domain formation. In: Nature. 2017 ; Vol. 547, No. 7662. pp. 241-245.
@article{2eaf6613fa984e0da5374b37f5db2e88,
title = "Phase separation drives heterochromatin domain formation",
abstract = "Constitutive heterochromatin is an important component of eukaryotic genomes that has essential roles in nuclear architecture, DNA repair and genome stability, and silencing of transposon and gene expression. Heterochromatin is highly enriched for repetitive sequences, and is defined epigenetically by methylation of histone H3 at lysine 9 and recruitment of its binding partner heterochromatin protein 1 (HP1). A prevalent view of heterochromatic silencing is that these and associated factors lead to chromatin compaction, resulting in steric exclusion of regulatory proteins such as RNA polymerase from the underlying DNA. However, compaction alone does not account for the formation of distinct, multi-chromosomal, membrane-less heterochromatin domains within the nucleus, fast diffusion of proteins inside the domain, and other dynamic features of heterochromatin. Here we present data that support an alternative hypothesis: That the formation of heterochromatin domains is mediated by phase separation, a phenomenon that gives rise to diverse non-membrane-bound nuclear, cytoplasmic and extracellular compartments. We show that Drosophila HP1a protein undergoes liquid-liquid demixing in vitro, and nucleates into foci that display liquid properties during the first stages of heterochromatin domain formation in early Drosophila embryos. Furthermore, in both Drosophila and mammalian cells, heterochromatin domains exhibit dynamics that are characteristic of liquid phase-separation, including sensitivity to the disruption of weak hydrophobic interactions, and reduced diffusion, increased coordinated movement and inert probe exclusion at the domain boundary. We conclude that heterochromatic domains form via phase separation, and mature into a structure that includes liquid and stable compartments. We propose that emergent biophysical properties associated with phase-separated systems are critical to understanding the unusual behaviours of heterochromatin, and how chromatin domains in general regulate essential nuclear functions.",
author = "Strom, {Amy R.} and Alexander Emelyanov and Mustafa Mir and Dmitry Fyodorov and Xavier Darzacq and Karpen, {Gary H.}",
year = "2017",
month = "7",
day = "13",
doi = "10.1038/nature22989",
language = "English (US)",
volume = "547",
pages = "241--245",
journal = "Nature",
issn = "0028-0836",
publisher = "Nature Publishing Group",
number = "7662",

}

TY - JOUR

T1 - Phase separation drives heterochromatin domain formation

AU - Strom, Amy R.

AU - Emelyanov, Alexander

AU - Mir, Mustafa

AU - Fyodorov, Dmitry

AU - Darzacq, Xavier

AU - Karpen, Gary H.

PY - 2017/7/13

Y1 - 2017/7/13

N2 - Constitutive heterochromatin is an important component of eukaryotic genomes that has essential roles in nuclear architecture, DNA repair and genome stability, and silencing of transposon and gene expression. Heterochromatin is highly enriched for repetitive sequences, and is defined epigenetically by methylation of histone H3 at lysine 9 and recruitment of its binding partner heterochromatin protein 1 (HP1). A prevalent view of heterochromatic silencing is that these and associated factors lead to chromatin compaction, resulting in steric exclusion of regulatory proteins such as RNA polymerase from the underlying DNA. However, compaction alone does not account for the formation of distinct, multi-chromosomal, membrane-less heterochromatin domains within the nucleus, fast diffusion of proteins inside the domain, and other dynamic features of heterochromatin. Here we present data that support an alternative hypothesis: That the formation of heterochromatin domains is mediated by phase separation, a phenomenon that gives rise to diverse non-membrane-bound nuclear, cytoplasmic and extracellular compartments. We show that Drosophila HP1a protein undergoes liquid-liquid demixing in vitro, and nucleates into foci that display liquid properties during the first stages of heterochromatin domain formation in early Drosophila embryos. Furthermore, in both Drosophila and mammalian cells, heterochromatin domains exhibit dynamics that are characteristic of liquid phase-separation, including sensitivity to the disruption of weak hydrophobic interactions, and reduced diffusion, increased coordinated movement and inert probe exclusion at the domain boundary. We conclude that heterochromatic domains form via phase separation, and mature into a structure that includes liquid and stable compartments. We propose that emergent biophysical properties associated with phase-separated systems are critical to understanding the unusual behaviours of heterochromatin, and how chromatin domains in general regulate essential nuclear functions.

AB - Constitutive heterochromatin is an important component of eukaryotic genomes that has essential roles in nuclear architecture, DNA repair and genome stability, and silencing of transposon and gene expression. Heterochromatin is highly enriched for repetitive sequences, and is defined epigenetically by methylation of histone H3 at lysine 9 and recruitment of its binding partner heterochromatin protein 1 (HP1). A prevalent view of heterochromatic silencing is that these and associated factors lead to chromatin compaction, resulting in steric exclusion of regulatory proteins such as RNA polymerase from the underlying DNA. However, compaction alone does not account for the formation of distinct, multi-chromosomal, membrane-less heterochromatin domains within the nucleus, fast diffusion of proteins inside the domain, and other dynamic features of heterochromatin. Here we present data that support an alternative hypothesis: That the formation of heterochromatin domains is mediated by phase separation, a phenomenon that gives rise to diverse non-membrane-bound nuclear, cytoplasmic and extracellular compartments. We show that Drosophila HP1a protein undergoes liquid-liquid demixing in vitro, and nucleates into foci that display liquid properties during the first stages of heterochromatin domain formation in early Drosophila embryos. Furthermore, in both Drosophila and mammalian cells, heterochromatin domains exhibit dynamics that are characteristic of liquid phase-separation, including sensitivity to the disruption of weak hydrophobic interactions, and reduced diffusion, increased coordinated movement and inert probe exclusion at the domain boundary. We conclude that heterochromatic domains form via phase separation, and mature into a structure that includes liquid and stable compartments. We propose that emergent biophysical properties associated with phase-separated systems are critical to understanding the unusual behaviours of heterochromatin, and how chromatin domains in general regulate essential nuclear functions.

UR - http://www.scopus.com/inward/record.url?scp=85024405877&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=85024405877&partnerID=8YFLogxK

U2 - 10.1038/nature22989

DO - 10.1038/nature22989

M3 - Article

VL - 547

SP - 241

EP - 245

JO - Nature

JF - Nature

SN - 0028-0836

IS - 7662

ER -