Mouse Heterochromatin Adopts Digital Compaction States Without Showing Hallmarks of HP1-Driven Liquid-Liquid Phase Separation

Overview

Journal Mol Cell

Publisher Cell Press

Specialty Cell Biology

Date 2020 Feb 27

PMID 32101700

Citations 147

Authors

Fabian Erdel

Anne Rademacher

Rifka Vlijm

Jana Tunnermann

Lukas Frank

Robin Weinmann

Elisabeth Schweigert

Klaus Yserentant

Johan Hummert

Caroline Bauer

Sabrina Schumacher

Ahmad Al Alwash

Christophe Normand

Dirk-Peter Herten

Johann Engelhardt

Karsten Rippe

Affiliations

Soon will be listed here.

Abstract

The formation of silenced and condensed heterochromatin foci involves enrichment of heterochromatin protein 1 (HP1). HP1 can bridge chromatin segments and form liquid droplets, but the biophysical principles underlying heterochromatin compartmentalization in the cell nucleus are elusive. Here, we assess mechanistically relevant features of pericentric heterochromatin compaction in mouse fibroblasts. We find that (1) HP1 has only a weak capacity to form liquid droplets in living cells; (2) the size, global accessibility, and compaction of heterochromatin foci are independent of HP1; (3) heterochromatin foci lack a separated liquid HP1 pool; and (4) heterochromatin compaction can toggle between two "digital" states depending on the presence of a strong transcriptional activator. These findings indicate that heterochromatin foci resemble collapsed polymer globules that are percolated with the same nucleoplasmic liquid as the surrounding euchromatin, which has implications for our understanding of chromatin compartmentalization and its functional consequences.

Citing Articles

Nanometer condensate organization in live cells derived from partitioning measurements.

Dollinger C, Potolitsyna E, Martin A, Anand A, Datar G, Schmit J bioRxiv. 2025; .

PMID: 40060647 PMC: 11888449. DOI: 10.1101/2025.02.26.640428.

Nuclear mechano-confinement induces geometry-dependent HP1α condensate alterations.

Hovet O, Nahali N, Halaburkova A, Haugen L, Paulsen J, Progida C Commun Biol. 2025; 8(1):308.

PMID: 40000755 PMC: 11862009. DOI: 10.1038/s42003-025-07732-6.

Biomolecular condensates in immune cell fate.

Kodali S, Sands C, Guo L, Huang Y, Di Stefano B Nat Rev Immunol. 2025; .

PMID: 39875604 DOI: 10.1038/s41577-025-01130-z.

HP1a promotes chromatin liquidity and drives spontaneous heterochromatin compartmentalization.

Brennan L, Kim H, Colmenares S, Ego T, Ryu J, Karpen G bioRxiv. 2025; .

PMID: 39868136 PMC: 11761810. DOI: 10.1101/2024.10.18.618981.

Chromatin enables precise and scalable gene regulation with factors of limited specificity.

Perkins M, Crocker J, Tkacik G Proc Natl Acad Sci U S A. 2025; 122(1):e2411887121.

PMID: 39793086 PMC: 11725945. DOI: 10.1073/pnas.2411887121.

References

Lieberman-Aiden E, van Berkum N, Williams L, Imakaev M, Ragoczy T, Telling A . Comprehensive mapping of long-range interactions reveals folding principles of the human genome. Science. 2009; 326(5950):289-93. PMC: 2858594. DOI: 10.1126/science.1181369. View

Chavez A, Scheiman J, Vora S, Pruitt B, Tuttle M, Iyer E . Highly efficient Cas9-mediated transcriptional programming. Nat Methods. 2015; 12(4):326-8. PMC: 4393883. DOI: 10.1038/nmeth.3312. View

Grussmayer K, Herten D . Time-resolved molecule counting by photon statistics across the visible spectrum. Phys Chem Chem Phys. 2017; 19(13):8962-8969. DOI: 10.1039/c7cp00363c. View

Casas-Delucchi C, van Bemmel J, Haase S, Herce H, Nowak D, Meilinger D . Histone hypoacetylation is required to maintain late replication timing of constitutive heterochromatin. Nucleic Acids Res. 2011; 40(1):159-69. PMC: 3245938. DOI: 10.1093/nar/gkr723. View

Kundaje A, Meuleman W, Ernst J, Bilenky M, Yen A, Heravi-Moussavi A . Integrative analysis of 111 reference human epigenomes. Nature. 2015; 518(7539):317-30. PMC: 4530010. DOI: 10.1038/nature14248. View

Machida S, Takizawa Y, Ishimaru M, Sugita Y, Sekine S, Nakayama J . Structural Basis of Heterochromatin Formation by Human HP1. Mol Cell. 2018; 69(3):385-397.e8. DOI: 10.1016/j.molcel.2017.12.011. View

Bancaud A, Huet S, Daigle N, Mozziconacci J, Beaudouin J, Ellenberg J . Molecular crowding affects diffusion and binding of nuclear proteins in heterochromatin and reveals the fractal organization of chromatin. EMBO J. 2009; 28(24):3785-98. PMC: 2797059. DOI: 10.1038/emboj.2009.340. View

Rothbauer U, Zolghadr K, Muyldermans S, Schepers A, Cardoso M, Leonhardt H . A versatile nanotrap for biochemical and functional studies with fluorescent fusion proteins. Mol Cell Proteomics. 2007; 7(2):282-9. DOI: 10.1074/mcp.M700342-MCP200. View

Kennedy M, Hughes R, Peteya L, Schwartz J, Ehlers M, Tucker C . Rapid blue-light-mediated induction of protein interactions in living cells. Nat Methods. 2010; 7(12):973-5. PMC: 3059133. DOI: 10.1038/nmeth.1524. View

10.

Pau G, Fuchs F, Sklyar O, Boutros M, Huber W . EBImage--an R package for image processing with applications to cellular phenotypes. Bioinformatics. 2010; 26(7):979-81. PMC: 2844988. DOI: 10.1093/bioinformatics/btq046. View

11.

Wang L, Gao Y, Zheng X, Liu C, Dong S, Li R . Histone Modifications Regulate Chromatin Compartmentalization by Contributing to a Phase Separation Mechanism. Mol Cell. 2019; 76(4):646-659.e6. DOI: 10.1016/j.molcel.2019.08.019. View

12.

Erdel F, Rippe K . Formation of Chromatin Subcompartments by Phase Separation. Biophys J. 2018; 114(10):2262-2270. PMC: 6129460. DOI: 10.1016/j.bpj.2018.03.011. View

13.

Thiru A, Nietlispach D, Mott H, Okuwaki M, Lyon D, Nielsen P . Structural basis of HP1/PXVXL motif peptide interactions and HP1 localisation to heterochromatin. EMBO J. 2004; 23(3):489-99. PMC: 1271814. DOI: 10.1038/sj.emboj.7600088. View

14.

Bracha D, Walls M, Wei M, Zhu L, Kurian M, Avalos J . Mapping Local and Global Liquid Phase Behavior in Living Cells Using Photo-Oligomerizable Seeds. Cell. 2018; 175(6):1467-1480.e13. PMC: 6724719. DOI: 10.1016/j.cell.2018.10.048. View

15.

Elgin S, Reuter G . Position-effect variegation, heterochromatin formation, and gene silencing in Drosophila. Cold Spring Harb Perspect Biol. 2013; 5(8):a017780. PMC: 3721279. DOI: 10.1101/cshperspect.a017780. View

16.

Strom A, Emelyanov A, Mir M, Fyodorov D, Darzacq X, Karpen G . Phase separation drives heterochromatin domain formation. Nature. 2017; 547(7662):241-245. PMC: 6022742. DOI: 10.1038/nature22989. View

17.

Taddei A, Maison C, Roche D, Almouzni G . Reversible disruption of pericentric heterochromatin and centromere function by inhibiting deacetylases. Nat Cell Biol. 2001; 3(2):114-20. DOI: 10.1038/35055010. View

18.

Schuster B, Reed E, Parthasarathy R, Jahnke C, Caldwell R, Bermudez J . Controllable protein phase separation and modular recruitment to form responsive membraneless organelles. Nat Commun. 2018; 9(1):2985. PMC: 6065366. DOI: 10.1038/s41467-018-05403-1. View

19.

Muller-Ott K, Erdel F, Matveeva A, Mallm J, Rademacher A, Hahn M . Specificity, propagation, and memory of pericentric heterochromatin. Mol Syst Biol. 2014; 10:746. PMC: 4299515. DOI: 10.15252/msb.20145377. View

20.

Weber S, Brangwynne C . Inverse size scaling of the nucleolus by a concentration-dependent phase transition. Curr Biol. 2015; 25(5):641-6. PMC: 4348177. DOI: 10.1016/j.cub.2015.01.012. View