Histone marks enable formation of immiscible phase-separated chromatin compartments

Wenjing Sun; Jiacheng Wang; Wenqian Liu; Baixue Tang; Hongyuan Qu; Huanxing Su; Jianwei Wang; Haitao Li; Wei Xie; Pilong Li

doi:10.1016/j.celrep.2025.116003

Histone marks enable formation of immiscible phase-separated chromatin compartments

Cell Rep. 2025 Jul 11;44(7):116003. doi: 10.1016/j.celrep.2025.116003. Online ahead of print.

Authors

Wenjing Sun¹, Jiacheng Wang², Wenqian Liu³, Baixue Tang⁴, Hongyuan Qu³, Huanxing Su⁵, Jianwei Wang⁴, Haitao Li³, Wei Xie⁶, Pilong Li⁷

Affiliations

¹ State Key Laboratory of Membrane Biology, Beijing Frontier Research Center for Biological Structure, School of Life Sciences, Tsinghua University, Tsinghua-Peking Center for Life Sciences, Beijing 100084, China.
² Center for Stem Cell Biology and Regenerative Medicine, MOE Key Laboratory of Bioinformatics, School of Life Sciences, Tsinghua University, Tsinghua-Peking Center for Life Sciences, Beijing 100084, China.
³ MOE Key Laboratory of Protein Sciences, Beijing Frontier Research Center for Biological Structure, Department of Basic Medical Sciences, School of Medicine, Tsinghua University, Beijing 100084, China.
⁴ State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin 300020, China.
⁵ State Key Laboratory of Mechanism and Quality of Chinese Medicine, Institute of Chinese Medical Sciences, University of Macau, Macau, China.
⁶ Center for Stem Cell Biology and Regenerative Medicine, MOE Key Laboratory of Bioinformatics, School of Life Sciences, Tsinghua University, Tsinghua-Peking Center for Life Sciences, Beijing 100084, China. Electronic address: xiewei121@mail.tsinghua.edu.cn.
⁷ State Key Laboratory of Membrane Biology, Beijing Frontier Research Center for Biological Structure, School of Life Sciences, Tsinghua University, Tsinghua-Peking Center for Life Sciences, Beijing 100084, China. Electronic address: pilongli@mail.tsinghua.edu.cn.

PMID: 40650903
DOI: 10.1016/j.celrep.2025.116003

Abstract

Eukaryotic chromatin is organized into compartments for gene expression regulation, but the underlying mechanisms remain unclear. Here, we demonstrate that multivalent H3K27me3 and its reader, the CBX7-PRC1 complex, regulate facultative heterochromatin via a phase separation mechanism. Facultative and constitutive heterochromatin represent distinct, coexisting condensates in nuclei. In vitro, H3K27me3- and H3K9me3-marked nucleosomal arrays and their reader complexes can phase separate into immiscible condensates that are analogous to the relationship between facultative and constitutive heterochromatin in vivo. Moreover, overexpression of CBX7-PRC1 causes aberrant chromatin compartmentalization as demonstrated by H3K9me3 CUT&Tag and up-regulation of genes related to cancer, such as acute myeloblastic leukemia (AML). Chromobox 7 (CBX7) inhibitor effectively inhibits cancer cell proliferation, possibly through phase-separation-mediated compartment reorganization. Our data demonstrate how the specificity of compartmentalization is achieved based on the formation of immiscible phase-separated condensates and offer potential epigenetic mechanistic insights into tumor development.

Keywords: CBX7-PRC1; CP: Molecular biology; chromatin compartmentalization; constitutive heterochromatin; cooperativity; facultative heterochromatin; immiscible condensates; liquid-liquid phase separation; multivalence.