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Histone marks enable formation of immiscible phase-separated chromatin compartments

ABSTRACT: Histone marks enable formation of immiscible phase-separated chromatin compartments

PROVIDER: PRJNA1007600 | ENA |

REPOSITORIES: ENA

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	SRR25708701_1.fastq.gz	Fastqsanger.gz
	SRR25708701_2.fastq.gz	Fastqsanger.gz
	SRR25708702_1.fastq.gz	Fastqsanger.gz
	SRR25708702_2.fastq.gz	Fastqsanger.gz

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Histone marks enable formation of immiscible phase-separated chromatin compartments

Project description: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, CBX7-PRC1, regulate facultative heterochromatin via a phase separation mechanism, similar to constitutive heterochromatin. Facultative and constitutive heterochromatin represent distinct, coexisting repressive condensates in nuclei. H3K27me3- and H3K9me3-marked nucleosomal arrays and their reader complexes phase separate into immiscible condensates, analogous to the relationship between facultative and constitutive heterochromatin in vivo. Overexpression of CBX7-PRC1 causes aberrant chromatin compartmentalization in vivo and up-regulation of cancer-related genes. CBX7 inhibitor effectively inhibits cancer cell proliferation possibly through phase separation-mediated compartment reorganization. Our data suggest that histone marks mediate chromatin compartmentalization via phase separation, and offer potential epigenetic mechanistic insights into tumor development and cancer therapy.

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Cancer Mutations of the Tumor Suppressor SPOP Disrupt the Formation of Active, Phase-Separated Compartments.

Project description:Mutations in the tumor suppressor SPOP (speckle-type POZ protein) cause prostate, breast, and other solid tumors. SPOP is a substrate adaptor of the cullin3-RING ubiquitin ligase and localizes to nuclear speckles. Although cancer-associated mutations in SPOP interfere with substrate recruitment to the ligase, mechanisms underlying assembly of SPOP with its substrates in liquid nuclear bodies and effects of SPOP mutations on assembly are poorly understood. Here, we show that substrates trigger phase separation of SPOP in vitro and co-localization in membraneless organelles in cells. Enzymatic activity correlates with cellular co-localization and in vitro mesoscale assembly formation. Disease-associated SPOP mutations that lead to the accumulation of proto-oncogenic proteins interfere with phase separation and co-localization in membraneless organelles, suggesting that substrate-directed phase separation of this E3 ligase underlies the regulation of ubiquitin-dependent proteostasis.

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PPARg marks splenic precursors of multiple nonlymphoid-tissue Treg compartments [scRNA-seq multiple tissues]

Project description:PPARg marks splenic precursors of multiple nonlymphoid-tissue Treg compartments [scRNA-seq multiple tissues]

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Human cytomegalovirus forms phase-separated compartments at viral genomes to facilitate viral replication.

Project description:Human cytomegalovirus (HCMV) replicates its DNA genome in specialized replication compartments (RCs) in the host cell nucleus. These membrane-less organelles originate as spherical structures and grow in size over time. However, the mechanism of RC biogenesis has remained understudied. Using live-cell imaging and photo-oligomerization, we show that a central component of RCs, the UL112-113 proteins, undergo liquid-liquid phase separation (LLPS) to form RCs in the nucleus. We show that the self-interacting domain and large intrinsically disordered regions of UL112-113 are required for LLPS. Importantly, viral DNA induces local clustering of these proteins and lowers the threshold for phase separation. The formation of phase-separated compartments around viral genomes is necessary to recruit the viral DNA polymerase for viral genome replication. Thus, HCMV uses its UL112-113 proteins to generate RCs around viral genomes by LLPS to ensure the formation of a pro-replicative environment.

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Project description:The nucleus is composed of membrane-less subnuclear compartments, containing intrinsically disordered proteins and RNAs that phase separate (PS) and contribute to specific nuclear reactions. However, whether and how different subnuclear compartments can intercommunicate remains elusive. Here we identified nuclear bodies with PS features composed of BAZ2A, a factor associating with active chromatin. BAZ2A-bodies depend on active transcription, RNAs, and the non-disordered BAZ2A RNA-binding TAM domain. Although BAZ2A and H3K27me3 occupancies anticorrelate in the linear genome, in the nuclear space BAZ2A-bodies contact H3K27me3-bodies. Disruption of BAZ2A-bodies promotes BAZ2A invasion into H3K27me3-domains, causing H3K27me3-bodies loss, H3K27me3 decrease, and gene upregulation. BAZ2A-bodies formation is negatively regulated by the nuclear-speckles associated lncRNA Malat1 that interacts with BAZ2A and mediates BAZ2A association to chromatin at nuclear speckles, which do not contact BAZ2A-bodies. The results unravel how active compartments protect repressive compartments using PS mechanisms that are promoted or impaired according to the type of RNA interactions with RNA-binding proteins.

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Cohesin-based chromatin interactions enable regulated gene expression within pre-existing architectural compartments.

Project description:Chromosome conformation capture approaches have shown that interphase chromatin is organized into an architectural framework of Mb-sized compartments and sub-Mb-sized topological domains. Cohesin controls chromosome topology to facilitate DNA repair and chromosome segregation in cycling cells, and also associates with active enhancers and promoters and with CTCF to form long-range interactions important for gene regulation. We find that architectural compartments - a major feature of interphase chromatin organization – are maintained in non-cycling mouse thymocytes after genetic depletion of cohesin in vivo. Cohesin was however required for specific long-range interactions within permissive (A-type) compartments, where cohesin-regulated genes reside. Cohesin depletion diminished interactions between cohesin-bound sites, while alternative interactions between chromatin features associated with transcriptional activation and repression became more prominent, with corresponding changes in gene expression. Our findings indicate that cohesin-mediated long-range interactions facilitate discrete gene expression states within pre-existing chromosomal compartments.

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