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Polycomb-mediated axial patterning requires nucleosome compaction [ChIP-seq]

ABSTRACT: We determined the genome-wide binding profiles of wild type and compaction mutant CBX2 (denoted as 'KRA') in mouse embryonic stem cells (mESCs) by ChIP-seq.

ORGANISM(S): Mus musculus

PROVIDER: GSE86084 | GEO | 2017/08/31

SECONDARY ACCESSION(S): PRJNA340228

REPOSITORIES: GEO

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Polycomb-mediated axial patterning requires nucleosome compaction [RNA-seq]

Project description:We determined by RNA-seq gene expression changes in mESCs following the induced expression of WT-, KRA- or DEA-CBX2 variants in Cbx2 null cells.

2017-08-31 | GSE86083 | GEO

Polycomb-mediated axial patterning requires nucleosome compaction

Project description:Polycomb-mediated axial patterning requires nucleosome compaction

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Polycomb-mediated axial patterning requires nucleosome compaction

Project description:This SuperSeries is composed of the SubSeries listed below.

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Mutation of a nucleosome compaction region disrupts Polycomb-mediated axial patterning.

Project description:Nucleosomes play important structural and regulatory roles by tightly wrapping the DNA that constitutes the metazoan genome. The Polycomb group (PcG) proteins modulate nucleosomes to maintain repression of key developmental genes, including Hox genes whose temporal and spatial expression is tightly regulated to guide patterning of the anterior-posterior body axis. CBX2, a component of the mammalian Polycomb repressive complex 1 (PRC1), contains a compaction region that has the biochemically defined activity of bridging adjacent nucleosomes. Here, we demonstrate that a functional compaction region is necessary for proper body patterning, because mutating this region leads to homeotic transformations similar to those observed with PcG loss-of-function mutations. We propose that CBX2-driven nucleosome compaction is a key mechanism by which PcG proteins maintain gene silencing during mouse development.

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Project description:Phase separation is increasingly recognized in facultative heterochromatinization of Polycomb target genes; however, the underlying mechanisms remain obscure. Using single-molecule imaging and tracking, we show that individual condensates in mESCs contain approximately 3 CBX2 molecules and numerous PRC1 and PRC2 subunits and indicate that the composition and dynamics of condensates are developmentally regulated. We reveal that CBX2 clusters PRC2 and controls the spatial distribution of both PRC2 and H3K27me3. Using genomic approaches, we demonstrate that CBX2 binds condensate initiation sites enriched for PRC2 nucleation sites. CBX2 deletion causes PRC2 and H3K27me3 to redistribute from their regular targets. By developing a separate-of-function variant, we determine that CBX2 relies on its self-clustering ability to function. These findings collectively support a novel phase-separation model driven by nucleation and bridging, in which low-abundance proteins self-cluster to initiate condensate assembly, a process tightly coupled to function.

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Sparse CBX2 nucleates many Polycomb proteins to promote facultative heterochromatinization of Polycomb target genes

Project description:Facultative heterochromatinization of genomic regulators by Polycomb repressive complex (PRC) 1 and 2 is essential in development and differentiation; however, the underlying molecular mechanisms remain obscure. Using genetic engineering, molecular approaches, and live-cell single-molecule imaging, we quantify the number of proteins within condensates formed through liquid-liquid phase separation (LLPS) and find that in mouse embryonic stem cells (mESCs), approximately 3 CBX2 proteins nucleate many PRC1 and PRC2 subunits to form one non-stoichiometric condensate. We demonstrate that sparse CBX2 prevents Polycomb proteins from migrating to constitutive heterochromatin, demarcates the spatial boundaries of facultative heterochromatin, controls the deposition of H3K27me3, regulates transcription, and impacts cellular differentiation. Furthermore, we show that LLPS of CBX2 is required for the demarcation and deposition of H3K27me3 and is essential for cellular differentiation. Our findings uncover new functional roles of LLPS in the formation of facultative heterochromatin and unravel a new mechanism by which low-abundant proteins nucleate many other proteins to form compartments that enable them to execute their functions.

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