The polycomb repressive complex 2 (PRC2) consists of core subunits SUZ12, EED, RBBP4/7, and EZH1/2 and is responsible for mono-, di-, and tri-methylation of lysine 27 on histone H3. Whereas two distinct forms exist, PRC2.1 (containing one polycomb-like protein) and PRC2.2 (containing AEBP2 and JARID2), little is known about their differential functions. Here, we report the discovery of a family of vertebrate-specific PRC2.1 proteins, "PRC2 associated LCOR isoform 1" (PALI1) and PALI2, encoded by the LCOR and LCORL gene loci, respectively. PALI1 promotes PRC2 methyltransferase activity in vitro and in vivo and is essential for mouse development. Pali1 and Aebp2 define mutually exclusive, antagonistic PRC2 subtypes that exhibit divergent H3K27-tri-methylation activities. The balance of these PRC2.1/PRC2.2 activities is required for the appropriate regulation of polycomb target genes during differentiation. PALI1/2 potentially link polycombs with transcriptional co-repressors in the regulation of cellular identity during development and in cancer.

The Polycomb repressor complex 2 (PRC2) is composed of the core subunits Ezh1/2, Suz12, and Eed, and it mediates all di- and tri-methylation of histone H3 at lysine 27 in higher eukaryotes. However, little is known about how the catalytic activity of PRC2 is regulated to demarcate H3K27me2 and H3K27me3 domains across the genome. To address this, we mapped the endogenous interactomes of Ezh2 and Suz12 in embryonic stem cells (ESCs), and we combined this with a functional screen for H3K27 methylation marks. We found that Nsd1-mediated H3K36me2 co-locates with H3K27me2, and its loss leads to genome-wide expansion of H3K27me3. These increases in H3K27me3 occurred at PRC2/PRC1 target genes and as de novo accumulation within what were previously broad H3K27me2 domains. Our data support a model in which Nsd1 is a key modulator of PRC2 function required for regulating the demarcation of genome-wide H3K27me2 and H3K27me3 domains in ESCs.

Sin3a is the central scaffold protein of the prototypical Hdac1/2 chromatin repressor complex, crucially required during early embryonic development for the growth of pluripotent cells of the inner cell mass. Here, we compare the composition of the Sin3a-Hdac complex between pluripotent embryonic stem (ES) and differentiated cells by establishing a method that couples two independent endogenous immunoprecipitations with quantitative mass spectrometry. We define the precise composition of the Sin3a complex in multiple cell types and identify the Fam60a subunit as a key defining feature of a variant Sin3a complex present in ES cells, which also contains Ogt and Tet1. Fam60a binds on H3K4me3-positive promoters in ES cells, together with Ogt, Tet1 and Sin3a, and is essential to maintain the complex on chromatin. Finally, we show that depletion of Fam60a phenocopies the loss of Sin3a, leading to reduced proliferation, an extended G1-phase and the deregulation of lineage genes. Taken together, Fam60a is an essential core subunit of a variant Sin3a complex in ES cells that is required to promote rapid proliferation and prevent unscheduled differentiation.

The regulation of gene expression through epigenetic mechanisms operates at several levels. These include modification of DNA itself, modification of the histone proteins in contact with DNA, as well as higher order regulation involving 'remodelling' and three-dimensional rearrangement of chromosomes to increase or decrease accessibility to the DNA by transcription factors 1 . Many of these changes are mediated by large heteromeric protein complexes possessing multiple activities that ensure that specific epigenetic changes occur at particular genes at the correct time.One family of such complexes are known as Polycomb Repressive Complexes (PRC) 2,3 . The genes encoding components of these complexes were originally isolated in genetic screens of Drosophila, where mutants display a variety of developmental phenotypes, suggesting a critical role for Polycomb genes in the regulating of genes involved in cell fate determination and differentiation 4,5 . Later biochemical work established that Polycomb function was mediated by two classes of multi-protein enzymatic complexes (PRC1 and PRC2) whose central catalytic functions include histone post-translational modification activities (i.e. ubiquitin ligase and methyltransferase activity respectively). The catalytic core of PRC1 in humans is a heterodimer comprising either of two related E3 ubiquitin ligases, RING1 (RING1A) or RNF2 (RING1B) and one of six PCGF orthologs [6][7][8][9][10] .

Highlights d We adapted the E-MAP approach to study genetic interactions underlying viral infection d We studied host gene pairs as well as gene-drug and geneviral mutant combinations d The HIV vE-MAP highlighted a role for the CNOT complex in mediating infection d CNOT mediates HIV infection in primary CD4+ T cells by suppression of innate immunity