GC-rich sequence elements recruit PRC2 in mammalian ES cells. PLoS Genet 6:e1001244

Howard Hughes Medical Institute and Department of Pathology, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts, United States of America.
PLoS Genetics (Impact Factor: 7.53). 12/2010; 6(12):e1001244. DOI: 10.1371/journal.pgen.1001244
Source: PubMed


Polycomb proteins are epigenetic regulators that localize to developmental loci in the early embryo where they mediate lineage-specific gene repression. In Drosophila, these repressors are recruited to sequence elements by DNA binding proteins associated with Polycomb repressive complex 2 (PRC2). However, the sequences that recruit PRC2 in mammalian cells have remained obscure. To address this, we integrated a series of engineered bacterial artificial chromosomes into embryonic stem (ES) cells and examined their chromatin. We found that a 44 kb region corresponding to the Zfpm2 locus initiates de novo recruitment of PRC2. We then pinpointed a CpG island within this locus as both necessary and sufficient for PRC2 recruitment. Based on this causal demonstration and prior genomic analyses, we hypothesized that large GC-rich elements depleted of activating transcription factor motifs mediate PRC2 recruitment in mammals. We validated this model in two ways. First, we showed that a constitutively active CpG island is able to recruit PRC2 after excision of a cluster of activating motifs. Second, we showed that two 1 kb sequence intervals from the Escherichia coli genome with GC-contents comparable to a mammalian CpG island are both capable of recruiting PRC2 when integrated into the ES cell genome. Our findings demonstrate a causal role for GC-rich sequences in PRC2 recruitment and implicate a specific subset of CpG islands depleted of activating motifs as instrumental for the initial localization of this key regulator in mammalian genomes.

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Available from: Manching Ku, Sep 29, 2015
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    • "This indicates that TFs might form a link between specific DNA sequences and the histone modifiers (Benveniste et al. 2014). Conversely, deletion of motifs for transcription activators from NMIs was found to be sufficient for PRC2 recruitment and H3K27me3 deposition in ESCs (Mendenhall et al. 2010). Minimal DNA sequence elements capable of autonomously recruiting PRC2 were recently defined by using iterative genome editing in mouse ESCs. "
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    ABSTRACT: Polycomb group (PcG) proteins are key regulators in establishing a transcriptional repressive state. Polycomb Repressive Complex 2 (PRC2), one of the two major PcG protein complexes, is essential for proper differentiation and maintenance of cellular identity. Multiple factors are involved in recruiting PRC2 to its genomic targets. In this review we will discuss the role of DNA sequence, transcription factors, pre-existing histone modifications, and RNA in guiding PRC2 towards specific genomic loci. The DNA sequence itself influences the DNA methylation state, which is an important determinant of PRC2 recruitment. Other histone modifications are also important for PRC2 binding as PRC2 can respond to different cellular states via crosstalk between histone modifications. Additionally, PRC2 might be able to sense the transcriptional status of genes by binding to nascent RNA, which could also guide the complex to chromatin. In this review we will discuss how all these molecular aspects define a local chromatin state which controls accurate, cell-type specific epigenetic silencing by PRC2. Copyright © 2015. Published by Elsevier Ltd.
    The international journal of biochemistry & cell biology 05/2015; 17. DOI:10.1016/j.biocel.2015.05.006 · 4.05 Impact Factor
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    • "However, a number of lines of evidence – most notably (i) the acquisition of H3K27me3 by bacterial non-methylated GC-rich sequences integrated into mouse genomes [156], (ii) the acquisition of H3K27me3 by CpG islands that have activating sequences removed [156], and (iii) the anticorrelation of H3K27me3 with DNA methylation [74] [146] – point to the requirement for CpG islands in establishing H3K27me3/polycomb repressed domains in mammals. In the absence of an obvious DNAbinding candidate for this role, indirect effects have been suggested, including the ability of H3K36me2 (which is removed from CpG islands through interactions with the ZF-CxxC-domain containing proteins Kdm2a/b, among other mechanisms) to inhibit PRC2 activity [157] [158]. "
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    ABSTRACT: DNA methylation acts as an epigenetic modification in vertebrate DNA. Recently it has become clear that the DNA and histone lysine methylation systems are highly interrelated and rely mechanistically on each other for normal chromatin function in vivo. Here we examine some of the functional links between these systems, with a particular focus on several recent discoveries suggesting how lysine methylation may help to target DNA methylation during development, and vice versa. In addition, the emerging role of non-methylated DNA found in CpG islands in defining histone lysine methylation profiles at gene regulatory elements will be discussed in the context of gene regulation. This article is part of a Special Issue entitled: Methylation: A Multifaceted Modification looking at transcription and beyond. (C) 2014 The Authors. Published by Elsevier B.V. This is an open access article under the CC BY-NC-ND license
    Biochimica et Biophysica Acta (BBA) - Gene Regulatory Mechanisms 12/2014; 1839(12). DOI:10.1016/j.bbagrm.2014.02.007 · 6.33 Impact Factor
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    • "PHO, in particular, binds numerous putative promoter and enhancer elements outside a PRE context (Schuettengruber et al., 2009), and it was shown to interact with the INO80 chromatin remodeling complex in addition to PcG complexes (Klymenko et al., 2006). Of note, the mammalian homolog of PHO, YY1, is able to rescue a pho zygotic mutant, but does not seem to play a major role in PcG recruitment in mammals (Atchison et al., 2003; Mendenhall et al., 2010). DSP1 was also shown to bind to many non-PRE loci in Drosophila embryos, which are marked strongly by GAGA motifs (Schuettengruber et al., 2009). "
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    ABSTRACT: Metazoan genomes are partitioned into modular chromosomal domains containing active or repressive chromatin. In flies, Polycomb group (PcG) response elements (PREs) recruit PHO and other DNA-binding factors and act as nucleation sites for the formation of Polycomb repressive domains. The sequence specificity of PREs is not well understood. Here, we use comparative epigenomics and transgenic assays to show that Drosophila domain organization and PRE specification are evolutionarily conserved despite significant cis-element divergence within Polycomb domains, whereas cis-element evolution is strongly correlated with transcription factor binding divergence outside of Polycomb domains. Cooperative interactions of PcG complexes and their recruiting factor PHO stabilize PHO recruitment to low-specificity sequences. Consistently, PHO recruitment to sites within Polycomb domains is stabilized by PRC1. These data suggest that cooperative rather than hierarchical interactions among low-affinity sequences, DNA-binding factors, and the Polycomb machinery are giving rise to specific and strongly conserved 3D structures in Drosophila.
    Cell Reports 10/2014; 9(1). DOI:10.1016/j.celrep.2014.08.072 · 8.36 Impact Factor
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