Polycomb Group Proteins Ezh2 and Rnf2 Direct Genomic Contraction and Imprinted Repression in Early Mouse Embryos

Abstract

Genomic imprinting regulates parental-specific expression of particular genes and is required for normal mammalian development. How imprinting is established during development is, however, largely unknown. To address this question, we studied the mouse Kcnq1 imprinted cluster at which paternal-specific silencing depends on expression of the noncoding RNA Kcnq1ot1. We show that Kcnq1ot1 is expressed from the zygote stage onward and rapidly associates with chromatin marked by Polycomb group (PcG) proteins and repressive histone modifications, forming a discrete repressive nuclear compartment devoid of RNA polymerase II, a configuration also observed at the Igf2r imprinted cluster. In this compartment, the paternal Kcnq1 cluster exists in a three-dimensionally contracted state. In vivo the PcG proteins Ezh2 and Rnf2 are independently required for genomic contraction and imprinted silencing. We propose that the formation of a parental-specific higher-order chromatin organization renders imprint clusters competent for monoallelic silencing and assign a central role to PcG proteins in this process.

Chromatin maps, histone modifications and leukemia

“…Finally, very recent data suggest a role in imprinting. 69,70 In drosophila, PRC2 binds specific polycomb response elements. It is less clear how PRC2 is recruited in higher species.…”

“…Recent data suggest that non-coding RNA may be involvedFHOTAIR 28 Fin the case of Hox loci, XIST in the case of X-chromosome inactivation, 27 and Kcnq1ot1 in the case of imprinting. 69,70 Genome-wide studies suggest that H3K27me3 may also mark developmental genes for future expression by participating in a 'bivalent domain' that carries both a repressive H3K27me3 mark and an activating H3K4me3 mark. 59 Evidence exists that H3K27me3 serves as a docking site for polycomb repressive complex 1 (PRC1), 71 a multiprotein complex that among other targets, mono-ubiquitinates H2A at K119.…”

Genomic Imprinting and Epigenetic Control of Development

“…In the case of XCI, Xist transcripts influence hundreds of megabases, making XCI a particularly attractive model for epigenetic phenomena. Although data suggest that Airn and Kcnq1ot1 may mediate the formation of a localized, transcriptionally silent nuclear compartment (Terranova et al 2008;Redrup et al 2009), Xist function during XCI has provided the best evidence of ncRNA-mediated formation of silent nuclear domains. A critical facet of XCI is the localization of the Xist RNA.…”

“…As in the embryo, Kcnq1ot1 is responsible for silencing of the placental genes; however, the locus has been observed to undergo a "compaction" specific to extraembryonic lineages (Terranova et al 2008;Redrup et al 2009). Reminiscent of the mechanism of Xist, the Kcnq1ot1 ncRNA forms a repressive nuclear compartment, devoid of Pol II and other marks of active chromatin (Terranova et al 2008).…”

Macro lncRNAs

“…29,41 Expression of the Kcnq1ot1 macro lncRNA correlates with accumulation of repressive histone H3K9me3 and H3K27me3 on the silenced flanking genes in placental but not in embryonic tissues. 49,50 However despite the demonstration that the responsible G9A/EHMT2 and PRC2 histone methyltransferases physically interact with Kcnq1ot1, 51 mice lacking G9A/EHMT2 and PRC2 only show stochastic loss of imprinted expression of some genes in the placenta. 52,53 A role for the Kcnq1ot1 macro lncRNA product was recently dismissed based on a siRNA-mediated knockdown experiment that did not change imprinted expression of these genes in undifferentiated embryonic stem cells.…”