Cooperation Between the H3K27me3 Chromatin Mark and Non-CG Methylation in Epigenetic Regulation

Plant Physiol. 2016 Oct;172(2):1131-1141. doi: 10.1104/pp.16.01238. Epub 2016 Aug 17.

Abstract

H3K27me3 is a repressive chromatin mark of genes and is catalyzed by homologs of Enhancer of zeste [E(z)], a component of Polycomb-repressive complex 2 (PRC2), while DNA methylation that occurs in CG and non-CG (CHG and CHH, where H is A, C, or T) contexts is a hallmark of transposon silencing in plants. However, the relationship between H3K27me3 and DNA methylation in gene repression remains unclear. In addition, the mechanism of PRC2 recruitment to specific genes is not known in plants. Here, we show that SDG711, a rice (Oryza sativa) E(z) homolog, is required to maintain H3K27me3 of many developmental genes after shoot meristem to leaf transition and that many H3K27me3-marked developmental genes are also methylated at non-CG sites in the body regions. SDG711-binding and SDG711-mediated ectopic H3K27me3 also target genes methylated at non-CG sites. Conversely, mutation of OsDRM2, a major rice CHH methyltransferase, resulted in loss of SDG711-binding and H3K27me3 from many genes and their de-repression. Furthermore, we show that SDG711 physically interacts with OsDRM2 and a putative CHG methylation-binding protein. These results together suggest that the repression of many developmental genes may involve both DRM2-mediated non-CG methylation and PRC2-mediated H3K27me3 and that the two marks are not generally mutually exclusive but may cooperate in repression of developmentally regulated genes in rice.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Chromatin / genetics
  • Chromatin / metabolism*
  • DNA Methylation*
  • Epigenesis, Genetic*
  • Gene Expression Profiling / methods
  • Gene Expression Regulation, Developmental
  • Gene Expression Regulation, Plant
  • Histones / genetics
  • Histones / metabolism*
  • Lysine / genetics
  • Lysine / metabolism*
  • Meristem / genetics
  • Meristem / growth & development
  • Meristem / metabolism
  • Methylation
  • Mutation
  • Oryza / genetics
  • Oryza / growth & development
  • Oryza / metabolism
  • Plant Leaves / genetics
  • Plant Leaves / growth & development
  • Plant Leaves / metabolism
  • Plant Proteins / genetics
  • Plant Proteins / metabolism
  • Plant Shoots / genetics
  • Plant Shoots / growth & development
  • Plant Shoots / metabolism
  • Polycomb Repressive Complex 2 / genetics
  • Polycomb Repressive Complex 2 / metabolism
  • Protein Binding
  • Reverse Transcriptase Polymerase Chain Reaction

Substances

  • Chromatin
  • Histones
  • Plant Proteins
  • Polycomb Repressive Complex 2
  • Lysine