NERD, a plant-specific GW protein, defines an additional RNAi-dependent chromatin-based pathway in Arabidopsis

Mol Cell. 2012 Oct 12;48(1):121-32. doi: 10.1016/j.molcel.2012.07.027. Epub 2012 Aug 30.


In Arabidopsis, transcriptional gene silencing (TGS) can be triggered by 24 nt small-interfering RNAs (siRNAs) through the RNA-directed DNA methylation (RdDM) pathway. By functional analysis of NERD, a GW repeat- and PHD finger-containing protein, we demonstrate that Arabidopsis harbors a second siRNA-dependent DNA methylation pathway targeting a subset of nonconserved genomic loci. The activity of the NERD-dependent pathway differs from RdDM by the fact that it relies both on silencing-related factors previously implicated only in posttranscriptional gene silencing (PTGS), including RNA-DEPENDENT RNA POLYMERASE1/6 and ARGONAUTE2, and most likely on 21 nt siRNAs. A central role for NERD in integrating RNA silencing and chromatin signals in transcriptional silencing is supported by data showing that it binds both to histone H3 and AGO2 proteins and contributes to siRNA accumulation at a NERD-targeted locus. Our results unravel the existence of a conserved chromatin-based RNA silencing pathway encompassing both PTGS and TGS components in plants.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Amino Acid Motifs
  • Amino Acid Sequence
  • Arabidopsis / genetics*
  • Arabidopsis / metabolism*
  • Arabidopsis Proteins / chemistry
  • Arabidopsis Proteins / genetics*
  • Arabidopsis Proteins / metabolism*
  • Argonaute Proteins
  • Chromatin / genetics
  • Chromatin / metabolism
  • Chromosomal Proteins, Non-Histone / chemistry
  • Chromosomal Proteins, Non-Histone / genetics*
  • Chromosomal Proteins, Non-Histone / metabolism*
  • DNA Methylation
  • Histones / metabolism
  • Molecular Sequence Data
  • Protein Binding
  • RNA Interference*
  • RNA, Small Interfering / genetics
  • RNA-Binding Proteins / metabolism
  • RNA-Dependent RNA Polymerase / metabolism
  • Recombinant Fusion Proteins / chemistry
  • Recombinant Fusion Proteins / genetics
  • Recombinant Fusion Proteins / metabolism
  • Signal Transduction


  • Arabidopsis Proteins
  • Argonaute Proteins
  • Chromatin
  • Chromosomal Proteins, Non-Histone
  • Histones
  • NERD protein, Arabidopsis
  • RNA, Small Interfering
  • RNA-Binding Proteins
  • Recombinant Fusion Proteins
  • argonaute 2 protein, Arabidopsis
  • RDR6 protein, Arabidopsis
  • RNA-Dependent RNA Polymerase

Associated data

  • GEO/GSE35346