RNA-directed DNA methylation requires stepwise binding of silencing factors to long non-coding RNA

Gudrun Böhmdorfer, M. Jordan Rowley, Jan Kuciński, Yongyou Zhu, Ivan Amies, Andrzej T. Wierzbicki

Research output: Contribution to journalArticlepeer-review

59 Scopus citations


Ribonucleic acid-mediated transcriptional gene silencing (known as RNA-directed DNA methylation, or RdDM, in Arabidopsis thaliana) is important for influencing gene expression and the inhibition of transposons by the deposition of repressive chromatin marks such as histone modifications and DNA methylation. A key event in de novo methylation of DNA by RdDM is the production of long non-coding RNA (lncRNA) by RNA polymerase V (Pol V). Little is known about the events that connect Pol V transcription to the establishment of repressive chromatin modifications. Using RNA immunoprecipitation, we elucidated the order of events downstream of lncRNA production and discovered interdependency between lncRNA-associated proteins. We found that the effector protein ARGONAUTE4 (AGO4) binds lncRNA independent of the RNA-binding protein INVOLVED IN DE NOVO2 (IDN2). In contrast, IDN2 binds lncRNA in an AGO4-dependent manner. We further found that the de novo DNA methyltransferase DOMAINS REARRANGED METHYLTRANSFERASE2 (DRM2) also associates with lncRNA produced by Pol V and that this event depends on AGO4 and IDN2. We propose a model where the silencing proteins AGO4, IDN2 and DRM2 bind to lncRNA in a stepwise manner, resulting in DNA methylation of RdDM target loci.

Original languageEnglish (US)
Pages (from-to)181-191
Number of pages11
JournalPlant Journal
Issue number2
StatePublished - Jul 2014
Externally publishedYes


  • Arabidopsis thaliana
  • Argonaute
  • DNA methyltransferase
  • non-coding RNA

ASJC Scopus subject areas

  • Genetics
  • Plant Science
  • Cell Biology


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