title: RNA-directed DNA methylation requires stepwise binding of silencing factors to long non-coding RNA.
abstract: 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.
authors.affiliation: Department of Molecular, Cellular and Developmental Biology, University of Michigan, Ann Arbor, MI, 48109, USA.
authors.forename: Gudrun
authors.initials: G
authors.lastname: Böhmdorfer
authors.forename: M Jordan
authors.initials: MJ
authors.lastname: Rowley
authors.forename: Jan
authors.initials: J
authors.lastname: Kuciński
authors.forename: Yongyou
authors.initials: Y
authors.lastname: Zhu
authors.forename: Ivan
authors.initials: I
authors.lastname: Amies
authors.forename: Andrzej T
authors.initials: AT
authors.lastname: Wierzbicki
mesh_terms: D017360:Arabidopsis / Q000235:genetics / Q000378:metabolism*; D029681:Arabidopsis Proteins / Q000235:genetics / Q000378:metabolism*; D019175:DNA Methylation / Q000235:genetics* / Q000502:physiology; D018506:Gene Expression Regulation, Plant; D020868:Gene Silencing; D062085:RNA, Long Noncoding / Q000378:metabolism*
chemical_list: D029681:Arabidopsis Proteins; D062085:RNA, Long Noncoding
keywords: Arabidopsis thaliana; Argonaute; DNA methyltransferase; INVOLVED IN DE NOVO2; non-coding RNA