Parallel action of AtDRB2 and RdDM in the control of transposable element expression

Marion Clavel,Julio Saez-Vásquez,Julie Descombin,Viviane Jean,Claire Picart,Thierry Pélissier,Cécile Bousquet-Antonelli,Cyril Charbonel,Jean-Marc Deragon

doi:10.1186/s12870-015-0455-z

Abstract

BackgroundIn plants and animals, a large number of double-stranded RNA binding proteins (DRBs) have been shown to act as non-catalytic cofactors of DICERs and to participate in the biogenesis of small RNAs involved in RNA silencing. We have previously shown that the loss of Arabidopsis thaliana’s DRB2 protein results in a significant increase in the population of RNA polymerase IV (p4) dependent siRNAs, which are involved in the RNA-directed DNA methylation (RdDM) process.ResultsSurprisingly, despite this observation, we show in this work that DRB2 is part of a high molecular weight complex that does not involve RdDM actors but several chromatin regulator proteins, such as MSI4, PRMT4B and HDA19. We show that DRB2 can bind transposable element (TE) transcripts in vivo but that drb2 mutants do not have a significant variation in TE DNA methylation.ConclusionWe propose that DRB2 is part of a repressive epigenetic regulator complex involved in a negative feedback loop, adjusting epigenetic state to transcription level at TE loci, in parallel of the RdDM pathway. Loss of DRB2 would mainly result in an increased production of TE transcripts, readily converted in p4-siRNAs by the RdDM machinery.Electronic supplementary materialThe online version of this article (doi:10.1186/s12870-015-0455-z) contains supplementary material, which is available to authorized users.

Highlights

In plants and animals, a large number of double-stranded RNA binding proteins (DRBs) have been shown to act as non-catalytic cofactors of DICERs and to participate in the biogenesis of small RNAs involved in RNA silencing
We proposed that the binding of nascent transcripts by DRB2 might facilitate the recruitment of repressing epigenetic factors that provide fine-tuning of transcription at targeted loci
DRB2 exists as a nuclear high molecular weight complex Since the drb2 mutation leads to an increase in the abundance of p4-siRNA of all sizes (21-nt to 24-nt) and classes (Type I and II) [50], we set out to document the role of DRB2 in the RNA-directed DNA methylation (RdDM) pathway

Summary

Introduction

A large number of double-stranded RNA binding proteins (DRBs) have been shown to act as non-catalytic cofactors of DICERs and to participate in the biogenesis of small RNAs involved in RNA silencing. The double-stranded RNA binding motif (DSRM) is an example of such module. DSRM-containing proteins have been essentially involved in the RNA interference process. Eighteen DSRM proteins are present in Arabidopsis thaliana, including four Dicer-Like (DCL) and five double-stranded RNA binding (DRBs) proteins [28,29,30]. DCLs are key enzymes involved in the biogenesis of the different classes of small interfering RNAs and are composed of one or two DSRM associated with RNase III, PAZ, DUF283 and helicase domains. DCL1 is responsible for the production of 21 nucleotides microRNAs from RNA polymerase II

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