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Background  The chromodomain helicase DNA-binding family of ATP-dependent chromatin remodeling factors play essential roles during eukaryote growth and development. They are recruited by specific transcription factors and regulate the expression of developmentally important genes. Here, we describe an unexpected role in non-coding RNA-directed DNA methylation in  Arabidopsis thaliana .    Results  Through forward genetic screens we identified  PKL , a gene required for developmental regulation in plants, as a factor promoting transcriptional silencing at the transgenic  RD29A  promoter. Mutation of  PKL  results in DNA methylation changes at more than half of the loci that are targeted by RNA-directed DNA methylation (RdDM). A small number of transposable elements and genes had reduced DNA methylation correlated with derepression in the  pkl  mutant, though for the majority, decreases in DNA methylation are not sufficient to cause release of silencing. The changes in DNA methylation in the  pkl  mutant are positively correlated with changes in 24-nt siRNA levels. In addition,  PKL  is required for the accumulation of Pol V-dependent transcripts and for the positioning of Pol V-stabilized nucleosomes at several tested loci, indicating that RNA polymerase V-related functions are impaired in the  pkl  mutant.    Conclusions    PKL  is required for transcriptional silencing and has significant effects on RdDM in plants. The changes in DNA methylation in the  pkl  mutant are correlated with changes in the non-coding RNAs produced by Pol IV and Pol V. We propose that at RdDM target regions,  PKL  may be required to create a chromatin environment that influences non-coding RNA production, DNA methylation, and transcriptional silencing.    Electronic supplementary material  The online version of this article (doi:10.1186/s13059-017-1226-y) contains supplementary material, which is available to authorized users.

The developmental regulator PKL is required to maintain correct DNA methylation patterns at RNA-directed DNA methylation loci