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A Pre-mRNA-splicing factor is required for RNA-directed DNA methylation in Arabidopsis.
- Source :
-
PLoS genetics [PLoS Genet] 2013; Vol. 9 (9), pp. e1003779. Date of Electronic Publication: 2013 Sep 12. - Publication Year :
- 2013
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Abstract
- Cytosine DNA methylation is a stable epigenetic mark that is frequently associated with the silencing of genes and transposable elements (TEs). In Arabidopsis, the establishment of DNA methylation is through the RNA-directed DNA methylation (RdDM) pathway. Here, we report the identification and characterization of RDM16, a new factor in the RdDM pathway. Mutation of RDM16 reduced the DNA methylation levels and partially released the silencing of a reporter gene as well as some endogenous genomic loci in the DNA demethylase ros1-1 mutant background. The rdm16 mutant had morphological defects and was hypersensitive to salt stress and abscisic acid (ABA). Map-based cloning and complementation test led to the identification of RDM16, which encodes a pre-mRNA-splicing factor 3, a component of the U4/U6 snRNP. RNA-seq analysis showed that 308 intron retention events occurred in rdm16, confirming that RDM16 is involved in pre-mRNA splicing in planta. RNA-seq and mRNA expression analysis also revealed that the RDM16 mutation did not affect the pre-mRNA splicing of known RdDM genes, suggesting that RDM16 might be directly involved in RdDM. Small RNA expression analysis on loci showing RDM16-dependent DNA methylation suggested that unlike the previously reported putative splicing factor mutants, rdm16 did not affect small RNA levels; instead, the rdm16 mutation caused a decrease in the levels of Pol V transcripts. ChIP assays revealed that RDM16 was enriched at some Pol V target loci. Our results suggest that RDM16 regulates DNA methylation through influencing Pol V transcript levels. Finally, our genome-wide DNA methylation analysis indicated that RDM16 regulates the overall methylation of TEs and gene-surrounding regions, and preferentially targets Pol IV-dependent DNA methylation loci and the ROS1 target loci. Our work thus contributes to the understanding of RdDM and its interactions with active DNA demethylation.<br />Competing Interests: The authors have declared that no competing interests exist.
- Subjects :
- Arabidopsis Proteins genetics
Arabidopsis Proteins metabolism
Histone Demethylases genetics
Mutation
Nuclear Proteins metabolism
RNA Precursors genetics
RNA Splicing Factors
Ribonucleoprotein, U4-U6 Small Nuclear metabolism
Alternative Splicing genetics
Arabidopsis genetics
Arabidopsis Proteins isolation & purification
DNA Methylation genetics
Nuclear Proteins genetics
RNA, Messenger genetics
Subjects
Details
- Language :
- English
- ISSN :
- 1553-7404
- Volume :
- 9
- Issue :
- 9
- Database :
- MEDLINE
- Journal :
- PLoS genetics
- Publication Type :
- Academic Journal
- Accession number :
- 24068953
- Full Text :
- https://doi.org/10.1371/journal.pgen.1003779