DOMAINS REARRANGED METHYLTRANSFERASE3 controls DNA methylation and regulates RNA polymerase V transcript abundance in Arabidopsis

Abstract

DNA methylation is a mechanism of epigenetic gene regulation and genome defense conserved in many eukaryotic organisms. In Arabidopsis, the DNA methyltransferase DOMAINS REARRANGED METHYLASE 2 (DRM2) controls RNA-directed DNA methylation in a pathway that also involves the plant-specific RNA Polymerase V (Pol V). Additionally, the Arabidopsis genome encodes an evolutionarily conserved but catalytically inactive DNA methyltransferase, DRM3. Here, we show that DRM3 has moderate effects on global DNA methylation and small RNA abundance and that DRM3 physically interacts with Pol V. In Arabidopsis drm3 mutants, we observe a lower level of Pol V-dependent noncoding RNA transcripts even though Pol V chromatin occupancy is increased at many sites in the genome. These findings suggest that DRM3 acts to promote Pol V transcriptional elongation or assist in the stabilization of Pol V transcripts. This work sheds further light on the mechanism by which long noncoding RNAs facilitate RNA-directed DNA methylation.DNA methylation | epigenetic regulation | RNA polymerase | non-coding RNA | gene silencing I n eukaryotes, DNA methylation plays significant roles in gene silencing and controls many important biological processes, including genome imprinting (1), X chromosome inactivation (2), genome stability, and the silencing of transposons, retroviruses, and other harmful DNA elements (3-5). In Arabidopsis, DNA methylation occurs in CG, CHG, and CHH (where H = A, T, or C) sequence contexts and is controlled by at least four DNA methyltransferases: METHYLTRANSFERASE 1 (MET1), CHROMOMETHYLASE2 (CMT2), CHROMOMETHYLASE3 (CMT3), and DOMAINS REARRANGED METHYLASE 2 (DRM2). MET1 and DRM2 are the plant homologs of mammalian methyltransferases Dnmt1 and Dnmt3, respectively, whereas CMT2 and CMT3 are plant-specific methyltransferases. MET1, like Dnmt1, is important for maintenance of CG methylation during DNA replication (6-8), and DRM2, CMT3, and CMT2 control the maintenance of non-CG methylation (9-13). The establishment of DNA methylation is controlled by DRM2 (9) via a process termed RNA-directed DNA methylation (RdDM) (14-16).In the current RdDM model, the DNA-DEPENDENT RNA POLYMERASE IV (Pol IV), RNA-DEPENDENT RNA POLYMERASE 2, and DICER-LIKE 3 function together to produce small interfering RNAs (siRNAs) that are bound by ARGONAUTE4 (AGO4). The AGO4/siRNA complex is thought to base pair with noncoding RNA transcripts produced by a DNA-DEPENDENT RNA POLYMERASE V (Pol V). Production of Pol V transcripts, as well as genome-wide Pol V chromatin occupancy, requires a complex termed DDR consisting of the putative chromatin-remodeling factor DEFECTIVE IN RNA-DIRECTED DNA METHYLATION 1 (DRD1), structural maintenance of chromosome domain protein DEFECTIVE IN MERISTEM SILENCING 3 (DMS3), and RNA-DIRECTED DNA METHYLATION 1 (17-20). The SUPPRESSOR OF VARIEGATION 3-9 HOMOLOG 2 (SUVH2) and -9 (SUVH9) proteins are required for genome-wide Pol V chromatin association by binding to DNA methylation (21,22). The cooccurrence of Pol IV-dependent siRNAs...

RNA‐based regulation of transposon expression

“…The binding of the AGO–siRNA complex to nascent Pol V transcripts leads to the recruitment of the plant Dnmt3 methyltransferase ortholog DRM2 to establish de novo DNA methylation at target loci, resulting in transcriptional silencing . Another ortholog, DRM3, presumably promotes Pol V transcriptional elongation or assists in the stabilization of Pol V transcripts …”

TEA: the epigenome platform for Arabidopsis methylome study

“…To help users become familiar with TEA, we provide a demo dataset from Zhong et al (2015) entitled “DOMAINS REARRANGED METHYLTRANSFERASE3 controls DNA methylation and regulates RNA polymerase V transcript abundance in Arabidopsis” [41]. Briefly, this study focused on elucidating the function of DRM3 (domain rearranged methyltransferase 3) in the RdDM pathway, which contains a catalytically inactive enzyme domain, but is required for de novo DNA methylation in vivo.…”

“…The demo datasets are from Zhong et al [41], which includes five previously published WGBS datasets, GSM881756, GSM1193638, GSM981015, GSM981017, and GSM981040 [31, 42]. All of these bisulfite sequencing reactions were carried out in 50-mer single-end format using an Illumina HiSeq2000.…”

Importance of DNA and histone methylation in in vitro plant propagation for crop improvement: a review

“…Epigenetic changes in chromosomal proteins and DNA (Simmons, 2008;Niederhuth & Schmitz, 2014;Stelpflug et al, 2014), and non-coding RNA-mediated pathways (Grant-Downton & Dickinson, 2005;Zhong et al, 2015) in plants can result in phenotypic variations, which may be either useful or detrimental. Epigenetic states in plants, once established, can be inherited through the transmission of epigenetic alleles (epialleles) over generations (Kakutani, 2002).…”