RNA Pol IV and V in gene silencing: Rebel polymerases evolving away from Pol II's rules

Abstract

Noncoding RNAs regulate gene expression at both the transcriptional and post-transcriptional levels, and play critical roles in development, imprinting and the maintenance of genome integrity in eukaryotic organisms [1–3]. Therefore, it is important to understand how the production of such RNAs are controlled. In addition to the three canonical DNA dependent RNA polymerases (Pol) Pol I, II and III, two non-redundant plant-specific RNA polymerases, Pol IV and Pol V, have been identified and shown to generate noncoding RNAs that are required for transcriptional gene silencing via the RNA-directed DNA methylation (RdDM) pathway. Thus, somewhat paradoxically, transcription is required for gene silencing. This paradox extends beyond plants, as silencing pathways in yeast, fungi, flies, worms, and mammals also require transcriptional machinery [4,5]. As plants have evolved specialized RNA polymerases to carry out gene silencing in a manner that is separate from the essential roles of Pol II, their characterization offers unique insight into how RNA polymerases facilitate gene silencing. In this review, we focus on the mechanisms of Pol IV and Pol V function, including their compositions, their transcripts, and their modes of recruitment to chromatin.

Transcriptional Gene Silencing Maintained by OTS1 SUMO Protease Requires a DNA-Dependent Polymerase V-Dependent Pathway

“…Pol V requires DDR complex (DRD1, DMS3, and RDM1) for function in producing noncoding scaffold RNAs and guiding sequence-specific DNA methylation (Kanno et al, 2004(Kanno et al, , 2005(Kanno et al, , 2008Herr et al, 2005;Onodera et al, 2005;Pontier et al, 2005;Gao et al, 2010;Law et al, 2010;Zhong et al, 2012;Zhou and Law, 2015). To test whether the DDR complex is required for the OTS1-mediated regulation of aberrant gene expression, we introduced drd1-6 or dms3-1 into ots1-3 background and obtained the corresponding double mutants ots1-3 drd1-6 and ots1-3 dms3-1.…”

“…The RdDM pathway is a conserved mechanism for mediating TGS of many endogenous transposons and repeat elements. Pol IV collaborating with RDR2 and DCL3 is responsible for 24-nucleotide small-interfering RNA (siRNA) biogenesis, whereas with the help of chromatin-remodeling DDR complex (DRD1, DMS3, and RDM1), Pol V functions to generate scaffold RNAs for guiding sequence-specific DNA methylation by siRNAs (Onodera et al, 2005;Pontier et al, 2005;Wierzbicki et al, 2008;Zhou and Law, 2015). Loss of Pol V or DRD1 disrupts heterochromatin organization during interphase; on the contrary, loss of Pol IV, RDR2, or DCL3 does not (Pontes et al, 2009).…”

Functional Dissection of the Pol V Largest Subunit CTD in RNA-Directed DNA Methylation

“…NUCLEAR RNA POLYMERASE V (Pol V) is a plant-specific multisubunit RNA polymerase important for siRNA-directed DNA methylation (RdDM) and transcriptional gene silencing, primarily of transposable elements (reviewed in: Haag and Pikaard, 2011; Ream et al, 2013; Zhou and Law, 2015). In the major RdDM pathway (reviewed in: Matzke and Mosher, 2014; Wendte and Pikaard, 2017), NUCLEAR RNA POLYMERASE IV (Pol IV) and RNA-DEPENDENT RNA POLYMERASE 2 (RDR2) generate short double-stranded RNAs that are then diced into 24 nt short interfering RNAs (siRNAs) (Blevins et al, 2015; Li et al, 2015; Zhai et al, 2015).…”

The MBD7 complex promotes expression of methylated transgenes without significantly altering their methylation status

“…Production of both 24-nt siRNAs and non-coding RNAs requires specialized RNA polymerases (Haag and Pikaard, 2011; Zhou et al, 2015). Pol IV transcripts were recently identified (Blevins et al, 2015; Zhai et al, 2015; Li et al, 2015a) and these short non-coding RNAs are processed into 24-nt siRNAs in a one precursor, one siRNA fashion (Blevins et al, 2015; Zhai et al, 2015) and then loaded into the ARGONAUTE 4 (AGO4) clade of effector proteins.…”