Plants have distinct RNA polymerase complexes (Pol IV and Pol V) with largely unknown roles in maintaining small RNA-associated gene silencing. Curiously, the eudicot Arabidopsis thaliana is not affected when either function is lost. By use of mutation selection and positional cloning, we showed that the largest subunit of the presumed maize Pol IV is involved in paramutation, an inherited epigenetic change facilitated by an interaction between two alleles, as well as normal maize development. Bioinformatics analyses and nuclear run-on transcription assays indicate that Pol IV does not engage in the efficient RNA synthesis typical of the three major eukaryotic DNA-dependent RNA polymerases. These results indicate that Pol IV employs abnormal RNA polymerase activities to achieve genome-wide silencing and that its absence affects both maize development and heritable epigenetic changes.

Mutations affecting the heritable maintenance of epigenetic states in maize identify multiple small RNA biogenesis factors including NRPD1, the largest subunit of the presumed maize Pol IV holoenzyme. Here we show that mutations defining the required to maintain repression7 locus identify a second RNA polymerase subunit related to Arabidopsis NRPD2a, the sole second largest subunit shared between Arabidopsis Pol IV and Pol V. A phylogenetic analysis shows that, in contrast to representative eudicots, grasses have retained duplicate loci capable of producing functional NRPD2-like proteins, which is indicative of increased RNA polymerase diversity in grasses relative to eudicots. Together with comparisons of rmr7 mutant plant phenotypes and their effects on the maintenance of epigenetic states with parallel analyses of NRPD1 defects, our results imply that maize utilizes multiple functional NRPD2-like proteins. Despite the observation that RMR7/NRPD2, like NRPD1, is required for the accumulation of most siRNAs, our data indicate that different Pol IV isoforms play distinct roles in the maintenance of meiotically-heritable epigenetic information in the grasses.

ABSTRACT

No abstract

All eukaryotes use three DNA-dependent RNA polymerases (RNAPs) to create cellular RNAs from DNA templates. Plants have additional RNAPs related to Pol II, but their evolutionary role(s) remain largely unknown. Zea mays (maize) RNA polymerase D1 (RPD1), the largest subunit of RNA polymerase IV (Pol IV), is required for normal plant development, paramutation, transcriptional repression of certain transposable elements (TEs), and transcriptional regulation of specific alleles. Here, we define the nascent transcriptomes of rpd1 mutant and wild-type (WT) seedlings using global run-on sequencing (GRO-seq) to identify the broader targets of RPD1-based regulation. Comparisons of WT and rpd1 mutant GRO-seq profiles indicate that Pol IV globally affects transcription at both transcriptional start sites and immediately downstream of polyadenylation addition sites. We found no evidence of divergent transcription from gene promoters as seen in mammalian GRO-seq profiles. Statistical comparisons identify genes and TEs whose transcription is affected by RPD1. Most examples of significant increases in genic antisense transcription appear to be initiated by 3ʹ-proximal long terminal repeat retrotransposons. These results indicate that maize Pol IV specifies Pol II-based transcriptional regulation for specific regions of the maize genome including genes having developmental significance.KEYWORDS RNA polymerase IV; transcription; gene regulation; transposons; paramutation E UKARYOTES use at least three DNA-dependent RNA polymerases (RNAPs) to transcribe their genomes into functional RNAs. RNAP Pol II generates messenger RNAs (mRNAs) and noncoding RNAs involved in various RNA-mediated regulatory pathways (reviewed by Sabin et al. 2013). Flowering plant genomes encode additional RNAP subunits comprising Pol IV and Pol V, which are central to a small interfering RNA (siRNA)-based silencing pathway primarily targeting repetitive sequences such as transposable elements (TEs) (Matzke and Mosher 2014;Matzke et al. 2015). These additional RNAPs derive from duplications of specific Pol II subunits followed by subfunctionalization during plant evolution (Tucker et al. 2011), yet the holoenzyme complexes still share some Pol II subunits (Ream et al. 2009;Haag et al. 2014).Zea mays (maize) has distinct largest subunits for Pol IV and V and, unlike Arabidopsis thaliana, three second-largest subunits Sidorenko et al. 2009;Stonaker et al. 2009) that in distinct combinations form two Pol IV and three Pol V isoforms (Haag et al. 2014). Genetic analyses of rna polymerase d/e 2a (rpd/e2a) encoding one of the secondlargest subunits (Sidorenko et al. 2009;Stonaker et al. 2009) together with recent proteomic data showing association of a putative RNA-dependent RNA polymerase (RDR2) with only RPD/E2a-containing isoforms (Haag et al. 2014) indicate that maize Pol IV isoforms have diverse functional roles in managing genome homeostasis.Loss of Pol IV function has different consequences in Arabidopsis, Brassica rapa (a close relative of Arabidops...