Diversity of Pol IV Function Is Defined by Mutations at the Maize rmr7 Locus

Abstract

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.

Diverse Gene-Silencing Mechanisms with Distinct Requirements for RNA Polymerase Subunits in Zea mays

“…This model accounts for the loss of silencing of b1 in plants deficient for MOP1, MOP2, and MOP3 activities and is consistent with the predicted function of all three predicted proteins (Alleman et al 2006;Sidorenko et al 2009;Stonaker et al 2009). However, prior findings indicate that the b1 enhancer repeats are predominantly transcribed by Pol II (Sidorenko et al 2009;, and although siRNA levels homologous with the b1 enhancer repeats are reduced in mop1-1 homozygous plants, in wild-type plants these siRNA levels are similar in transcriptionally silenced B9, transcriptionally active B-I, and neutral b1 alleles .…”

“…Molecular cloning of these trans-acting factors, including the products of the mediator of paramutation (mop) and required for maintenance of repression (rmr) genes, indicates that paramutation requires the activity of proteins homologous with Arabidopsis thaliana proteins involved in small RNA-induced DNA methylation and heterochromatin formation (referred to as RNA-directed DNA methylation, or RdDM) (Alleman et al 2006;Hale et al 2007;Erhard et al 2009;Sidorenko et al 2009;Stonaker et al 2009). …”

Epigenetic Regulation of Abiotic Stress Tolerance in Plants

“…33 Recent studies demonstrated that MOP1, ZmRPD1, and RMR7 (orthologs of ArabidopsisRDR2, NRPD1, and NRPD2, respectively) are required for paramutation in maize, and suggested that RdDM pathway is needed for the establishment and maintenance of silencing in paramutation. 34,35 A spontaneous mutant Epi-d1 in rice showed a metastable dwarf phenotype which is mitotically and meiotically heritable and corresponds to the metastable epigenetic silencing of the DWARF1 (D1) gene. 36 The silenced state is correlated with DNA hypermethylation in the D1 promoter region.…”

The Pea (Pisum sativum L.) Rogue Paramutation is Accompanied by Alterations in the Methylation Pattern of Specific Genomic Sequences

“…Among the above mentioned maize loci, the most significant progresses have been achieved in the study of b1 and pl1 and the identified genes required for paramutation at these two loci: mediator of paramutation (mop1 [9] and mop2 [10]) and required to maintain repression (rmr1 [11], rmr2 [12], rmr6 [13], and rmr7 [14]) were found to encode proteins involved in small interfering RNA (siRNA) biogenesis and RNA directed DNA methylation (RdDM).…”