RNA Polymerase IV Functions in Paramutation in Zea mays

Abstract

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.

Genome-Wide Characterization of Maize Small RNA Loci and Their Regulation in the required to maintain repression6-1 (rmr6-1) Mutant and Long-Term Abiotic Stresses

“…Plants from inbred B73 (Zea mays) and rmr6-1 (loss-of-function allele introgressed in B73; Erhard et al, 2009) stocks were grown in pots in a greenhouse with temperatures between 28°C and 30°C during the day and 20°C to 22°C at night and relative humidity between 60% and 80%. Plants were watered to pot capacity until V5/V6 stage (plants with 5/6 visible leaf collars), when stress treatments were applied as described in detail in Morari et al, 2015, with some changes compared to the original protocol.…”

RNA-mediated trans -communication can establish paramutation at the b1 locus in maize

“…The mediator of paramutation (mop) genes (1,(4)(5)(6) and the required to maintain repression (rmr) genes (6,(8)(9)(10) have been isolated using the b1 and pl1 systems, respectively. To date, all characterized genes required for paramutation identified through forward genetic screens encode proteins that have been associated with siRNA biogenesis in other species (1).…”

siRNA-mediated DNA methylation and H3K9 dimethylation in plants

“…siRNAs are usually 24 nt in length and tend to be produced from repeats and transposable elements, although many are also found in intergenic regions. siRNA production, which requires a potential chromatin remodeling protein, CLASSY1 (Herr et al, 2005;Onodera et al, 2005), is initiated by a plant-specific DNA-dependent RNA polymerase: Pol IV, generating single stranded RNAs from a transposon or repeats-containing region (Herr et al, 2005;Onodera et al, 2005;Erhard et al, 2009;Sidorenko et al, 2009;Havecker et al, 2010). It has been recently discovered that the recruitment of Pol IV to target loci requires the assistance of certain proteins, such as SHH1 (Law et al, 2013) and DTF1 (Zhang et al, 2013).…”