required to maintain repression2 Is a Novel Protein That Facilitates Locus-Specific Paramutation in Maize

Abstract

Meiotically heritable epigenetic changes in gene regulation known as paramutations are facilitated by poorly understood trans-homolog interactions. Mutations affecting paramutations in maize (Zea mays) identify components required for the accumulation of 24-nucleotide RNAs. Some of these components have Arabidopsis thaliana orthologs that are part of an RNA-directed DNA methylation (RdDM) pathway. It remains unclear if small RNAs actually mediate paramutations and whether the maize-specific molecules identified to date define a mechanism distinct from RdDM. Here, we identify a novel protein required for paramutation at the maize purple plant1 locus. This required to maintain repression2 (RMR2) protein represents the founding member of a plant-specific clade of predicted proteins. We show that RMR2 is required for transcriptional repression at the Pl1-Rhoades haplotype, for accumulation of 24-nucleotide RNA species, and for maintenance of a 5-methylcytosine pattern distinct from that maintained by RNA polymerase IV. Genetic tests indicate that RMR2 is not required for paramutation occurring at the red1 locus. These results distinguish the paramutation-type mechanisms operating at specific haplotypes. The RMR2 clade of proteins provides a new entry point for understanding the diversity of epigenomic control operating in higher plants.

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

“…The association of plant paramutation with DNA-methylation has been established in multiple plant paramutation systems [12,[15][16][17][18][19][20][21]. Bearing in mind these results we carried out a comparative analysis of the genome-wide 5-cytosine methylation and a random identification of specific differentially methylated sequences in cv.…”

“…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).…”

“…In maize, the hypermethylation of specific loci sequences correlates with different epigenetic states at the p1 and r1 loci [17][18][19], while the restoration of the wild dark color is associated with the hypomethylation of CHG sites at the 3' regions of the pl1 locus [12]. Also in maize, the paramutagenic B' epiallele of the locus b1 is hypermethylated at the junction sequences between the required for paramutation heptarepeats located 100 kb upstream of the locus [20], and in the paramutation induced by the presence of transgenic b1 repeats, the increasing DNA methylation at the endogenous b1 repeats correlates with stronger silencing of b1 locus [21].…”

Genetic Perturbation of the Maize Methylome

“…Genetic screens have successfully identified mutants that are defective in the establishment and/ or maintenance of paramutation (Dorweiler et al, 2000;Hollick and Chandler, 2001). The molecular characterization of these mutants has revealed that most affect components of the RdDM pathway (Alleman et al, 2006;Erhard et al, 2009;Sidorenko et al, 2009;Sloan et al, 2014), while others are novel proteins (Barbour et al, 2012). In some cases, these mutants have been shown to have locus-specific effects on DNA methylation (Lisch et al, 2002;McGinnis et al, 2006;Sloan et al, 2014), but the genome-wide effect of these mutations on DNA methylation has not been characterized.…”

Nascent Transcription Affected by RNA Polymerase IV inZea mays

“…The developmental defects observed in rpd1 mutants are both distinct and nonheritable (Parkinson et al 2007) and therefore unlikely to be related to TE-derived mutations. These defects also appear unrelated to siRNA-induced silencing because other maize mutants affecting siRNA biogenesis, including rpd/e2a, are developmentally normal (Hale et al 2007;Stonaker et al 2009;Barbour et al 2012). We hypothesize that maize has co-opted RPD1/Pol IV to transcriptionally control specific alleles of genes for which TEs and TE-like repeats act as regulatory elements.…”