Maize RNA Polymerase IV Definestrans-Generational Epigenetic Variation

Abstract

The maize (Zea mays) RNA Polymerase IV (Pol IV) largest subunit, RNA Polymerase D1 (RPD1 or NRPD1), is required for facilitating paramutations, restricting expression patterns of genes required for normal development, and generating small interfering RNA (siRNAs). Despite this expanded role for maize Pol IV relative to Arabidopsis thaliana, neither the general characteristics of Pol IV–regulated haplotypes, nor their prevalence, are known. Here, we show that specific haplotypes of the purple plant1 locus, encoding an anthocyanin pigment regulator, acquire and retain an expanded expression domain following transmission from siRNA biogenesis mutants. This conditioned expression pattern is progressively enhanced over generations in Pol IV mutants and then remains heritable after restoration of Pol IV function. This unusual genetic behavior is associated with promoter-proximal transposon fragments but is independent of sequences required for paramutation. These results indicate that trans-generational Pol IV action defines the expression patterns of haplotypes using co-opted transposon-derived sequences as regulatory elements. Our results provide a molecular framework for the concept that induced changes to the heterochromatic component of the genome are coincident with heritable changes in gene regulation. Alterations of this Pol IV–based regulatory system can generate potentially desirable and adaptive traits for selection to act upon.

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

“…We propose that loss of RMR6-dependent siRNAs targeting this intron allowed de-repression of both the intron-located TE and the associated gene. This observation supports the hypothesis that TE-like sequences and repeats targeted by siRNAs can function as controlling elements influencing the expression of close or overlapping genes (Liu et al, 2004;Kinoshita et al, 2007;Erhard et al, 2013). We examined the effects of our long-term stress treatments on leaf-expressed non-MIRNA sRNA loci in wild-type plants.…”

“…The enrichment of RdDM-associated siRNAs near maize genes (Wang et al, 2009;Gent et al, 2013;Gent et al, 2014;Xin et al, 2014) has been suggested to ensure the continuous silencing of potentially deleterious TEs and TE-like sequences in an active and accessible chromatin environment required for the Pol II transcription of close genes (Gent et al, 2014). In maize, gene expression can be influenced by gene-proximal TEs and repeats (Erhard et al, 2013), and both genes and TEs can be regulated by the direct competition between Pol IV and Pol II occupancy at their promoters Erhard et al, 2015). At the genome-wide level, the expression of maize genes positively correlates with the accumulation levels of upstream 24-nt siRNAs (Gent et al, 2013).…”

Nascent Transcription Affected by RNA Polymerase IV inZea mays

“…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. Supporting this concept, specific purple plant1 (pl1) alleles having an upstream doppia TE fragment are regulated by RPD1 (Erhard et al 2013). As the maize genome is composed of .85% TE-like sequences (Schnable et al 2009), many of which occur within 5 kb of genes (Baucom et al 2009;Gent et al 2013), a large number of alleles using TE-like sequences as regulatory elements is possible.…”

“…Ten homozygous wild-type (WT; Rpd1-B73/Rpd1-B73) and 10 homozygous rpd1-1 mutant (rpd1 mutant) siblings were identified with a dCAPs marker for the rpd1-1 lesion (Erhard et al 2013) and used for nuclei isolations. Nuclei were isolated from whole shoots (roots removed) of 8-day-old seedlings.…”

“…Because Pol IV is required for siRNA-directed cytosine methylation (reviewed by Mosher 2014 andMatzke et al 2015), it is expected that the regulation of many alleles might be affected by RPD1/NRPD1 action although few such alleles have been identified in maize (Hollick et al 2005;Parkinson et al 2007;Erhard et al 2013) and Arabidopsis (Matzke et al 2007;Ariel et al 2014). To date there have been no reports of genome-wide effects of RPD1/NRPD1 on gene regulation in any species although several studies have noted correlations between siRNA profiles and nearby genic mRNA abundance (Hollister et al 2011;Eichten et al 2012;Greaves et al 2012).…”