A dicer-like3 protein affects paramutation at multiple loci in Zea mays

Paramutation is a process by which meiotically-heritable gene regulation is altered by trans-homolog interactions. In Zea mays, genetic screens for functions maintaining paramutation-induced repressed states have identified loci encoding small RNA biogenesis components, thus implicating small RNAs in mediating these trans-homolog communications. Here we report that the required to maintain repression5 locus encodes the sole dicer-like3 protein responsible for non-anther-specific 24-nucleotide RNA production. We found dicer-like3 is essential for mediating paramutation at the booster1 locus and for the meiotic maintenance of transcriptionally repressed states at the purple plant1 locus. Despite an expected role in mediating RNA-directed DNA methylation, we found 5-methylcytosine levels largely unchanged at multiple repetitive sequences in dicer-like3 mutants, with minimal compensation from other small RNA sizes. The minor effects on plant heights and flowering time seen in the absence of dicer-like3 contrasts with other paramutation mutants and we highlight one specific allele repressed by RNA polymerase IV yet unaffected by dicer-like3 loss. These findings highlight diverse regulatory functions for individual components of 24-nucleotide biogenesis occurring in the grasses and support a working model in which this small RNA size class mediates trans-homolog interactions that drive meiotically-heritable changes in gene regulation.