A dicer-like3 protein affects paramutation at multiple loci inZea mays

Abstract

ABSTRACTParamutation is a process by which meiotically-heritable gene regulation is altered bytrans-homolog interactions. InZea mays, genetic screens for functions maintaining paramutation-induced repressed states have identified loci encoding small RNA biogenesis components, thus implicating small RNAs in mediating thesetrans-homolog communications. Here we report that therequired to maintain repression5locus 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 thebooster1locus and for the meiotic maintenance of transcriptionally repressed states at thepurple plant1locus. Despite an expected role in mediating RNA-directed DNA methylation, we found 5-methylcytosine levels largely unchanged at multiple repetitive sequences indicer-like3mutants, 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 mediatestrans-homolog interactions that drive meiotically-heritable changes in gene regulation.