Ovule siRNAs methylate and silence protein-coding genes in trans

Abstract

Abstract24-nt small interfering siRNAs maintain asymmetric DNA methylation at thousands of euchromatic transposable elements in plant genomes in a process call RNA-directed DNA Methylation (RdDM). Although this methylation occasionally causes transcriptional silencing of nearby protein-coding genes, direct targeting of methylation at coding sequences is rare. RdDM is dispensable for growth and development in Arabidopsis, but is required for reproduction in other plant species, such as Brassica rapa. 24-nt siRNAs are particularly abundant in reproductive tissue, due largely to overwhelming expression from a small number of loci in the ovule and developing seed coat, termed siren loci. Here we show that siRNAs are often produced from gene fragments embedded in siren loci, and that these siRNAs can trigger methylation in trans at related protein-coding genes. This trans-methylation is associated with transcriptional silencing of target genes and may be responsible for seed abortion in RdDM mutants. Furthermore, we demonstrate that a consensus sequence in at least two families of DNA transposons is associated with abundant siren expression, most likely through recruitment of the CLSY3 putative chromatin remodeller. This research describes a new mechanism whereby RdDM influences gene expression and sheds light on the role of RdDM during plant reproduction.