Abundant Phased, Secondary siRNAs in Plant Reproductive Organs

The major classes of plant small RNAs include microRNAs (miRNAs) and small interfering RNAs (siRNAs); one specific type of the latter are secondary siRNAs, a group well known for including trans-acting siRNAs (tasiRNAs). My lab has developed and applied a suite of computational tools and laboratory methods for the analysis of small RNAs and cleaved mRNA targets of small RNAs. By applied these tools to a range of plant species, dissected tissues, and mutants, we have characterized new miRNAs and their targets, and identified diverse populations of phased, secondary siRNAs (phasiRNAs) as well as their miRNA triggers. Our recent work focuses on secondary siRNAs in anthers, particularly grasses in which hundreds or even thousands of long, noncoding RNAs (lncRNAs) are expressed and processed into phasiRNAs. In grass anthers, these lncRNA-derived phased siRNAs are highly enriched, produced by loci dispersed in the genome, and synthesized either pre-meiotically (and are 21 nt) or coordinate with germinal cell maturation for meiosis (and are 24 nt). In addition to their function, our experiments are designed to understand the evolutionary origin and divergence of these phased siRNAs, their lncRNA precursors, and their miRNA “triggers”.