Base-pairing requirements for small RNA mediated gene silencing of recessive self incompatibility alleles in Arabidopsis halleri.

Small RNAs (sRNA) are central regulators of gene expression, yet identifying the molecular alphabet of sRNA-target interactions remains challenging. Here, we take advantage of the dominance hierarchy among self-incompatibility alleles in Arabidopsis halleri to evaluate the base-pairing requirements for effective transcriptional silencing by a highly diversified set of sRNA-target interactions. We used RT-qPCR to follow temporal expression of the pollen (SCR) and pistil (SRK) determinants of self-incompatibility in numerous heterozygous combinations. SCR and SRK had sharply distinct expression dynamics through flower development. Recessive SCR alleles were transcriptionally silenced in all heterozygote combinations examined, bringing levels of SCR transcripts below detection limits regardless of the position of the sRNA target along the SCR sequence. A simple threshold model of base-pairing for the sRNA-target interaction captures most of the variation in SCR transcript levels. In contrast, both SRK alleles were expressed at similar levels in all heterozygote genotypes. We show that the base-pairing requirements for effective transcriptional silencing by these sRNAs are broadly similar to those of canonical microRNAs, even though they are believed to function in sharply different ways. We discuss the implications for the evolutionary processes associated with the origin and maintenance of the dominance hierarchy among self-incompatibility alleles.