TY - JOUR T1 - Base-pairing requirements for small RNA-mediated gene silencing of recessive self-incompatibility alleles in <em>Arabidopsis halleri</em> JF - bioRxiv DO - 10.1101/370239 SP - 370239 AU - N. Burghgraeve AU - S. Simon AU - S. Barral AU - I. Fobis-Loisy AU - A-C Holl AU - C. Poniztki AU - E. Schmitt AU - X. Vekemans AU - V. Castric Y1 - 2018/01/01 UR - http://biorxiv.org/content/early/2018/07/19/370239.abstract N2 - 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.Author summary Small non-coding RNAs are important regulatory molecules that achieve their function through sequence similarity with their target sites. In many cases however, the precise base-pairing requirements for effective regulation are poorly known. At the self-incompatibility (SI) locus in Arabidopsis, dominance between alleles is pervasive and is controlled in pollen by small non-coding RNAs produced by dominant alleles that target specific sequence motifs on recessive alleles. Here we use a large number of heterozygote combinations of SI alleles to show that dominance is tightly associated with strong transcriptional silencing of the recessive alleles in presence of a more dominant allele. We take advantage of this highly diversified system of multiple sRNAs and their diversified target sites to determine the base-pairing requirements for successful small-RNA mediated transcriptional silencing. The threshold model that we identify has important functional and evolutionary implications for this complex regulatory mechanism. ER -