Most metazoan microRNAs (miRNAs) target many genes for repression, but the nematode lsy-6 miRNA is much less proficient. Here, we show that the low proficiency of lsy-6 can be recapitulated in HeLa cells and that miR-23 (a mammalian miRNA) also has low proficiency in these cells. Reporter results and array data both indicate two properties of these miRNAs that impart low proficiency: their weak predicted seed-pairing stability (SPS) and their high target-site abundance (TA). These two properties also explain differential propensities of small interfering RNAs (siRNAs) to repress unintended targets. Using these insights, we expand the TargetScan tool for quantitatively predicting miRNA regulation (and siRNA off-targeting) so as to model differential miRNA (siRNA) proficiencies, thereby improving prediction performance. Moreover, we propose that siRNAs designed to have both weaker SPS and higher TA will have fewer off-targets without compromised on-target activity.

Summary Prions are a paradigm-shifting mechanism of inheritance in which phenotypes are encoded by self-templating protein conformations rather than nucleic acids. Here we examine the breadth of protein-based inheritance across the yeast proteome by assessing the ability of nearly every open reading frame (∼5,300 ORFs) to induce heritable traits. Transient overexpression of nearly 50 proteins created traits that remained heritable long after their expression returned to normal. These traits were beneficial, had prion-like patterns of inheritance, were common in wild yeasts, and could be transmitted to naïve cells with protein alone. Most inducing proteins were not known prions and did not form amyloid. Instead, they are highly enriched in nucleic acid binding proteins with large intrinsically disordered domains that have been widely conserved across evolution. Our data thus establish a common type of protein-based inheritance through which intrinsically disordered proteins can drive the emergence of new traits and adaptive opportunities.

Highlights d The Vts1 IDR promotes its condensation into the non-amyloid prion [SMAUG + ] d [SMAUG + ] hyperactivates Vts1 function d [SMAUG + ] rewires post-transcriptional gene regulation to promote proliferation d Self-assembly is conserved in the human Vts1 homolog hSmaug1