Large-scale profiling of noncoding RNA function in yeast.

Noncoding RNAs (ncRNAs) are emerging as key regulators of cellular function. We have exploited the recently developed barcoded ncRNA gene deletion strain collections in the yeast Saccharomyces cerevisiae to investigate the numerous ncRNAs in yeast with no known function. The ncRNA deletion collection contains deletions of tRNAs, snoRNAs, snRNAs, stable unannotated transcripts (SUTs), cryptic unstable transcripts (CUTs) and other annotated ncRNAs encompassing 532 different individual ncRNA deletions. We have profiled the fitness of the diploid heterozygous ncRNA deletion strain collection in six conditions using batch and continuous liquid culture, as well as the haploid ncRNA deletion strain collections arrayed individually onto solid rich media. These analyses revealed many novel environmental-specific haplo-insufficient and haplo-proficient phenotypes providing key information on the importance of each specific ncRNA in every condition. Co-fitness analysis using fitness data from the heterozygous ncRNA deletion strain collection identified two ncRNA groups required for growth during heat stress and nutrient deprivation. The extensive fitness data for each ncRNA deletion strain has been compiled into an easy to navigate database called Yeast ncRNA Analysis (YNCA). By expanding the original ncRNA deletion strain collection we identified four novel essential ncRNAs; SUT527, SUT075, SUT367 and SUT259/691. We defined the effects of each new essential ncRNA on adjacent gene expression in the heterozygote background identifying both repression and induction of nearby genes. Additionally, we discovered a function for SUT527 in the expression, 3' end formation and localization of SEC4, an essential protein coding mRNA. Finally, using plasmid complementation we rescued the SUT075 lethal phenotype revealing that this ncRNA acts in trans. Overall, our findings provide important new insights into the function of ncRNAs.

The evolution of sexual imprinting in socially monogamous populations.

Sexual imprinting is a common mechanism of mate preference learning. It is thought to influence how traits evolve and in some cases to promote speciation. Recently there has been increasing interest in how sexual imprinting itself evolves. Theoretical work on polygynous mating systems predicts that females will evolve paternal imprinting, which means they learn to prefer phenotypes expressed by their fathers. In nature however, females of some species learn to prefer phenotypes expressed by their mothers instead. We used a dynamical systems model and tools from adaptive dynamics to study how sexual imprinting evolves in species with socially monogamous mating systems. We considered cases in which the target trait for imprinting is under viability selection but is not a reliable signal of paternal investment. Thus, the target trait signals the genetic benefits rather than the parental care benefits of mate choice. When mating is socially monogamous and there is some extra-pair paternity, we show that maternal imprinting can be favored over paternal imprinting. Counterintuitively, females often become choosier when selecting social partners in systems where extra-pair mating is more frequent. That is, females may be more selective when choosing social partners that will sire a smaller percentage of their offspring. Our results offer new testable hypotheses, and advance our understanding of the mechanisms that drive the evolution of mate choice strategies in nature.