12 research outputs found
Second Annual Workshop of the Association of Early-Career Social Learning Researchers in St Andrews, Scotland
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
Identifying cues for self-organised nest wall building behaviour in the rock ant, Temnothorax rugatulus (dataset)
Identifying cues for self-organized nest wall-building behaviour in the rock ant, Temnothorax rugatulus, using hidden Markov models (dataset & code)
Haploid deletion strain phenotypic screen.
<p>Scatter plot of the normalized colony size values for each of the haploid ncRNA deletion strains growing on YPD plates at 30°C. Any strains falling outside the grey shaded area are significantly different than the wild-type strain (p < 0.05). Data can be seen in <b><a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1007253#pgen.1007253.s014" target="_blank">S14</a> and <a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1007253#pgen.1007253.s015" target="_blank">S15</a> Tables</b>.</p
Spot assays for strains containing <i>EMP46</i>, <i>GAL2</i>, <i>EMP46/GAL2</i> or empty pBEVY-GA overexpression plasmids.
<p>The comparative fitness of the identified strain when grown on galactose media or glucose media, which activates and inactivates the GAL1/10 promoter, respectively.</p