Dedicated transcriptomics combined with power analysis lead to functional understanding of genes with weak phenotypic changes in knockout lines

Author summary Knockout mice benefit the understanding of gene functions in mammals. However, it has proven difficult for many genes to identify clear phenotypes, related due to lack of sufficient assays. As Lewis Wolpert put it in a famous quote “But did you take them to the opera?”, thus metaphorically alluding to the need to extend phenotyping efforts. This insight led to the establishment of phenotyping pipelines that are nowadays routinely used to characterize knock-out lines. However, transcriptomic approaches based on RNA-Seq have been much less explored for such deep-level studies. We conducted here both, a theoretical power analysis and practical RNA-Seq experiments on two knockout lines with small phenotypic effects to investigate the parameters including sample size, sequencing depth, fold change, and dispersion. Our dedicated RNA-Seq studies discovered thousands of genes with small transcriptional changes and enriched in specific functions in both knockout lines. We find that it is more important to increase the number of samples than to increase the sequencing depth. Our work shows that a deep RNA-Seq study on knockouts is powerful for understanding gene functions in cases of weak phenotypic effects, and provides a guideline for the experimental design of such studies

Copy number variation in small nucleolar RNAs regulates personality behavior

Animals show behavioral traits that can collectively be called personality. We focus here on the role of the Prader-Willi Syndrom gene region in regulating personality behavior. It includes two clusters of tandem repeats coding for small nucleolar RNAs, SNORD115 and SNORD116. SNORD115 is known to regulate splicing of the serotonin receptor Ht2cr and SNORD116 is predicted to interact with the transcript of the chromatin regulator Ankrd11. We show that both snoRNA clusters display major copy number variation within and between populations, as well as in an inbred mouse strain and that this affects the expression of their specific target genes. Using a set of behavioral scores related to personality in populations of two species of wild mice, guinea pigs and humans, we find a strong correlation between the snoRNA copy number and these scores. Our results suggest that the SNORD clusters are major regulators of personality and correlated traits