Identifying key regulatory networks and predicting targets of orphan box C/D SNORD116 snoRNAs in Prader-Willi Syndrome

To identify the targets and functions of SNORD116 snoRNAs, we engineered two different deletions mimicking those seen in Prader-Willi Syndrome (PWS) patients into two distinct human embryonic stem cell lines to control for effects of genetic background. We also introduced an inducible Neurogenin-2 cassette into the safe-harbor AAVS1 locus to enable quick and reproducible differentiation into neurons. We verified wild type and deletion genotypes across both genetic background generated comparable neruons at a gene expression level by comparing them to wild type hESCs. We then performed differential gene expression analysis using data obtained from bulk RNA-sequencing to compare the two distinct deletion types to their isogenic wild type pair and each other. Overall design: Comparative differential gene expression analysis of bulk RNA-seq data for 4-6 biological replicates of wild type H9 and CT2 inducible neurons and their PWS-like deletion derivatives.