Non-coding RNAs Associated With Prader-Willi Syndrome Regulate Transcription Of Neurodevelopmental Genes In Human Induced Pluripotent Stem Cells

We generated knockdowns (KD) of long non-coding RNAs (lncRNAs) arising from locus 15q11-q13, deletions in which result in Prader-Willi syndrome, in induced pluripotent stem cells. We extracted chromatin-associated RNA (chRNA) and total RNA and sequenced those using Illumina platform. There were four conditions for chRNA: control, KD of sno-lncRNAs, KD of SPA-lncRNAs, KD of both sno/SPA-lncRNAs, in biological duplicate. There were only two conditions for the total RNA seq: control and sno/SPA-lncRNAs. We found differential expression of genes relating to neurodevelopment and cell death between control and sno/SPA-lncRNAs only in chRNA samples. Differential gene expression between KDs of lncRNAs in locus 15q11-q13 in induced pluripotent stem cells and controls