Schizophrenia-associated long non-coding RNAs in neurons derived from iPS cells

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DESCRIPTION (provided by applicant): Many functional RNAs do not code for proteins, such as the well-established small RNA subtypes tRNA, snoRNA, and miRNA, among others. More recently, families of long non-coding RNAs (lncRNAs) have been identified through genome-wide expression studies. There is increasing evidence that these molecules play an important role in regulating pluripotency, cellular differentiation, and neuronal function. Although several thousand lncRNAs have been identified, the function has been established for only a few. Of those that have been well-characterized, regulation of gene expression by modulating the chromatin state is the most common functional mechanism. For example, some lncRNAs associate with polycomb repressive complex 2, directing this ubiquitous chromatin organizing complex to specific gene targets. We recently carried out a whole genome transcriptome analysis (RNA-Seq) in human neurons derived from induced pluripotent stem cells (iPSCs) and identified significant changes in the expression of nearly 10,000 genes during neuronal differentiation, of which a substantial fraction were lncRNAs. Among those that showed the most significant increases in expression were several in the HOXA and HOXB loci, most notably HOTAIRM1. In addition, two lncRNAs that increase in expression during early neurogenesis - RP11-586K2.1 and RP11-319G6.1 contain or are near association signals identified in genome-wide association studies carried out in schizophrenia (SZ). We hypothesize that these lncRNAs are the biologically functional elements responsible for the association signals found in a subgroup of patients, presumably caused by genetic variation within these non-coding genes that are in linkage disequilibrium with associated SNPs. We also hypothesize that lncRNAs in general, through their capacity to influence tissue specific expression and signal transduction pathways, have a more important role in the development of neuropsychiatric disorders than is currently recognized. This proposal is designed to test these hypotheses in differentiating human neurons derived from iPSCs. This will be accomplished using a gene knockdown approach followed by RNA-Seq, and by identifying lncRNAs that bind to chromatin using an immunoprecipitation-based strategy called RIP-Seq (chromatin immunoprecipitation followed by deep sequencing of bound RNA). These studies will help elucidate the role of lncRNAs in the development SZ and other neuropsychiatric disorders.