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

描述(申请人提供)：许多功能RNA不编码蛋白质，如成熟的小RNA亚型tRNA、snoRNA和miRNA等。最近，通过全基因组表达研究发现了长非编码RNA家族(LncRNAs)。越来越多的证据表明，这些分子在调节多能性、细胞分化和神经元功能方面发挥着重要作用。尽管已经确定了数千个LncRNA，但只为少数几个建立了这一功能。在这些已被很好描述的基因中，通过调节染色质状态来调节基因表达是最常见的作用机制。例如，一些lncRNA与多梳抑制复合体2相关联，将这种普遍存在的染色质组织复合体导向特定的基因靶点。我们最近在人类诱导多能干细胞(IPSCs)来源的神经元中进行了全基因组转录组分析(RNA-Seq)，发现在神经元分化过程中近10,000个基因的表达发生了显著变化，其中很大一部分是lncRNAs。在那些表现出最显著的表达增加的基因中，有几个是在HOXA和HOXB基因座上，最著名的是HOTAIRM1。此外，在早期神经发生过程中表达增加的两个lncRNAs-RP11-586K2.1和RP11-319G6.1包含或接近于在精神分裂症(SZ)全基因组关联研究中发现的关联信号。我们假设这些LncRNAs是在亚组患者中发现的关联信号的生物功能元件，可能是由于这些非编码基因与相关SNPs处于连锁不平衡的遗传变异所致。我们还假设，一般来说，lncRNAs通过其影响组织特异性表达和信号转导途径的能力，在神经精神障碍的发展中具有比目前所认识的更重要的作用。这一提议旨在测试这些假设在区分来自ipscs的人类神经元方面的作用。这将使用基因敲除方法，然后是RNA-Seq，并通过使用一种名为RIP-Seq(染色质免疫沉淀随后对结合的RNA进行深度测序)的免疫沉淀策略来识别与染色质结合的lncRNA。这些研究将有助于阐明lncRNAs在SZ和其他神经精神障碍的发生发展中的作用。

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.