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

描述（由申请人提供）：许多功能性RNA不编码蛋白质，例如已确立的小RNA亚型tRNA、snoRNA和miRNA等。最近，长链非编码RNA（lncRNA）家族已经通过全基因组表达研究被鉴定。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中发挥重要作用。尽管已经鉴定了几千种lncRNA，但仅对少数几种确立了功能。在那些已经被充分表征的功能机制中，通过调节染色质状态来调节基因表达是最常见的功能机制。例如，一些lncRNA与polycomb抑制复合物2结合，将这种普遍存在的染色质组织复合物引导至特定的基因靶标。我们最近在诱导多能干细胞（iPSC）衍生的人类神经元中进行了全基因组转录组分析（RNA-Seq），并确定了神经元分化过程中近10，000个基因表达的显著变化，其中相当一部分是lncRNA。在那些表现出最显著的表达增加的基因中，有几个在HOXA和HOXB基因座中，最显著的是HOTAIRM 1。此外，在早期神经发生期间表达增加的两种lncRNA-RP 11 -586K2.1和RP 11 -319G6.1包含或接近在精神分裂症（SZ）中进行的全基因组关联研究中鉴定的关联信号。我们假设这些lncRNA是负责在患者亚组中发现的关联信号的生物学功能元件，推测是由这些与相关SNP连锁不平衡的非编码基因内的遗传变异引起的。我们还假设lncRNA一般通过其影响组织特异性表达和信号转导途径的能力，在神经精神疾病的发展中具有比目前公认的更重要的作用。该提议旨在测试这些假设，以区分来自iPSC的人类神经元。这将使用基因敲除方法，然后是RNA-Seq，并通过使用称为RIP-Seq的基于免疫沉淀的策略（染色质免疫沉淀，然后是结合RNA的深度测序）鉴定与染色质结合的lncRNA来实现。这些研究将有助于阐明lncRNA在SZ和其他神经精神疾病发展中的作用。

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.