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

iPS 细胞神经元中与精神分裂症相关的长非编码 RNA

基本信息

批准号：
8583003
负责人：
HERBERT M LACHMAN
金额：
$ 25.05万
依托单位：
ALBERT EINSTEIN COLLEGE OF MEDICINE
依托单位国家：
美国
项目类别：
财政年份：
2013
资助国家：
美国
起止时间：
2013-08-01 至 2015-07-31
项目状态：
已结题

来源：
https://reporter.nih.gov/project-details/8583003
关键词：
Affect Autistic Disorder Biological Process Candidate Disease Gene Cell Culture System Cells Chromatin Chromatin Remodeling Factor Chromatin Structure Code Complex Development Disease Elements Exons Family Functional RNA Gene Expression Profile Gene Expression Regulation Gene Targeting Genes Genetic Variation Genome Human Human Genome Immunoprecipitation Laboratories Linkage Disequilibrium MicroRNAs Molecular Neuronal Differentiation Neurons Nucleotides Patients Pharmaceutical Preparations Play Polycomb Process Proteins RNA RNA Binding Retinol Binding Proteins Role SMARCA2 gene Schizophrenia Signal Transduction Signal Transduction Pathway Small Nucleolar RNA Small RNA Subgroup Testing Tissue-Specific Gene Expression Tissues Transfer RNA autism spectrum disorder base chromatin immunoprecipitation deep sequencing design drug development embryonic stem cell genome wide association study genome-wide histone methyltransferase induced pluripotent stem cell inhibitor/antagonist intein member neurogenesis neuropsychiatry pluripotency promoter public health relevance stem cell technology transcriptome sequencing

项目摘要

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.

描述（由申请人提供）：许多功能性RNA不为蛋白质编码，例如良好的小RNA子类型tRNA，SNORNA和miRNA等。最近，已经通过全基因组表达研究确定了长期非编码RNA（LNCRNA）的家族。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起着重要作用。尽管已经确定了数千个LNCRNA，但仅建立了少数功能。在经过良好特征的人中，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相关，将这种无处不在的染色质组织复合物引导到特定基因靶标。最近，我们在源自诱导的多能干细胞（IPSC）的人神经元中进行了整个基因组转录组分析（RNA-SEQ），并确定了神经元分化过程中近10,000个基因表达的显着变化，其中大量分数为LNCRNA。在表达最显着增加的hoxa和HoxB基因座中，最显着的表达增加，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LNCRNA-RP11-586K2.1和RP11-319G6.1包含或接近在基因组范围的关联研究中在精神分裂症（SZ）进行的均质信号。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，这可能是由这些非编码基因内的遗传变异引起的，这些基因与相关SNP链接不平衡。我们还假设LNCRNA通常通过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所认识到的更重要的作用。该建议旨在检验这些假设，以区分源自IPSC的人类神经元。这将使用基因敲低方法，然后是RNA-seq，并通过使用基于免疫沉淀的策略（称为RIP-SEQ（染色质免疫沉淀）鉴定与染色质结合的LNCRNA，然后对结合RNA进行深度测序）。这些研究将有助于阐明LNCRNA在SZ发育和其他神经精神疾病中的作用。