Global Analysis of the Human RNA Degradome

描述（由申请方提供）：人RNA降解组的全球分析。用微阵列或测序方法分析转录组已经成为基础和应用生物医学研究的支柱。2005年，PI的实验室开创了小RNA的深度测序，这种方法现在是检查真核系统中miRNA群体的常规方法。对于某些肿瘤的分型，miRNA谱分析可能比mRNA谱分析更有效，这一发现强调了对转录组的其他主要组分进行谱分析可能导致新的和更有效的疾病关联。转录组的一个组分在很大程度上被忽略了，那就是RNA衰变产物的数量，即，RNA降解组。该项目的长期目标是促进使用RNA降解组信息来解决生物学问题和识别人类疾病的新标志物。为了实现这一目标，必须证明RNA降解组可以在全基因组范围内进行分析，并提供重要信息。该项目旨在实现这一目标的人类degradome，并测试的假设，RNA衰变的调节比以前认为的更广泛。一种称为RNA末端平行分析（帕雷）的方法将被应用于这个问题。与第一个miRNA分析研究一样，帕雷是使用拟南芥植物开发的，其中miRNA通常指导其mRNA靶点的切割，类似于哺乳动物中RNAi期间发生的情况。通过检查与这些事件相对应的RNA衰变产物的群体（具有5'单磷酸的聚腺苷酸化RNA），几乎所有经验证的和许多新的miRNA靶被鉴定。虽然这种方法提供了一种很好的方法来鉴定潜在的重要靶点的miRNA或其他内源性小RNA，在人类中引起切割，这些情况被认为是罕见的。使用帕雷检查转录组中每个转录本的衰变模式，预计会产生最大的影响。在该项目下，将从不同的ENCODE系、敲低突变体和不同类型的衰变产物中制备帕雷文库并进行深度测序。将生成并比较每个文库的每个注释的人cDNA的衰减图。将识别并验证在单个或多个样本中表现出降解改变的转录本。这项工作将为现有的基因表达数据增加一个新的维度，并对其做出重大贡献。此外，它将鼓励研究人员研究RNA降解组的变化与一系列人类疾病的关联。 公共卫生相关性：这项工作将为现有的基因表达数据增加一个新的维度，并对其做出重大贡献。此外，它将鼓励研究人员研究RNA降解组的变化与一系列人类疾病的关联。

DESCRIPTION (provided by applicant): Global Analysis of the Human RNA Degradome. Profiling the transcriptome with microarrays or sequencing approaches has become a mainstay of basic and applied biomedical research. In 2005, the deep sequencing of small RNAs was pioneered in the PI's lab, an approach that is now routine for examining miRNA populations in eukaryotic systems. The finding that miRNA profiling can be more effective than mRNA profiling for typing certain tumors emphasizes that profiling other major components of the transcriptome can lead to new and more potent disease associations. One component of the transcriptome that has been largely ignored is the population of RNA decay products, i.e., the RNA degradome. The long-term goal of this project is to facilitate the use of RNA degradome information to solve biological problems and identify new markers of human disease. To accomplish this, it is essential to demonstrate that the RNA degradome can be analyzed on a genome-wide scale and provide important information. This project seeks to achieve this for the human degradome, and test the hypothesis that regulation of RNA decay is more widespread than previously thought. An approach called Parallel Analysis of RNA Ends (PARE) will be applied to the problem. Like the first miRNA profiling studies, PARE was developed using Arabidopsis plants, in which miRNAs typically guide the cleavage of their mRNA targets, similar to what happens during RNAi in mammals. By examining the population of RNA decay products corresponding to these events (polyadenylated RNAs with a 5' monophosphate), nearly all the validated and many new miRNA targets were identified. Although this approach provides an excellent way to identify potentially important targets of miRNAs or other endogenous small RNAs that cause cleavage in human, these cases are thought to be rare. It is the use of PARE to examine the patterns of decay for each transcript in the transcriptome that is expected to have the greatest impact. Under this project, PARE libraries will be made and deeply sequenced from different ENCODE lines, knockdown mutants, and different types of decay products. Decay plots for each annotated human cDNA for each library will be generated and compared. Transcripts that exhibit altered degradation in individual or multiple samples will be identified and validated. This work will add a new dimension to existing gene expression data, and contribute significantly to it. Moreover, it will encourage investigators to examine the associations of changes in the RNA degradome with a range of human diseases. PUBLIC HEALTH RELEVANCE: This work will add a new dimension to existing gene expression data, and contribute significantly to it. Moreover, it will encourage investigators to examine the associations of changes in the RNA degradome with a range of human diseases.