Global Analysis of the Human RNA Degradome

描述(申请人提供)：人类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的实验室率先对小RNA进行了深度测序，这一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图谱可能比mRNA图谱更有效，这一发现强调了图谱转录组的其他主要成分可以导致新的、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衰变产物的群体，即RNA降解组。该项目的长期目标是促进利用RNA降解组信息来解决生物学问题和识别人类疾病的新标记。要做到这一点，至关重要的是证明RNA降解穹顶可以在全基因组范围内进行分析，并提供重要信息。这个项目试图在人类的降解穹顶上实现这一点，并测试对RNA衰变的调节比之前认为的更广泛的假设。一种名为RNA末端并行分析(PARE)的方法将应用于该问题。与第一次miRNA谱研究一样，PAE是使用拟南芥植物开发的，其中miRNAs通常指导其mRNA靶标的切割，类似于哺乳动物在RNAi过程中发生的事情。通过检查与这些事件相对应的RNA衰退产物(带有5‘一磷酸的多腺苷RNAs)的群体，几乎所有有效的和许多新的miRNA靶标都被识别出来。虽然这种方法提供了一种很好的方法来识别导致人类切割的miRNAs或其他内源性小RNA的潜在重要靶标，但这些情况被认为是罕见的。使用PARE来检查转录组中每个转录本的衰退模式，预计会产生最大的影响。在该项目下，将从不同的ENCODE品系、击倒突变体和不同类型的衰变产物中建立PARE文库并进行深度测序。将为每个文库生成并比较每个带注释的人类基因的衰变曲线图。将识别和验证在单个或多个样本中显示发生变化的降解的转录本。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，它还将鼓励研究人员检查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，它还将鼓励研究人员检查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.