Computational analysis of causality between miRNAs and antisense transcription

描述（由申请人提供）：反义转录是一种普遍存在的现象，影响约25%的真核基因，但其起源和功能尚不清楚。小RNA，如microRNAs （miRNAs）和反式小干扰RNA （ta- sirna）也普遍存在于后生动物和植物中，在基因调控、发育和疾病中发挥重要作用，但迄今为止，计算方法对植物和动物小RNA发现的预测能力有限。基于对四个独立的拟南芥转录组数据库的计算分析，我们假设mirna和ta- sirna是拟南芥反义转录的触发因子。这一假设将使用计算和统计方法在整个拟南芥和水稻基因组上进行严格的测试。以已知和假设的miRNA和ta-siRNA靶基因反义转录为学习集，基于反义转录结合已建立的miRNA预测方法，开发新的算法来发现新的候选miRNA、ta-siRNA及其假设的靶基因。作为生长和发育的潜在关键调节因子，已确定的假定的小RNA靶基因将是固有的“有趣”。预测的新型小RNA及其靶标将通过简单的瞬态分析系统、RNA印迹和cDNA末端快速扩增（RACE）进行实验验证，以证明新型小RNA定向切割靶标。对影响小rna和反义转录的已知突变体的全基因组平铺阵列的转录组分析将确定反义rna和小rna的因果关系程度。基于植物和动物之间共同现象的小RNA预测新算法可能对任何存在深层基因组资源的生物体中的小RNA发现，基因组注释以及更好地了解人类疾病病因具有普遍效用。这种预测工具在功能基因组学和进化生物学领域也会有用处。更好地了解小RNA及其在基因调控中的作用，可能有助于揭示“RNA世界”和生命的起源。

DESCRIPTION (provided by applicant): Antisense transcription is a widespread and pervasive phenomenon affecting about 25% of eukaryotic genes, but its origins and functions are unknown. Small RNAs such as microRNAs (miRNAs) and trans- acting small-interfering RNAs (ta-siRNAs) are also pervasive in metazoans and plants and play important roles in gene regulation, development, and disease, but to date the predictive power of computational methods for plant and animal small RNA discovery is limited. Based on computational analysis of four independent Arabidopsis transcriptome databases, it is hypothesized that miRNAs and ta-siRNAs are triggers for antisense transcription in Arabidopsis. This hypothesis will be rigorously tested using computational and statistical methods on the entire Arabidopsis and rice genomes. Using known and hypothesized miRNA and ta-siRNA target gene antisense transcription as a learning set, a new algorithm will be developed based on antisense transcription combined with established miRNA prediction methods to discover new candidate miRNAs, ta-siRNAs and their hypothetical target genes. The identified putative small RNA target genes would be inherently "interesting" as potential key regulators of growth and development. The predicted novel small RNAs and their targets will be experimentally validated with a facile transient assay system, RNA blots and rapid amplification of cDNA ends (RACE) to prove novel small RNA- directed cleavage of targets. Transcriptome profiling on whole genome tiling arrays of known mutants that affect small RNAs and antisense transcription will determine the extent of causality of antisense and small RNAs. A novel algorithm for small RNA prediction based on a phenomenon shared between plants and animals may have general utility for small RNA discovery in any organism for which deep genomic resources exist, for genome annotation, and for better understanding of human disease etiologies. Such a predictive tool would also have utility in the fields of functional genomics and evolutionary biology. A better understanding of small RNAs and their roles in gene regulation may shed light on "the RNA World" and the origins of life.