Identification of small RNA pathway genes using patterns of phylogenetic conservation and divergence
Identification of small RNA pathway genes using patterns of phylogenetic conservation and divergence
复制标题
DOI：
10.1038/nature11779
复制
发表时间：
2013-01-31
期刊：
影响因子：
64.8
通讯作者：
Ruvkun, Gary
中科院分区：
文献类型：
--
作者：
Tabach, Yuval;Billi, Allison C.;Ruvkun, Gary
RNA干扰（RNAi）和microRNA（miRNA）途径的遗传和生物化学分析显示，Argonaute和Dicer等蛋白质是加工小RNA并将其呈递给靶标的重要辅因子。经过充分验证的小RNA途径辅因子，如这些显示出独特的模式，特别是动物，植物，真菌和原生生物物种的保护或分歧。我们比较了86个不同的真核生物基因组序列，以辨别与已知小RNA辅因子显示相似系统发育特征的蛋白质组。从秀丽隐杆线虫和黑腹果蝇中miRNA或短干扰RNA（siRNA）介导的抑制缺陷的功能基因组筛选中，以及从与经验证的小RNA途径蛋白共纯化的蛋白质的蛋白质组学分析中，已经出现了大量额外的候选小RNA辅因子（3，4）。许多这些候选小RNA途径蛋白的系统发育概况与已知的小RNA辅因子蛋白的系统发育概况相似。我们使用贝叶斯方法将系统发育分析与来自不同转录共调控和蛋白质组相互作用数据集的预测相结合，为每个蛋白质在小RNA途径中的作用分配概率。测试来自该分析的高置信度候选者的RNAi沉默缺陷，我们发现大约一半的预测小RNA辅因子是RNAi沉默所需的。许多新鉴定的小RNA途径蛋白是参与RNA剪接的蛋白质的直向同源物。为了支持RNA剪接机制和小RNA介导的基因沉默之间的深层联系，在分析的许多物种中Argonaute蛋白和其他小RNA组分的存在与这些物种中内含子的数量密切相关。
Genetic and biochemical analyses of RNA interference (RNAi) and microRNA (miRNA) pathways have revealed proteins such as Argonaute and Dicer as essential cofactors that process and present small RNAs to their targets. Well-validated small RNA pathway cofactors such as these show distinctive patterns of conservation or divergence in particular animal, plant, fungal and protist species. We compared 86 divergent eukaryotic genome sequences to discern sets of proteins that show similar phylogenetic profiles with known small RNA cofactors. A large set of additional candidate small RNA cofactors have emerged from functional genomic screens for defects in miRNA-or short interfering RNA (siRNA)-mediated repression in Caenorhabditis elegans and Dro-sophila melanogaster(1,2), and from proteomic analyses of proteins co-purifying with validated small RNA pathway proteins(3,4). The phylogenetic profiles of many of these candidate small RNA pathway proteins are similar to those of known small RNA cofactor proteins. We used a Bayesian approach to integrate the phylogenetic profile analysis with predictions from diverse transcriptional coregulation and proteome interaction data sets to assign a probability for each protein for a role in a small RNA pathway. Testing high-confidence candidates from this analysis for defects in RNAi silencing, we found that about one-half of the predicted small RNA cofactors are required for RNAi silencing. Many of the newly identified small RNA pathway proteins are orthologues of proteins implicated in RNA splicing. In support of a deep connection between the mechanism of RNA splicing and small-RNA-mediated gene silencing, the presence of the Argonaute proteins and other small RNA components in the many species analysed strongly correlates with the number of introns in those species.