Identification of 11 candidate structured noncoding RNA motifs in humans by comparative genomics.
Identification of 11 candidate structured noncoding RNA motifs in humans by comparative genomics.
复制标题
通过比较基因组学鉴定人类 11 个候选结构非编码 RNA 基序
DOI：
10.1186/s12864-021-07474-9
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发表时间：
2021-03-09
期刊：
影响因子：
4.4
通讯作者：
Li S
中科院分区：
文献类型：
--
作者：
Hou L;Xie J;Wu Y;Wang J;Duan A;Ao Y;Liu X;Yu X;Yan H;Perreault J;Li S
研究背景人类基因组中只有1.5%编码蛋白质，其余大部分编码非编码RNA（ncRNA）。许多ncRNA形成结构并执行许多重要功能。准确地识别结构化的ncRNA在人类基因组中，发现它们的生物学功能仍然是一个重大的挑战。ResultsHere，我们已经建立了一个管道（CM线），具有以下功能，用于分析人类和其他动物的大基因组。首先，我们选择了具有较大遗传距离的物种，以便于发现协变和相容突变。其次，我们使用CMfinder，它可以生成有用的比对，即使序列保守性低。第三，我们删除了重复序列和已知结构的ncRNA，以减少CMfinder的工作量。第四，我们使用《无间道》来寻找更多的代表人物并优化结构。我们报道了11类在人类中具有显著共变异的结构化ncRNA候选物。功能分析表明，这些ncRNA可能具有不同的功能。有些人可能会调节生物钟基因通过聚（A）信号（PAS），有些可能会调节延伸因子（EEF 1A）和T细胞受体信号通路通过合作与RNA结合proteins.ConclusionsBy寻找RNA结构的重要功能，从大基因组，CM-线揭示了各种新结构的ncRNA的存在。功能分析表明，一些新发现的ncRNA模体可能具有生物学功能。我们为发现结构化ncRNA和鉴定其功能而建立的管道也可以应用于分析其他大型基因组。
BackgroundOnly 1.5% of the human genome encodes proteins, while large part of the remaining encodes noncoding RNAs (ncRNA). Many ncRNAs form structures and perform many important functions. Accurately identifying structured ncRNAs in the human genome and discovering their biological functions remain a major challenge.ResultsHere, we have established a pipeline (CM-line) with the following features for analyzing the large genomes of humans and other animals. First, we selected species with larger genetic distances to facilitate the discovery of covariations and compatible mutations. Second, we used CMfinder, which can generate useful alignments even with low sequence conservation. Third, we removed repetitive sequences and known structured ncRNAs to reduce the workload of CMfinder. Fourth, we used Infernal to find more representatives and refine the structure. We reported 11 classes of structured ncRNA candidates with significant covariations in humans. Functional analysis showed that these ncRNAs may have variable functions. Some may regulate circadian clock genes through poly (A) signals (PAS); some may regulate the elongation factor (EEF1A) and the T-cell receptor signaling pathway by cooperating with RNA binding proteins.ConclusionsBy searching for important features of RNA structure from large genomes, the CM-line has revealed the existence of a variety of novel structured ncRNAs. Functional analysis suggests that some newly discovered ncRNA motifs may have biological functions. The pipeline we have established for the discovery of structured ncRNAs and the identification of their functions can also be applied to analyze other large genomes.
影响因子：
1.6
作者：
Ye, Wenfeng;Zhou, Yi;Jiang, Jingting
通讯作者：
Jiang, Jingting