A common set of distinct features that characterize noncoding RNAs   across multiple species

doi:10.1093/nar/gku1316

CORC > 北京大学 > 生命科学学院

	A common set of distinct features that characterize noncoding RNAs across multiple species
	Hu, Long ; Di, Chao ; Kai, Mingxuan ; Yang, Yu-Cheng T. ; Li, Yang ; Qiu, Yunjiang ; Hu, Xihao ; Yip, Kevin Y. ; Zhang, Michael Q. ; Lu, Zhi John
刊名	核酸研究
	2015
关键词	SEQUENCE FEATURES IN-VIVO GENOME CHROMATIN PROTEIN BINDING IDENTIFICATION EXPRESSION REVEALS EVOLUTION
DOI	10.1093/nar/gku1316
英文摘要	To find signature features shared by various ncRNA sub-types and characterize novel ncRNAs, we have developed a method, RNAfeature, to investigate > 600 sets of genomic and epigenomic data with various evolutionary and biophysical scores. RNAfeature utilizes a fine-tuned intra-species wrapper algorithm that is followed by a novel feature selection strategy across species. It considers long distance effect of certain features (e.g. histone modification at the promoter region). We finally narrow down on 10 informative features (including sequences, structures, expression profiles and epigenetic signals). These features are complementary to each other and as a whole can accurately distinguish canonical ncRNAs from CDSs and UTRs (accuracies: > 92% in human, mouse, worm and fly). Moreover, the feature pattern is conserved across multiple species. For instance, the supervised 10-feature model derived from animal species can predict ncRNAs in Arabidopsis (accuracy: 82%). Subsequently, we integrate the 10 features to define a set of noncoding potential scores, which can identify, evaluate and characterize novel noncoding RNAs. The score covers all transcribed regions (including unconserved ncRNAs), without requiring assembly of the full-length transcripts. Importantly, the noncoding potential allows us to identify and characterize potential functional domains with feature patterns similar to canonical ncRNAs (e.g. tRNA, snRNA, miRNA, etc) on similar to 70% of human long ncRNAs (lncRNAs).; Biochemistry & Molecular Biology; SCI(E); PubMed; 0; ARTICLE; zhilu@tsinghua.edu.cn; 1; 104-114; 43
语种	英语
内容类型	期刊论文
源URL	[http://ir.pku.edu.cn/handle/20.500.11897/341745]
专题	生命科学学院
推荐引用方式 GB/T 7714	Hu, Long,Di, Chao,Kai, Mingxuan,et al. A common set of distinct features that characterize noncoding RNAs across multiple species[J]. 核酸研究,2015.
APA	Hu, Long.,Di, Chao.,Kai, Mingxuan.,Yang, Yu-Cheng T..,Li, Yang.,...&Lu, Zhi John.(2015).A common set of distinct features that characterize noncoding RNAs across multiple species.核酸研究.
MLA	Hu, Long,et al."A common set of distinct features that characterize noncoding RNAs across multiple species".核酸研究 (2015).