Integrative annotation of human large intergenic noncoding RNAs reveals global properties and specific subclasses
dechang 添加于 2012-3-31 10:32
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作 者
Cabili MN, Trapnell C, Goff L, Koziol M, Tazon-Vega B, Regev A, Rinn JL 摘 要
Large intergenic noncoding RNAs (lincRNAs) are emerging as key regulators of diverse cellular processes. Determining the function of individual lincRNAs remains a challenge. Recent advances in RNA sequencing (RNA-seq) and computational methods allow for an unprecedented analysis of such transcripts. Here, we present an integrative approach to define a reference catalog of >8000 human lincRNAs. Our catalog unifies previously existing annotation sources with transcripts we assembled from RNA-seq data collected from approximately 4 billion RNA-seq reads across 24 tissues and cell types. We characterize each lincRNA by a panorama of >30 properties, including sequence, structural, transcriptional, and orthology features. We found that lincRNA expression is strikingly tissue-specific compared with coding genes, and that lincRNAs are typically coexpressed with their neighboring genes, albeit to an extent similar to that of pairs of neighboring protein-coding genes. We distinguish an additional subset of transcripts that have high evolutionary conservation but may include short ORFs and may serve as either lincRNAs or small peptides. Our integrated, comprehensive, yet conservative reference catalog of human lincRNAs reveals the global properties of lincRNAs and will facilitate experimental studies and further functional classification of these genes.-
详细资料
- 关键词: Alternative Splicing; Enhancer Elements, Genetic/genetics; Gene Expression Regulation; Genes, Overlapping; Humans; Molecular Sequence Annotation/*methods; RNA, Untranslated/classification/*genetics; Sequence Homology, Nucleic Acid
- 文献种类:期刊
- 期刊名称: Genes & Development
- 期刊缩写: Genes Dev
- 期卷页: 2011年 第25卷 第18期 1915-1927页
- 地址: Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, Massachusetts 02142, USA
- ISBN: 0890-9369
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DOI URL
Multilayered Control of Alternative Splicing Regulatory Networks by Transcription Factors
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