title: Ribosome profiling reveals resemblance between long non-coding RNAs and 5' leaders of coding RNAs.
abstract: Large-scale genomics and computational approaches have identified thousands of putative long non-coding RNAs (lncRNAs). It has been controversial, however, as to what fraction of these RNAs is truly non-coding. Here, we combine ribosome profiling with a machine-learning approach to validate lncRNAs during zebrafish development in a high throughput manner. We find that dozens of proposed lncRNAs are protein-coding contaminants and that many lncRNAs have ribosome profiles that resemble the 5' leaders of coding RNAs. Analysis of ribosome profiling data from embryonic stem cells reveals similar properties for mammalian lncRNAs. These results clarify the annotation of developmental lncRNAs and suggest a potential role for translation in lncRNA regulation. In addition, our computational pipeline and ribosome profiling data provide a powerful resource for the identification of translated open reading frames during zebrafish development.
authors.affiliation: Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA 02138, USA.
authors.forename: Guo-Liang
authors.initials: GL
authors.lastname: Chew
authors.forename: Andrea
authors.initials: A
authors.lastname: Pauli
authors.forename: John L
authors.initials: JL
authors.lastname: Rinn
authors.forename: Aviv
authors.initials: A
authors.lastname: Regev
authors.forename: Alexander F
authors.initials: AF
authors.lastname: Schier
authors.forename: Eivind
authors.initials: E
authors.lastname: Valen
mesh_terms: D000818:Animals; D047108:Embryonic Development / Q000235:genetics / Q000502:physiology; D012313:RNA / Q000235:genetics*; D062085:RNA, Long Noncoding / Q000235:genetics*; D012270:Ribosomes / Q000235:genetics*; D015027:Zebrafish / Q000235:genetics / Q000254:growth & development
chemical_list: D062085:RNA, Long Noncoding; D012313:RNA
keywords: ES cells; Embryogenesis; Long non-coding RNAs; Ribosome profiling; Zebrafish