title: Cytoplasmic long noncoding RNAs are frequently bound to and degraded at ribosomes in human cells.
abstract: Recent footprinting studies have made the surprising observation that long noncoding RNAs (lncRNAs) physically interact with ribosomes. However, these findings remain controversial, and the overall proportion of cytoplasmic lncRNAs involved is unknown. Here we make a global, absolute estimate of the cytoplasmic and ribosome-associated population of stringently filtered lncRNAs in a human cell line using polysome profiling coupled to spike-in normalized microarray analysis. Fifty-four percent of expressed lncRNAs are detected in the cytoplasm. The majority of these (70%) have >50% of their cytoplasmic copies associated with polysomal fractions. These interactions are lost upon disruption of ribosomes by puromycin. Polysomal lncRNAs are distinguished by a number of 5' mRNA-like features, including capping and 5'UTR length. On the other hand, nonpolysomal "free cytoplasmic" lncRNAs have more conserved promoters and a wider range of expression across cell types. Exons of polysomal lncRNAs are depleted of endogenous retroviral insertions, suggesting a role for repetitive elements in lncRNA localization. Finally, we show that blocking of ribosomal elongation results in stabilization of many associated lncRNAs. Together these findings suggest that the ribosome is the default destination for the majority of cytoplasmic long noncoding RNAs and may play a role in their degradation.
authors.affiliation: Centre for Genomic Regulation (CRG), 08003 Barcelona, Spain Universitat Pompeu Fabra (UPF), 08003 Barcelona, Spain Institut Hospital del Mar d'Investigacions Mèdiques (IMIM), 08003 Barcelona, Spain.
authors.forename: Joana
authors.initials: J
authors.lastname: Carlevaro-Fita
authors.affiliation: A*STAR Institute of Medical Biology, Singapore 138648, Singapore.
authors.forename: Anisa
authors.initials: A
authors.lastname: Rahim
authors.affiliation: Centre for Genomic Regulation (CRG), 08003 Barcelona, Spain Universitat Pompeu Fabra (UPF), 08003 Barcelona, Spain Institut Hospital del Mar d'Investigacions Mèdiques (IMIM), 08003 Barcelona, Spain.
authors.forename: Roderic
authors.initials: R
authors.lastname: Guigó
authors.affiliation: A*STAR Institute of Medical Biology, Singapore 138648, Singapore School of Biological Sciences, Nanyang Technological University, 637551 Singapore.
authors.forename: Leah A
authors.initials: LA
authors.lastname: Vardy
authors.affiliation: Centre for Genomic Regulation (CRG), 08003 Barcelona, Spain Universitat Pompeu Fabra (UPF), 08003 Barcelona, Spain Institut Hospital del Mar d'Investigacions Mèdiques (IMIM), 08003 Barcelona, Spain.
authors.forename: Rory
authors.initials: R
authors.lastname: Johnson
mesh_terms: D020121:5' Untranslated Regions; D001665:Binding Sites; D003593:Cytoplasm / Q000378:metabolism*; D006367:HeLa Cells; D006801:Humans; D006868:Hydrolysis; D017404:In Situ Hybridization, Fluorescence; D020014:K562 Cells; D062085:RNA, Long Noncoding / Q000378:metabolism*; D012270:Ribosomes / Q000378:metabolism*
chemical_list: D020121:5' Untranslated Regions; D062085:RNA, Long Noncoding
keywords: cytoplasm; degradation; long noncoding RNA; ribosome; ribosome profiling; translation; transposable element