Cytoplasmic long noncoding RNAs are frequently bound to and degraded at ribosomes in human cells.

Carlevaro Fita, Joana; Rahim, Anisa; Guigó, Roderic; Vardy, Leah A; Johnson, Rory Baldwin (2016). Cytoplasmic long noncoding RNAs are frequently bound to and degraded at ribosomes in human cells. RNA - a publication of the RNA Society, 22(6), pp. 867-882. Cold Spring Harbor Laboratory Press 10.1261/rna.053561.115

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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.

Item Type:

Journal Article (Original Article)

Division/Institute:

04 Faculty of Medicine > Department of Haematology, Oncology, Infectious Diseases, Laboratory Medicine and Hospital Pharmacy (DOLS) > Clinic of Medical Oncology
04 Faculty of Medicine > Pre-clinic Human Medicine > BioMedical Research (DBMR)

UniBE Contributor:

Carlevaro Fita, Joana and Johnson, Rory Baldwin

Subjects:

600 Technology > 610 Medicine & health

ISSN:

1355-8382

Publisher:

Cold Spring Harbor Laboratory Press

Language:

English

Submitter:

Marianne Zahn

Date Deposited:

23 Dec 2016 15:08

Last Modified:

12 Jan 2017 12:15

Publisher DOI:

10.1261/rna.053561.115

PubMed ID:

27090285

Uncontrolled Keywords:

cytoplasm; degradation; long noncoding RNA; ribosome; ribosome profiling; translation; transposable element

BORIS DOI:

10.7892/boris.92067

URI:

https://boris.unibe.ch/id/eprint/92067

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