Cytoplasmic long noncoding RNAs are frequently bound to and degraded at ribosomes in human cells
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...
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| Format: | Journal Article |
| Language: | English |
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2016
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| Online Access: | https://hdl.handle.net/10356/81504 http://hdl.handle.net/10220/40809 |
| _version_ | 1824456955151777792 |
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| author | Carlevaro-Fita, Joana Rahim, Anisa Guigó, Roderic Johnson, Rory Vardy, Leah Karen Anne |
| author2 | School of Biological Sciences |
| author_facet | School of Biological Sciences Carlevaro-Fita, Joana Rahim, Anisa Guigó, Roderic Johnson, Rory Vardy, Leah Karen Anne |
| author_sort | Carlevaro-Fita, Joana |
| collection | NTU |
| description | 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. |
| first_indexed | 2025-02-19T04:02:19Z |
| format | Journal Article |
| id | ntu-10356/81504 |
| institution | Nanyang Technological University |
| language | English |
| last_indexed | 2025-02-19T04:02:19Z |
| publishDate | 2016 |
| record_format | dspace |
| spelling | ntu-10356/815042023-02-28T16:58:51Z Cytoplasmic long noncoding RNAs are frequently bound to and degraded at ribosomes in human cells Carlevaro-Fita, Joana Rahim, Anisa Guigó, Roderic Johnson, Rory Vardy, Leah Karen Anne School of Biological Sciences Cytoplasm Transposable element Ribosome profiling Degradation Long noncoding RNA Ribosome Translation 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. ASTAR (Agency for Sci., Tech. and Research, S’pore) Published version 2016-06-27T09:00:29Z 2019-12-06T14:32:29Z 2016-06-27T09:00:29Z 2019-12-06T14:32:29Z 2016 Journal Article Carlevaro-Fita, J., Rahim, A., Guigó, R., Vardy, L. A., & Johnson, R. (2016). Cytoplasmic long noncoding RNAs are frequently bound to and degraded at ribosomes in human cells. RNA, 22(6), 867-882. 1355-8382 https://hdl.handle.net/10356/81504 http://hdl.handle.net/10220/40809 10.1261/rna.053561.115 27090285 en RNA © 2016 Carlevaro-Fita et al. This article, published in RNA, is available under a Creative Commons License (Attribution 4.0 International), as described at http://creativecommons.org/licenses/by/4.0/. 16 p. application/pdf |
| spellingShingle | Cytoplasm Transposable element Ribosome profiling Degradation Long noncoding RNA Ribosome Translation Carlevaro-Fita, Joana Rahim, Anisa Guigó, Roderic Johnson, Rory Vardy, Leah Karen Anne Cytoplasmic long noncoding RNAs are frequently bound to and degraded at ribosomes in human cells |
| title | Cytoplasmic long noncoding RNAs are frequently bound to and degraded at ribosomes in human cells |
| title_full | Cytoplasmic long noncoding RNAs are frequently bound to and degraded at ribosomes in human cells |
| title_fullStr | Cytoplasmic long noncoding RNAs are frequently bound to and degraded at ribosomes in human cells |
| title_full_unstemmed | Cytoplasmic long noncoding RNAs are frequently bound to and degraded at ribosomes in human cells |
| title_short | Cytoplasmic long noncoding RNAs are frequently bound to and degraded at ribosomes in human cells |
| title_sort | cytoplasmic long noncoding rnas are frequently bound to and degraded at ribosomes in human cells |
| topic | Cytoplasm Transposable element Ribosome profiling Degradation Long noncoding RNA Ribosome Translation |
| url | https://hdl.handle.net/10356/81504 http://hdl.handle.net/10220/40809 |
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