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Context-specific effects of sequence elements on subcellular localization of linear and circular RNAs

Long RNAs vary extensively in their post-transcriptional fates, and this variation is attributed in part to short sequence elements. We used massively parallel RNA assays to study how sequences derived from noncoding RNAs influence the subcellular localization and stability of circular and linear RN...

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Autores principales: Ron, Maya, Ulitsky, Igor
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Nature Publishing Group UK 2022
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9072321/
https://www.ncbi.nlm.nih.gov/pubmed/35513423
http://dx.doi.org/10.1038/s41467-022-30183-0
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author Ron, Maya
Ulitsky, Igor
author_facet Ron, Maya
Ulitsky, Igor
author_sort Ron, Maya
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description Long RNAs vary extensively in their post-transcriptional fates, and this variation is attributed in part to short sequence elements. We used massively parallel RNA assays to study how sequences derived from noncoding RNAs influence the subcellular localization and stability of circular and linear RNAs, including spliced and unspliced forms. We find that the effects of sequence elements strongly depend on the host RNA context, with limited overlap between sequences that drive nuclear enrichment of linear and circular RNAs. Binding of specific RNA binding proteins underpins some of these differences—SRSF1 binding leads to nuclear enrichment of circular RNAs; SAFB binding is associated with nuclear enrichment of predominantly unspliced linear RNAs; and IGF2BP1 promotes export of linear spliced RNA molecules. The post-transcriptional fate of long RNAs is thus dictated by combinatorial contributions of specific sequence elements, of splicing, and of the presence of the terminal features unique to linear RNAs.
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spelling pubmed-90723212022-05-07 Context-specific effects of sequence elements on subcellular localization of linear and circular RNAs Ron, Maya Ulitsky, Igor Nat Commun Article Long RNAs vary extensively in their post-transcriptional fates, and this variation is attributed in part to short sequence elements. We used massively parallel RNA assays to study how sequences derived from noncoding RNAs influence the subcellular localization and stability of circular and linear RNAs, including spliced and unspliced forms. We find that the effects of sequence elements strongly depend on the host RNA context, with limited overlap between sequences that drive nuclear enrichment of linear and circular RNAs. Binding of specific RNA binding proteins underpins some of these differences—SRSF1 binding leads to nuclear enrichment of circular RNAs; SAFB binding is associated with nuclear enrichment of predominantly unspliced linear RNAs; and IGF2BP1 promotes export of linear spliced RNA molecules. The post-transcriptional fate of long RNAs is thus dictated by combinatorial contributions of specific sequence elements, of splicing, and of the presence of the terminal features unique to linear RNAs. Nature Publishing Group UK 2022-05-05 /pmc/articles/PMC9072321/ /pubmed/35513423 http://dx.doi.org/10.1038/s41467-022-30183-0 Text en © The Author(s) 2022 https://creativecommons.org/licenses/by/4.0/Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/ (https://creativecommons.org/licenses/by/4.0/) .
spellingShingle Article
Ron, Maya
Ulitsky, Igor
Context-specific effects of sequence elements on subcellular localization of linear and circular RNAs
title Context-specific effects of sequence elements on subcellular localization of linear and circular RNAs
title_full Context-specific effects of sequence elements on subcellular localization of linear and circular RNAs
title_fullStr Context-specific effects of sequence elements on subcellular localization of linear and circular RNAs
title_full_unstemmed Context-specific effects of sequence elements on subcellular localization of linear and circular RNAs
title_short Context-specific effects of sequence elements on subcellular localization of linear and circular RNAs
title_sort context-specific effects of sequence elements on subcellular localization of linear and circular rnas
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9072321/
https://www.ncbi.nlm.nih.gov/pubmed/35513423
http://dx.doi.org/10.1038/s41467-022-30183-0
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