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Importance of the RNA secondary structure for the relative accumulation of clustered viral microRNAs

Micro (mi)RNAs are small non-coding RNAs with key regulatory functions. Recent advances in the field allowed researchers to identify their targets. However, much less is known regarding the regulation of miRNAs themselves. The accumulation of these tiny regulators can be modulated at various levels...

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Autores principales: Contrant, Maud, Fender, Aurélie, Chane-Woon-Ming, Béatrice, Randrianjafy, Ramy, Vivet-Boudou, Valérie, Richer, Delphine, Pfeffer, Sébastien
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Oxford University Press 2014
Materias:
RNA
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4081064/
https://www.ncbi.nlm.nih.gov/pubmed/24831544
http://dx.doi.org/10.1093/nar/gku424
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author Contrant, Maud
Fender, Aurélie
Chane-Woon-Ming, Béatrice
Randrianjafy, Ramy
Vivet-Boudou, Valérie
Richer, Delphine
Pfeffer, Sébastien
author_facet Contrant, Maud
Fender, Aurélie
Chane-Woon-Ming, Béatrice
Randrianjafy, Ramy
Vivet-Boudou, Valérie
Richer, Delphine
Pfeffer, Sébastien
author_sort Contrant, Maud
collection PubMed
description Micro (mi)RNAs are small non-coding RNAs with key regulatory functions. Recent advances in the field allowed researchers to identify their targets. However, much less is known regarding the regulation of miRNAs themselves. The accumulation of these tiny regulators can be modulated at various levels during their biogenesis from the transcription of the primary transcript (pri-miRNA) to the stability of the mature miRNA. Here, we studied the importance of the pri-miRNA secondary structure for the regulation of mature miRNA accumulation. To this end, we used the Kaposi's sarcoma herpesvirus, which encodes a cluster of 12 pre-miRNAs. Using small RNA profiling and quantitative northern blot analysis, we measured the absolute amount of each mature miRNAs in different cellular context. We found that the difference in expression between the least and most expressed viral miRNAs could be as high as 60-fold. Using high-throughput selective 2′-hydroxyl acylation analyzed by primer extension, we then determined the secondary structure of the long primary transcript. We found that highly expressed miRNAs derived from optimally structured regions within the pri-miRNA. Finally, we confirmed the importance of the local structure by swapping stem-loops or by targeted mutagenesis of selected miRNAs, which resulted in a perturbed accumulation of the mature miRNA.
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spelling pubmed-40810642014-07-10 Importance of the RNA secondary structure for the relative accumulation of clustered viral microRNAs Contrant, Maud Fender, Aurélie Chane-Woon-Ming, Béatrice Randrianjafy, Ramy Vivet-Boudou, Valérie Richer, Delphine Pfeffer, Sébastien Nucleic Acids Res RNA Micro (mi)RNAs are small non-coding RNAs with key regulatory functions. Recent advances in the field allowed researchers to identify their targets. However, much less is known regarding the regulation of miRNAs themselves. The accumulation of these tiny regulators can be modulated at various levels during their biogenesis from the transcription of the primary transcript (pri-miRNA) to the stability of the mature miRNA. Here, we studied the importance of the pri-miRNA secondary structure for the regulation of mature miRNA accumulation. To this end, we used the Kaposi's sarcoma herpesvirus, which encodes a cluster of 12 pre-miRNAs. Using small RNA profiling and quantitative northern blot analysis, we measured the absolute amount of each mature miRNAs in different cellular context. We found that the difference in expression between the least and most expressed viral miRNAs could be as high as 60-fold. Using high-throughput selective 2′-hydroxyl acylation analyzed by primer extension, we then determined the secondary structure of the long primary transcript. We found that highly expressed miRNAs derived from optimally structured regions within the pri-miRNA. Finally, we confirmed the importance of the local structure by swapping stem-loops or by targeted mutagenesis of selected miRNAs, which resulted in a perturbed accumulation of the mature miRNA. Oxford University Press 2014-08-01 2014-05-15 /pmc/articles/PMC4081064/ /pubmed/24831544 http://dx.doi.org/10.1093/nar/gku424 Text en © The Author(s) 2014. Published by Oxford University Press on behalf of Nucleic Acids Research. http://creativecommons.org/licenses/by/3.0/ This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/3.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited.
spellingShingle RNA
Contrant, Maud
Fender, Aurélie
Chane-Woon-Ming, Béatrice
Randrianjafy, Ramy
Vivet-Boudou, Valérie
Richer, Delphine
Pfeffer, Sébastien
Importance of the RNA secondary structure for the relative accumulation of clustered viral microRNAs
title Importance of the RNA secondary structure for the relative accumulation of clustered viral microRNAs
title_full Importance of the RNA secondary structure for the relative accumulation of clustered viral microRNAs
title_fullStr Importance of the RNA secondary structure for the relative accumulation of clustered viral microRNAs
title_full_unstemmed Importance of the RNA secondary structure for the relative accumulation of clustered viral microRNAs
title_short Importance of the RNA secondary structure for the relative accumulation of clustered viral microRNAs
title_sort importance of the rna secondary structure for the relative accumulation of clustered viral micrornas
topic RNA
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4081064/
https://www.ncbi.nlm.nih.gov/pubmed/24831544
http://dx.doi.org/10.1093/nar/gku424
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