High-affinity RNA targets of the Survival Motor Neuron protein reveal diverse preferences for sequence and structural motifs

The Survival Motor Neuron (SMN) protein is essential for survival of all animal cells. SMN harbors a nucleic acid-binding domain and plays an important role in RNA metabolism. However, the RNA-binding property of SMN is poorly understood. Here we employ iterative in vitro selection and chemical stru...

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Autores principales: Ottesen, Eric W, Singh, Natalia N, Luo, Diou, Singh, Ravindra N
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Oxford University Press 2018
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6237763/
https://www.ncbi.nlm.nih.gov/pubmed/30165668
http://dx.doi.org/10.1093/nar/gky770
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author Ottesen, Eric W
Singh, Natalia N
Luo, Diou
Singh, Ravindra N
author_facet Ottesen, Eric W
Singh, Natalia N
Luo, Diou
Singh, Ravindra N
author_sort Ottesen, Eric W
collection PubMed
description The Survival Motor Neuron (SMN) protein is essential for survival of all animal cells. SMN harbors a nucleic acid-binding domain and plays an important role in RNA metabolism. However, the RNA-binding property of SMN is poorly understood. Here we employ iterative in vitro selection and chemical structure probing to identify sequence and structural motif(s) critical for RNA–SMN interactions. Our results reveal that motifs that drive RNA–SMN interactions are diverse and suggest that tight RNA–SMN interaction requires presence of multiple contact sites on the RNA molecule. We performed UV crosslinking and immunoprecipitation coupled with high-throughput sequencing (HITS-CLIP) to identify cellular RNA targets of SMN in neuronal SH-SY5Y cells. Results of HITS-CLIP identified a wide variety of targets, including mRNAs coding for ribosome biogenesis and cytoskeleton dynamics. We show critical determinants of ANXA2 mRNA for a direct SMN interaction in vitro. Our data confirms the ability of SMN to discriminate among close RNA sequences, and represent the first validation of a direct interaction of SMN with a cellular RNA target. Our findings suggest direct RNA–SMN interaction as a novel mechanism to initiate the cascade of events leading to the execution of SMN-specific functions.
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spelling pubmed-62377632018-11-21 High-affinity RNA targets of the Survival Motor Neuron protein reveal diverse preferences for sequence and structural motifs Ottesen, Eric W Singh, Natalia N Luo, Diou Singh, Ravindra N Nucleic Acids Res RNA and RNA-protein complexes The Survival Motor Neuron (SMN) protein is essential for survival of all animal cells. SMN harbors a nucleic acid-binding domain and plays an important role in RNA metabolism. However, the RNA-binding property of SMN is poorly understood. Here we employ iterative in vitro selection and chemical structure probing to identify sequence and structural motif(s) critical for RNA–SMN interactions. Our results reveal that motifs that drive RNA–SMN interactions are diverse and suggest that tight RNA–SMN interaction requires presence of multiple contact sites on the RNA molecule. We performed UV crosslinking and immunoprecipitation coupled with high-throughput sequencing (HITS-CLIP) to identify cellular RNA targets of SMN in neuronal SH-SY5Y cells. Results of HITS-CLIP identified a wide variety of targets, including mRNAs coding for ribosome biogenesis and cytoskeleton dynamics. We show critical determinants of ANXA2 mRNA for a direct SMN interaction in vitro. Our data confirms the ability of SMN to discriminate among close RNA sequences, and represent the first validation of a direct interaction of SMN with a cellular RNA target. Our findings suggest direct RNA–SMN interaction as a novel mechanism to initiate the cascade of events leading to the execution of SMN-specific functions. Oxford University Press 2018-11-16 2018-08-27 /pmc/articles/PMC6237763/ /pubmed/30165668 http://dx.doi.org/10.1093/nar/gky770 Text en © The Author(s) 2018. Published by Oxford University Press on behalf of Nucleic Acids Research. http://creativecommons.org/licenses/by-nc/4.0/ This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/4.0/), which permits non-commercial re-use, distribution, and reproduction in any medium, provided the original work is properly cited. For commercial re-use, please contact journals.permissions@oup.com
spellingShingle RNA and RNA-protein complexes
Ottesen, Eric W
Singh, Natalia N
Luo, Diou
Singh, Ravindra N
High-affinity RNA targets of the Survival Motor Neuron protein reveal diverse preferences for sequence and structural motifs
title High-affinity RNA targets of the Survival Motor Neuron protein reveal diverse preferences for sequence and structural motifs
title_full High-affinity RNA targets of the Survival Motor Neuron protein reveal diverse preferences for sequence and structural motifs
title_fullStr High-affinity RNA targets of the Survival Motor Neuron protein reveal diverse preferences for sequence and structural motifs
title_full_unstemmed High-affinity RNA targets of the Survival Motor Neuron protein reveal diverse preferences for sequence and structural motifs
title_short High-affinity RNA targets of the Survival Motor Neuron protein reveal diverse preferences for sequence and structural motifs
title_sort high-affinity rna targets of the survival motor neuron protein reveal diverse preferences for sequence and structural motifs
topic RNA and RNA-protein complexes
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6237763/
https://www.ncbi.nlm.nih.gov/pubmed/30165668
http://dx.doi.org/10.1093/nar/gky770
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