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Deciphering targeting rules of splicing modulator compounds: case of TG003

BACKGROUND: Recent advances in the development of small chemical compounds that can modulate RNA splicing brought excitement to the field of splicing-targeting therapy. Splicing-targeting therapy tries to ameliorate the disease by altering the exon combination of transcripts to reduce the undesired...

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Autores principales: Sakuma, Maki, Iida, Kei, Hagiwara, Masatoshi
Formato: Online Artículo Texto
Lenguaje:English
Publicado: BioMed Central 2015
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4580995/
https://www.ncbi.nlm.nih.gov/pubmed/26400733
http://dx.doi.org/10.1186/s12867-015-0044-6
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author Sakuma, Maki
Iida, Kei
Hagiwara, Masatoshi
author_facet Sakuma, Maki
Iida, Kei
Hagiwara, Masatoshi
author_sort Sakuma, Maki
collection PubMed
description BACKGROUND: Recent advances in the development of small chemical compounds that can modulate RNA splicing brought excitement to the field of splicing-targeting therapy. Splicing-targeting therapy tries to ameliorate the disease by altering the exon combination of transcripts to reduce the undesired effect of genetic mutations. However, the knowledge and tools to understand factors contributing to splicing modulator compound sensitivity have been lacking. Our goal was to establish a method to characterize sequence features found in compound sensitive exons. RESULTS: Here we developed a comparative transcriptomic approach to explore features that make an exon sensitive to a chemical compound. In this study, we chose TG003, a potential drug for Duchenne muscular dystrophy, and performed RNA-sequencing on samples from human and mouse skeletal muscle cells, with and without TG003 treatments. We compared TG003 responsiveness between homologous exon pairs and identified 21 pairs in which human exons were skip-enhanced but not mouse exons. We compared the sequence features; splice site scores, number of splicing factor binding sites, and properties of branch sequence and polypyrimidine tracts, and found that polypyrimidine tracts were stronger (longer stretches and richer content of consecutive polypyrimidine) in the mouse TG003 insensitive exons. We also compared the features between TG003 skip-enhanced and insensitive exons within the species, and discovered that human TG003 skip-enhanced exons were shorter and had less splicing factor binding sites than the group of human TG003 insensitive exons. Mouse insensitive exons homologous to human TG003 skip-enhanced exons shared these properties. Our results suggested that these features are prerequisites for TG003 skip-enhanced exons and weak polypyrimidine tracts are defining features, which were supported by a decision tree analysis on all cassette exons in human. CONCLUSIONS: In this study we established a comparative transcriptomic approach, which shed lights on how small chemical compounds modulate RNA splicing. The results described here was the first attempt to decipher the targeting rules of a splicing modulator compound. We expect that this approach would contribute to the precise understanding of the mechanism of TG003-induced splicing modulation, expand target diseases of splicing modulators in general, as well as the development of new splicing modulators. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/s12867-015-0044-6) contains supplementary material, which is available to authorized users.
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spelling pubmed-45809952015-09-25 Deciphering targeting rules of splicing modulator compounds: case of TG003 Sakuma, Maki Iida, Kei Hagiwara, Masatoshi BMC Mol Biol Research Article BACKGROUND: Recent advances in the development of small chemical compounds that can modulate RNA splicing brought excitement to the field of splicing-targeting therapy. Splicing-targeting therapy tries to ameliorate the disease by altering the exon combination of transcripts to reduce the undesired effect of genetic mutations. However, the knowledge and tools to understand factors contributing to splicing modulator compound sensitivity have been lacking. Our goal was to establish a method to characterize sequence features found in compound sensitive exons. RESULTS: Here we developed a comparative transcriptomic approach to explore features that make an exon sensitive to a chemical compound. In this study, we chose TG003, a potential drug for Duchenne muscular dystrophy, and performed RNA-sequencing on samples from human and mouse skeletal muscle cells, with and without TG003 treatments. We compared TG003 responsiveness between homologous exon pairs and identified 21 pairs in which human exons were skip-enhanced but not mouse exons. We compared the sequence features; splice site scores, number of splicing factor binding sites, and properties of branch sequence and polypyrimidine tracts, and found that polypyrimidine tracts were stronger (longer stretches and richer content of consecutive polypyrimidine) in the mouse TG003 insensitive exons. We also compared the features between TG003 skip-enhanced and insensitive exons within the species, and discovered that human TG003 skip-enhanced exons were shorter and had less splicing factor binding sites than the group of human TG003 insensitive exons. Mouse insensitive exons homologous to human TG003 skip-enhanced exons shared these properties. Our results suggested that these features are prerequisites for TG003 skip-enhanced exons and weak polypyrimidine tracts are defining features, which were supported by a decision tree analysis on all cassette exons in human. CONCLUSIONS: In this study we established a comparative transcriptomic approach, which shed lights on how small chemical compounds modulate RNA splicing. The results described here was the first attempt to decipher the targeting rules of a splicing modulator compound. We expect that this approach would contribute to the precise understanding of the mechanism of TG003-induced splicing modulation, expand target diseases of splicing modulators in general, as well as the development of new splicing modulators. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/s12867-015-0044-6) contains supplementary material, which is available to authorized users. BioMed Central 2015-09-24 /pmc/articles/PMC4580995/ /pubmed/26400733 http://dx.doi.org/10.1186/s12867-015-0044-6 Text en © Sakuma et al. 2015 Open AccessThis article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided 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 Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.
spellingShingle Research Article
Sakuma, Maki
Iida, Kei
Hagiwara, Masatoshi
Deciphering targeting rules of splicing modulator compounds: case of TG003
title Deciphering targeting rules of splicing modulator compounds: case of TG003
title_full Deciphering targeting rules of splicing modulator compounds: case of TG003
title_fullStr Deciphering targeting rules of splicing modulator compounds: case of TG003
title_full_unstemmed Deciphering targeting rules of splicing modulator compounds: case of TG003
title_short Deciphering targeting rules of splicing modulator compounds: case of TG003
title_sort deciphering targeting rules of splicing modulator compounds: case of tg003
topic Research Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4580995/
https://www.ncbi.nlm.nih.gov/pubmed/26400733
http://dx.doi.org/10.1186/s12867-015-0044-6
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