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Comparative analysis of the transcriptomes of EDL, psoas, and soleus muscles from mice
BACKGROUND: Individual skeletal muscles have evolved to perform specific tasks based on their molecular composition. In general, muscle fibers are characterized as either fast-twitch or slow-twitch based on their myosin heavy chain isoform profiles. This approach made sense in the early days of musc...
Autores principales: | , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
BioMed Central
2020
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7678079/ https://www.ncbi.nlm.nih.gov/pubmed/33213377 http://dx.doi.org/10.1186/s12864-020-07225-2 |
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author | Hettige, Pabodha Tahir, Uzma Nishikawa, Kiisa C. Gage, Matthew J. |
author_facet | Hettige, Pabodha Tahir, Uzma Nishikawa, Kiisa C. Gage, Matthew J. |
author_sort | Hettige, Pabodha |
collection | PubMed |
description | BACKGROUND: Individual skeletal muscles have evolved to perform specific tasks based on their molecular composition. In general, muscle fibers are characterized as either fast-twitch or slow-twitch based on their myosin heavy chain isoform profiles. This approach made sense in the early days of muscle studies when SDS-PAGE was the primary tool for mapping fiber type. However, Next Generation Sequencing tools permit analysis of the entire muscle transcriptome in a single sample, which allows for more precise characterization of differences among fiber types, including distinguishing between different isoforms of specific proteins. We demonstrate the power of this approach by comparing the differential gene expression patterns of extensor digitorum longus (EDL), psoas, and soleus from mice using high throughput RNA sequencing. RESULTS: EDL and psoas are typically classified as fast-twitch muscles based on their myosin expression pattern, while soleus is considered a slow-twitch muscle. The majority of the transcriptomic variability aligns with the fast-twitch and slow-twitch characterization. However, psoas and EDL exhibit unique expression patterns associated with the genes coding for extracellular matrix, myofibril, transcription, translation, striated muscle adaptation, mitochondrion distribution, and metabolism. Furthermore, significant expression differences between psoas and EDL were observed in genes coding for myosin light chain, troponin, tropomyosin isoforms, and several genes encoding the constituents of the Z-disk. CONCLUSIONS: The observations highlight the intricate molecular nature of skeletal muscles and demonstrate the importance of utilizing transcriptomic information as a tool for skeletal muscle characterization. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s12864-020-07225-2. |
format | Online Article Text |
id | pubmed-7678079 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2020 |
publisher | BioMed Central |
record_format | MEDLINE/PubMed |
spelling | pubmed-76780792020-11-20 Comparative analysis of the transcriptomes of EDL, psoas, and soleus muscles from mice Hettige, Pabodha Tahir, Uzma Nishikawa, Kiisa C. Gage, Matthew J. BMC Genomics Research Article BACKGROUND: Individual skeletal muscles have evolved to perform specific tasks based on their molecular composition. In general, muscle fibers are characterized as either fast-twitch or slow-twitch based on their myosin heavy chain isoform profiles. This approach made sense in the early days of muscle studies when SDS-PAGE was the primary tool for mapping fiber type. However, Next Generation Sequencing tools permit analysis of the entire muscle transcriptome in a single sample, which allows for more precise characterization of differences among fiber types, including distinguishing between different isoforms of specific proteins. We demonstrate the power of this approach by comparing the differential gene expression patterns of extensor digitorum longus (EDL), psoas, and soleus from mice using high throughput RNA sequencing. RESULTS: EDL and psoas are typically classified as fast-twitch muscles based on their myosin expression pattern, while soleus is considered a slow-twitch muscle. The majority of the transcriptomic variability aligns with the fast-twitch and slow-twitch characterization. However, psoas and EDL exhibit unique expression patterns associated with the genes coding for extracellular matrix, myofibril, transcription, translation, striated muscle adaptation, mitochondrion distribution, and metabolism. Furthermore, significant expression differences between psoas and EDL were observed in genes coding for myosin light chain, troponin, tropomyosin isoforms, and several genes encoding the constituents of the Z-disk. CONCLUSIONS: The observations highlight the intricate molecular nature of skeletal muscles and demonstrate the importance of utilizing transcriptomic information as a tool for skeletal muscle characterization. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s12864-020-07225-2. BioMed Central 2020-11-19 /pmc/articles/PMC7678079/ /pubmed/33213377 http://dx.doi.org/10.1186/s12864-020-07225-2 Text en © The Author(s) 2020 Open AccessThis 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 licence, and indicate if changes were made. The images or other third party material in this article are included in the article's Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article's Creative Commons licence 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 licence, visit http://creativecommons.org/licenses/by/4.0/. 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 in a credit line to the data. |
spellingShingle | Research Article Hettige, Pabodha Tahir, Uzma Nishikawa, Kiisa C. Gage, Matthew J. Comparative analysis of the transcriptomes of EDL, psoas, and soleus muscles from mice |
title | Comparative analysis of the transcriptomes of EDL, psoas, and soleus muscles from mice |
title_full | Comparative analysis of the transcriptomes of EDL, psoas, and soleus muscles from mice |
title_fullStr | Comparative analysis of the transcriptomes of EDL, psoas, and soleus muscles from mice |
title_full_unstemmed | Comparative analysis of the transcriptomes of EDL, psoas, and soleus muscles from mice |
title_short | Comparative analysis of the transcriptomes of EDL, psoas, and soleus muscles from mice |
title_sort | comparative analysis of the transcriptomes of edl, psoas, and soleus muscles from mice |
topic | Research Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7678079/ https://www.ncbi.nlm.nih.gov/pubmed/33213377 http://dx.doi.org/10.1186/s12864-020-07225-2 |
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