Comparative analysis of the transcriptomes of EDL, psoas, and soleus muscles from mice
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RESEARCH ARTICLE
Open Access
Comparative analysis of the transcriptomes of EDL, psoas, and soleus muscles from mice Pabodha Hettige1,2, Uzma Tahir3, Kiisa C. Nishikawa3 and Matthew J. Gage1,2*
Abstract 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. Keywords: RNA sequencing, Fast-twitch muscle, Slow-twitch muscle, Transcriptome, Muscle specialization, Differential gene expression
Background Muscle sarcomere is a complex network of proteins that work together to generate force. Specific fiber types have evolved to express a unique array of proteins according to the tasks that muscles perform [1–3]. The basic principles associated with muscle contraction were established with * Correspondence: [email protected] 1 Department of Chemistry, University of Massachusetts Lowell, Lowell, MA 01854, USA 2 UMass Movement Center, University of Massachusetts Lowell, Lowell, MA 01854, USA Full list of author information is available at the end of the article
the development of the sliding filament model [4, 5]. However, there remain many unanswered questions associated with muscle function and the differences among skeletal muscle fiber types [2, 6, 7], even after close to a century of work. Transcriptomic variability among different types of skeletal muscle is one particular area that has been poorly characterized. A complete understanding o
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