Transcriptomic dissection of myogenic differentiation signature in caprine by RNA-Seq
Open accessAbstract
Muscle growth and development from the embryonic to the adult stage of an organism consists of a series of exquisitely regulated and orchestrated changes in expression of genes leading to muscle maturation. In this study, we performed whole transcriptome profiling of adult caprine skeletal muscle derived myoblast and fused myotubes. Using Ion Torrent PGM sequencing platform, a total of 948,776 and 799,976 reads were generated in myoblasts and fused myotubes, respectively. The sequence reads were analyzed on CLC Genomics Workbench using Bos taurus RNA database to study the gene expression in both stages to study different genes responsible for muscle development and regeneration. The up and down-regulated genes were analyzed for gene ontology (GO) and KEGG pathways by Database for Annotation, Visualization and Integrated Discovery (DAVID) database. We found many genes exclusive to multinuclear fused myotubes and contractile nature of skeletal muscle, whereas up-regulated genes in myoblast stage were related to cell division and transcriptional regulation. Out of 27 genes selected for expression validation by RT-qPCR (reverse transcriptase-quantitative polymerase chain reaction), 19 genes showed the expression pattern comparable with CLC Genomics Workbench findings. Further, mRNA originated muscle specific microRNAs (miRNA-1 and miRNA-133b) were also observed in the fused myotubes along with other miRNAs with possible importance in muscle development. This study highlights important genes responsible for muscle development and differentiation in adult skeletal muscle system.
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The recommendations and most of the observations presented are likely to be applicable to any sequencing platform used for RNA-seq.
“the recommendations and most of our observations presented here will likely be applicable to any sequencing platform used for RNA-seq46,47.”
From Detecting and correcting systematic variation in large-scale RNA sequencing data (2014) · cites this paper as [47]
Many aspects of library preparation and normalization, including isolation, purification, priming, amplification, reagent batch and kit version, are universal to working with RNA.
“Because many aspects of library preparation and normalization are universal aspects of working with RNA, including isolation, purification, priming, amplification, reagent batch and kit version”
From Detecting and correcting systematic variation in large-scale RNA sequencing data (2014) · cites this paper as [47]
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- Authors
- Tripathi, A. K., Patel, A. K., Shah, R. K., Patel, A. B., Shah, T. M., Bhatt, V. D., & Joshi, C. G.
- Affiliations
- Anand Agricultural University (IN)
- ORCID
- Venue
- Mechanisms of Development
- Publisher
- Elsevier BV
- Published
- 2014-05
- Volume
- 132
- Pages
- 79-92
- ISSN
- 0925-4773 (ISSN-L)
- OpenAlex
- W2022691086
- Cited by
- 18
- References
- 44
- Citations by year
- 2024: 1 · 2022: 5 · 2021: 2 · 2020: 1 · 2019: 3 · 2017: 3 · 2016: 2 · 2014: 1
- FWCI
- 0.82
- Type
- journal article
- Language
- en
- Open access
- bronze
- doi.org
- Licence
- Locations
- Mechanisms of Development (publishedVersion)
- PubMed (publishedVersion)
- Funders
- National Agriculture Innovation Project, Indian council of Agricultural Research (NAIP-ICAR), Government of India
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Muscle Physiology and Disorders
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Developmental Biology and Gene Regulation
- Life Sciences › Agricultural and Biological Sciences › Animal Science and Zoology › Meat and Animal Product Quality
- Keywords
- myogenesis, myoblasts, myotubes, gene expression profiling, muscle regeneration, miR-1, miR-133b, muscle-specific microRNAs
- MeSH terms
- Animals, Cell Differentiation, Cells, Cultured, Goats, RNA, Transcription, Genetic, Down-Regulation, Up-Regulation, Muscle Fibers, Skeletal, Gene Expression Regulation, Developmental, Gene Expression Profiling, Muscle Development, Myoblasts, Skeletal, MicroRNAs, Transcriptome
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