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Biomolecules
Special Issues
Omics Approaches to Understanding Skeletal Muscle Biology
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Omics Approaches to Understanding Skeletal Muscle Biology

A special issue of Biomolecules (ISSN 2218-273X). This special issue belongs to the section "Bioinformatics and Systems Biology".

Deadline for manuscript submissions: closed (20 June 2022) | Viewed by 11384

Special Issue Editors

Prof. Dr. Zhonglin Tang

E-Mail Website
Guest Editor
Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518124, China
Interests: Skeletal muscle; Myogenesis; Gene Expression; Non-coding RNAs; Regulation Network; Epigenetics; Functional genomics; Multi-omics
Prof. Dr. Qinghua Nie

E-Mail Website
Guest Editor
College of Animal Science, South China Agricultural University, Guangzhou 510642, China
Interests: poultry genetics and breeding; genomics; bioinformation
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

Skeletal muscle is the most abundant tissue, accounting for 30–40% of body mass in adult humans and 35–60% of that in domesticated animals. It is well known that skeletal muscle development is an extremely complex regulatory process orchestrated by myogenic genes, transcription factors, and noncoding RNAs. However, the regulatory mechanisms of skeletal muscle biology at different levels, such as histone modification, RNA editing, splicing, and RNA methylation, still need to be explored. In past decades, we have witnessed the rapid development of high-throughput multi-omics technologies, which provides a powerful tool for understanding skeletal muscle biology. This Special Issue aims to integrate multi-omics data, such as genomics, transcriptomics, proteomics, and metabolomics, to construct interaction networks and deeply explore the regulatory mechanism of skeletal muscle development, regeneration, aging, diseases and other related areas. We welcome both experimental and bioinformatics studies proving mechanistic insights into skeletal muscle biology. Both original research and review papers are welcome.

Prof. Dr. Zhonglin Tang
Prof. Dr. Qinghua Nie
Guest Editors

Manuscript Submission Information

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All submissions that pass pre-check are peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as short communications are invited. For planned papers, a title and short abstract (about 100 words) can be sent to the Editorial Office for announcement on this website.

Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. Biomolecules is an international peer-reviewed open access monthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 2700 CHF (Swiss Francs). Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

Keywords

  • Skeletal muscle
  • Myogenesis
  • Regulation network
  • Gene expression
  • Functional genomics

Published Papers (4 papers)

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Research

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24 pages, 12284 KiB  
Article
Comparative Transcriptomic Analysis of mRNAs, miRNAs and lncRNAs in the Longissimus dorsi Muscles between Fat-Type and Lean-Type Pigs
by Jian Zhang, Jiying Wang, Cai Ma, Wenlei Wang, Heng Wang and Yunliang Jiang
Biomolecules 2022, 12(9), 1294; https://doi.org/10.3390/biom12091294 - 13 Sep 2022
Cited by 6 | Viewed by 2898
Abstract
In pigs, meat quality and production are two important traits affecting the pig industry and human health. Compared to lean-type pigs, fat-type pigs contain higher intramuscular fat (IMF) contents, better taste and nutritional value. To uncover genetic factors controlling differences related to IMF [...] Read more.
In pigs, meat quality and production are two important traits affecting the pig industry and human health. Compared to lean-type pigs, fat-type pigs contain higher intramuscular fat (IMF) contents, better taste and nutritional value. To uncover genetic factors controlling differences related to IMF in pig muscle, we performed RNA-seq analysis on the transcriptomes of the Longissimus dorsi (LD) muscle of Laiwu pigs (LW, fat-type pigs) and commercial Duroc × Landrace × Yorkshire pigs (DLY, lean-type pigs) at 150 d to compare the expression profiles of mRNA, miRNA and lncRNA. A total of 225 mRNAs, 12 miRNAs and 57 lncRNAs were found to be differentially expressed at the criteria of |log2(foldchange)| > 1 and q < 0.05. The mRNA expression of LDHB was significantly higher in the LD muscle of LW compared to DLY pigs with log2(foldchange) being 9.66. Using protein interaction prediction method, we identified more interactions of estrogen-related receptor alpha (ESRRA) associated with upregulated mRNAs, whereas versican (VCAN) and proenkephalin (PENK) were associated with downregulated mRNAs in LW pigs. Integrated analysis on differentially expressed (DE) mRNAs and miRNAs in the LD muscle between LW and DLY pigs revealed two network modules: between five upregulated mRNA genes (GALNT15, FKBP5, PPARGC1A, LOC110258214 and LOC110258215) and six downregulated miRNA genes (ssc-let-7a, ssc-miR190-3p, ssc-miR356-5p, ssc-miR573-5p, ssc-miR204-5p and ssc-miR-10383), and between three downregulated DE mRNA genes (IFRD1, LOC110258600 and LOC102158401) and six upregulated DE miRNA genes (ssc-miR1379-3p, ssc-miR1379-5p, ssc-miR397-5p, ssc-miR1358-5p, ssc-miR299-5p and ssc-miR1156-5p) in LW pigs. Based on the mRNA and ncRNA binding site targeting database, we constructed a regulatory network with miRNA as the center and mRNA and lncRNA as the target genes, including GALNT15/ssc-let-7a/LOC100523888, IFRD1/ssc-miR1379-5p/CD99, etc., forming a ceRNA network in the LD muscles that are differentially expressed between LW and DLY pigs. Collectively, these data may provide resources for further investigation of molecular mechanisms underlying differences in meat traits between lean- and fat-type pigs. Full article
(This article belongs to the Special Issue Omics Approaches to Understanding Skeletal Muscle Biology)
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14 pages, 3786 KiB  
Article
miR-27b-3p Attenuates Muscle Atrophy by Targeting Cbl-b in Skeletal Muscles
by Xin Yang, Zhenhui Li, Zhijun Wang, Jiaao Yu, Manting Ma and Qinghua Nie
Biomolecules 2022, 12(2), 191; https://doi.org/10.3390/biom12020191 - 23 Jan 2022
Cited by 5 | Viewed by 3040
Abstract
As it is well known, muscle atrophy is a process in which protein degradation increases and protein synthesis decreases. This process is regulated by a variety of links. Among them, microRNAs play an essential role in this process, which has attracted widespread attention. [...] Read more.
As it is well known, muscle atrophy is a process in which protein degradation increases and protein synthesis decreases. This process is regulated by a variety of links. Among them, microRNAs play an essential role in this process, which has attracted widespread attention. In this paper, we find that miR-27b-3p and Cbl-b genes are significantly differentially expressed in the induced atrophy model. The dual-luciferase experiment and Western blot analysis confirmed that miR-27b-3p could regulate the expression of Cbl-b. In C2C12-differentiated myotubes, the overexpression of the Cbl-b gene showed that Cbl-b could upregulate the expression of MuRF-1 and Atrogin-1, which are related marker genes of muscle atrophy, at both the mRNA and protein levels, indicating that the Cbl-b gene can specifically affect muscle atrophy. The knockdown of the Cbl-b gene after C2C12-differentiated myotubes induced atrophy treatment can downregulate the expression of muscle-atrophy-related genes, indicating that manual intervention to downregulate the expression of Cbl-b has a certain alleviating effect on muscle atrophy. These data suggest that miR-27b-3p can regulate the expression of the Cbl-b gene and then exert a particular influence on muscle atrophy through the Cbl-b gene. Full article
(This article belongs to the Special Issue Omics Approaches to Understanding Skeletal Muscle Biology)
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17 pages, 26188 KiB  
Article
Characterization of Alternative Splicing Events in Porcine Skeletal Muscles with Different Intramuscular Fat Contents
by Wanjun Hao, Zewei Yang, Yuanlu Sun, Jiaxin Li, Dongjie Zhang, Di Liu and Xiuqin Yang
Biomolecules 2022, 12(2), 154; https://doi.org/10.3390/biom12020154 - 18 Jan 2022
Cited by 11 | Viewed by 2419
Abstract
Meat quality is one of the most important economic traits in pig breeding and production. Intramuscular fat (IMF) is a major factor that improves meat quality. To better understand the alternative splicing (AS) events underlying meat quality, long-read isoform sequencing (Iso-seq) was used [...] Read more.
Meat quality is one of the most important economic traits in pig breeding and production. Intramuscular fat (IMF) is a major factor that improves meat quality. To better understand the alternative splicing (AS) events underlying meat quality, long-read isoform sequencing (Iso-seq) was used to identify differential (D)AS events between the longissimus thoracis (LT) and semitendinosus (ST), which differ in IMF content, together with short-read RNA-seq. Through Iso-seq analysis, we identified a total of 56,789 novel transcripts covering protein-coding genes, lncRNA, and fusion transcripts that were not previously annotated in pigs. We also identified 456,965 AS events, among which 3930 were DAS events, corresponding to 2364 unique genes. Through integrative analysis of Iso-seq and RNA-seq, we identified 1174 differentially expressed genes (DEGs), among which 122 were DAS genes, i.e., DE-DAS genes. There are 12 overlapped pathways between the top 20 DEGs and DE-DAS genes, as revealed by KEGG (Kyoto Encyclopedia of Genes and Genomes) analysis, indicating that DE-DAS genes play important roles in the differential phenotype of LT and ST. Further analysis showed that upregulated DE-DAS genes are more important than downregulated ones in IMF deposition. Fatty acid degradation and the PPAR (peroxisome proliferator-activated receptor) signaling pathway were found to be the most important pathways regulating the differential fat deposition of the two muscles. The results update the existing porcine genome annotations and provide data for the in-depth exploration of the mechanisms underlying meat quality and IMF deposition. Full article
(This article belongs to the Special Issue Omics Approaches to Understanding Skeletal Muscle Biology)
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Review

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18 pages, 782 KiB  
Review
Recent Progress on Circular RNAs in the Development of Skeletal Muscle and Adipose Tissues of Farm Animals
by Shanying Yan, Yangli Pei, Jiju Li, Zhonglin Tang and Yalan Yang
Biomolecules 2023, 13(2), 314; https://doi.org/10.3390/biom13020314 - 7 Feb 2023
Cited by 4 | Viewed by 2118
Abstract
Circular RNAs (circRNAs) are a highly conserved and specifically expressed novel class of covalently closed non-coding RNAs. CircRNAs can function as miRNA sponges, protein scaffolds, and regulatory factors, and play various roles in development and other biological processes in mammals. With the rapid [...] Read more.
Circular RNAs (circRNAs) are a highly conserved and specifically expressed novel class of covalently closed non-coding RNAs. CircRNAs can function as miRNA sponges, protein scaffolds, and regulatory factors, and play various roles in development and other biological processes in mammals. With the rapid development of high-throughput sequencing technology, thousands of circRNAs have been discovered in farm animals; some reportedly play vital roles in skeletal muscle and adipose development. These are critical factors affecting meat yield and quality. In this review, we have highlighted the recent advances in circRNA-related studies of skeletal muscle and adipose in farm animals. We have also described the biogenesis, properties, and biological functions of circRNAs. Furthermore, we have comprehensively summarized the functions and regulatory mechanisms of circRNAs in skeletal muscle and adipose development in farm animals and their effects on economic traits such as meat yield and quality. Finally, we propose that circRNAs are putative novel targets to improve meat yield and quality traits during animal breeding. Full article
(This article belongs to the Special Issue Omics Approaches to Understanding Skeletal Muscle Biology)
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