Genome-Wide Analysis Reveals Extensive Changes in LncRNAs during Skeletal Muscle Development in Hu Sheep

AbstractDNA methylation is an important epigenetic modification in vertebrate and is essential for epigenetic gene regulation in skeletal muscle development. We showed the genome-wide DNA methylation profile in skeletal muscle tissue of larval 7dph (JP1), juvenile 90dph (JP2), adult female 24 months (JP3) and adult male 24 months (JP4) Japanese flounder. The distribution and levels of methylated DNA within genomic features (1stexons, gene body, introns, TSS200, TSS1500 and intergenic) show different developmental landscapes. We also successfully identified differentially methylated regions (DMRs) and different methylated genes (DMGs) through a comparative analysis, indicating that DMR in gene body, intron and intergenic regions were more compared to other regions of all DNA elements. A gene ontology analysis indicated that the DMGs were mainly related to regulation of skeletal muscle fiber development process, Axon guidance, Adherens junction, and some ATPase activity. Methylome and transcriptome clearly revealed a exhibit a negative correlation. And integration analysis revealed a total of 425, 398 and 429 negatively correlated genes with methylation in the JP2_VS_JP1, JP3_VS_JP1 and JP4_VS_JP1 comparison groups, respectively. And these genes were functionally associated with pathways including Adherens junction, Axon guidance, Focal adhesion, cell junctions, Actin cytoskeleton and Wnt signaling pathways. In addition, we validated the MethylRAD results by bisulfite sequencing PCR (BSP) in some of the differentially methylated skeletal muscle growth-related genes (Myod1, Six1 and Ctnnb1). In this study, we have generated the genome-wide profile of methylome and transcriptome in Japanese flounder for the first time, and our results bring new insights into the epigenetic regulation of developmental processes in Japanese flounder. This study contributes to the knowledge on epigenetics in vertebrates.Author summaryEpigenetic mechanisms like DNA methylation have recently reported as vital regulators of some species skeletal muscle development through the control of genes related to growth. To date, although genome-wide DNA methylation profiles of many organisms have been reported and the Japanese flounder reference genome and whole transcriptome data are publically available, the methylation pattern of Japanese flounder skeletal muscle tissue remains minimally studied and the global DNA methylation data are yet to be known. Here we investigated the genome-wide DNA methylation patterns in Japanese flounder, throughout its development. These findings help to enrich research in molecular and developmental biology in vertebrates.

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The SMYD3 methyltransferase promotes myogenesis by activating the myogenin regulatory network

Scientific Reports ◽

10.1038/s41598-019-53577-5 ◽

2019 ◽

Vol 9 (1) ◽

Cited By ~ 4

Author(s):

Roberta Codato ◽

Martine Perichon ◽

Arnaud Divol ◽

Ella Fung ◽

Athanassia Sotiropoulos ◽

...

Keyword(s):

Skeletal Muscle ◽

Muscle Development ◽

Myogenic Differentiation ◽

Muscle Differentiation ◽

Skeletal Muscle Differentiation ◽

Skeletal Muscle Development ◽

Genome Wide ◽

Coordinated Expression

AbstractThe coordinated expression of myogenic regulatory factors, including MyoD and myogenin, orchestrates the steps of skeletal muscle development, from myoblast proliferation and cell-cycle exit, to myoblast fusion and myotubes maturation. Yet, it remains unclear how key transcription factors and epigenetic enzymes cooperate to guide myogenic differentiation. Proteins of the SMYD (SET and MYND domain-containing) methyltransferase family participate in cardiac and skeletal myogenesis during development in zebrafish, Drosophila and mice. Here, we show that the mammalian SMYD3 methyltransferase coordinates skeletal muscle differentiation in vitro. Overexpression of SMYD3 in myoblasts promoted muscle differentiation and myoblasts fusion. Conversely, silencing of endogenous SMYD3 or its pharmacological inhibition impaired muscle differentiation. Genome-wide transcriptomic analysis of murine myoblasts, with silenced or overexpressed SMYD3, revealed that SMYD3 impacts skeletal muscle differentiation by targeting the key muscle regulatory factor myogenin. The role of SMYD3 in the regulation of skeletal muscle differentiation and myotube formation, partially via the myogenin transcriptional network, highlights the importance of methyltransferases in mammalian myogenesis.

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The SMYD3 methyltransferase promotes myogenesis by activating the myogenin regulatory network

10.1101/804633 ◽

2019 ◽

Author(s):

Roberta Codato ◽

Martine Perichon ◽

Arnaud Divol ◽

Ella Fung ◽

Athanassia Sotiropoulos ◽

...

Keyword(s):

Skeletal Muscle ◽

Muscle Development ◽

Myogenic Differentiation ◽

Muscle Differentiation ◽

Skeletal Muscle Differentiation ◽

Skeletal Muscle Development ◽

Genome Wide ◽

Coordinated Expression

ABSTRACTThe coordinated expression of myogenic regulatory factors, including MyoD and myogenin, orchestrates the steps of skeletal muscle development, from myoblast proliferation and cell-cycle exit, to myoblast fusion and myotubes maturation. Yet, it remains unclear how key transcription factors and epigenetic enzymes cooperate to guide myogenic differentiation. Proteins of the SMYD (SET and MYND domain-containing) methyltransferase family participate in cardiac and skeletal myogenesis during development in zebrafish, Drosophila and mice. Here, we show that the mammalian SMYD3 methyltransferase coordinates skeletal muscle differentiation in vitro. Overexpression of SMYD3 in myoblasts promoted muscle differentiation and myoblasts fusion. Conversely, silencing of endogenous SMYD3 or its pharmacological inhibition impaired muscle differentiation. Genome-wide transcriptomic analysis of murine myoblasts, with silenced or overexpressed SMYD3, revealed that SMYD3 impacts skeletal muscle differentiation by targeting the key muscle regulatory factor myogenin. The role of SMYD3 in the regulation of skeletal muscle differentiation and myotube formation, partially via the myogenin transcriptional network, highlights the importance of methyltransferases in mammalian myogenesis.

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Effect of protein nutrition and amino acid balance early in life on porcine skeletal muscle development

10.31274/rtd-180813-3788 ◽

1976 ◽

Author(s):

Maynard Gordon Hogberg

Keyword(s):

Skeletal Muscle ◽

Amino Acid ◽

Muscle Development ◽

Skeletal Muscle Development ◽

Protein Nutrition ◽

Amino Acid Balance

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Effect of protein nutrition and amino acid balance early in life on porcine skeletal muscle development

10.31274/rtd-180817-3788 ◽

1976 ◽

Author(s):

Maynard Gordon Hogberg

Keyword(s):

Skeletal Muscle ◽

Amino Acid ◽

Muscle Development ◽

Skeletal Muscle Development ◽

Protein Nutrition ◽

Amino Acid Balance

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Key Genes Regulating Skeletal Muscle Development and Growth in Farm Animals

Animals ◽

10.3390/ani11030835 ◽

2021 ◽

Vol 11 (3) ◽

pp. 835

Author(s):

Mohammadreza Mohammadabadi ◽

Farhad Bordbar ◽

Just Jensen ◽

Min Du ◽

Wei Guo

Keyword(s):

Skeletal Muscle ◽

Candidate Genes ◽

Meat Quality ◽

Muscle Development ◽

Muscle Growth ◽

Farm Animals ◽

Meat Production ◽

Skeletal Muscle Development ◽

Extrinsic Factors ◽

Myogenic Regulatory Factor

Farm-animal species play crucial roles in satisfying demands for meat on a global scale, and they are genetically being developed to enhance the efficiency of meat production. In particular, one of the important breeders’ aims is to increase skeletal muscle growth in farm animals. The enhancement of muscle development and growth is crucial to meet consumers’ demands regarding meat quality. Fetal skeletal muscle development involves myogenesis (with myoblast proliferation, differentiation, and fusion), fibrogenesis, and adipogenesis. Typically, myogenesis is regulated by a convoluted network of intrinsic and extrinsic factors monitored by myogenic regulatory factor genes in two or three phases, as well as genes that code for kinases. Marker-assisted selection relies on candidate genes related positively or negatively to muscle development and can be a strong supplement to classical selection strategies in farm animals. This comprehensive review covers important (candidate) genes that regulate muscle development and growth in farm animals (cattle, sheep, chicken, and pig). The identification of these genes is an important step toward the goal of increasing meat yields and improves meat quality.

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