Integrated miRNA–mRNA transcriptomic analysis reveals epigenetic-mediated embryonic muscle growth differences between Wuzhishan and Landrace pigs1

Zhang, Xumeng; Cai, Shaohui; Chen, Luxi; Yuan, Renqiang; Nie, Yaping; Ding, Suying; Fāng, Yīng; Zhu, Qi; Chen, Keren; Wang, Hong; Chen, Yaosheng; Mo, Delin

doi:10.1093/jas/skz091

Cited by 15 publications

(10 citation statements)

References 35 publications

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“…Multiple genes are targeted by a single miRNA and multiple miRNAs can target a single gene, which makes miRNAs a major player in gene regulation and important biological processes, including fetal and placental development [9][10][11]. Several studies have showed the role of miRNAs and their target genes in skeletal muscle development at different prenatal and postnatal stages across different breeds of pigs [7,[12][13][14][15][16][17].…”

Section: Introductionmentioning

confidence: 99%

“…The number and density of myoblasts and myogenesis intensity also varies with the animal species and breed. For instance, prenatal myogenesis intensity and the number of myoblasts are higher in fat pig breeds compared to lean pig breeds [7,14,20]. In addition to variation in myogenesis intensity, the expression of miRNAs and genes regulating muscle development also differs across different pig breeds.…”

Section: Introductionmentioning

confidence: 99%

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In Utero Fetal Weight in Pigs Is Regulated by microRNAs and Their Target Genes

Ali

Muráni

Hadlich

et al. 2021

Genes

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Impaired skeletal muscle growth in utero can result in reduced birth weight and poor carcass quality in pigs. Recently, we showed the role of microRNAs (miRNAs) and their target genes in prenatal skeletal muscle development and pathogenesis of intrauterine growth restriction (IUGR). In this study, we performed an integrative miRNA-mRNA transcriptomic analysis in longissimus dorsi muscle (LDM) of pig fetuses at 63 days post conception (dpc) to identify miRNAs and genes correlated to fetal weight. We found 13 miRNAs in LDM significantly correlated to fetal weight, including miR-140, miR-186, miR-101, miR-15, miR-24, miR-29, miR-449, miR-27, miR-142, miR-99, miR-181, miR-199, and miR-210. The expression of these miRNAs decreased with an increase in fetal weight. We also identified 1315 genes significantly correlated to fetal weight at 63 dpc, of which 135 genes were negatively correlated as well as identified as potential targets of the above-listed 13 miRNAs. These miRNAs and their target genes enriched pathways and biological processes important for fetal growth, development, and metabolism. These results indicate that the transcriptomic profile of skeletal muscle can be used to predict fetal weight, and miRNAs correlated to fetal weight can serve as potential biomarkers of prenatal fetal health and growth.

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Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

In Utero Fetal Weight in Pigs Is Regulated by microRNAs and Their Target Genes

Ali

Muráni

Hadlich

et al. 2021

Genes

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“…ACTNs (α-actinins) are widely expressed cytoskeleton proteins that cross-link actin filaments at the adherens junctions in epithelial and focal adhesions at the leading edge of migrating cells [ 55 , 56 ], and play a key role in the maintenance and regulation of the cytoskeleton. In mammalian cells, there are four kinds of ACTNs, which are the components of all three kinds of stress fibers (ventral stress fibers, dorsal stress fibers, and transverse arcs) [ 57 , 58 ]. ACTN 3 is a prominent actin filament associated protein that is expressed in skeletal muscle [ 59 ], and its function is to maintain the microfilament spacing at the Z-disc.…”

Section: Discussionmentioning

confidence: 99%

Skeletal Muscle Transcriptome Analysis of Hanzhong Ma Duck at Different Growth Stages Using RNA-Seq

Cao

Zhang

et al. 2021

Biomolecules

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As one of the most important poultry worldwide, ducks (Anas platyrhynchos) are raised mainly for meat and egg products, and muscle development in ducks is important for meat production. Therefore, an investigation of gene expression in duck skeletal muscle would significantly contribute to our understanding of muscle development. In this study, twenty-four cDNA libraries were constructed from breast and leg muscles of Hanzhong Ma ducks at day 17, 21, 27 of the embryo and postnatal at 6-month-old. High-throughput sequencing and bioinformatics were used to determine the abundances and characteristics of transcripts. A total of 632,172,628 (average 52,681,052) and 637,213,938 (average 53,101,162) reads were obtained from the sequencing data of breast and leg muscles, respectively. Over 71.63% and 77.36% of the reads could be mapped to the Anas platyrhynchos genome. In the skeletal muscle of Hanzhong duck, intron variant (INTRON), synonymous variant (SYNONYMOUS_CODING), and prime 3′ UTR variant (UTR_3_PRIME) were the main single nucleotide polymorphisms (SNP) annotation information, and “INTRON”, “UTR_3_PRIME”, and downstream-gene variant (DOWNSTREAM) were the main insertion-deletion (InDel) annotation information. The predicted number of alternative splicing (AS) in all samples were mainly alternative 5′ first exon (transcription start site)-the first exon splicing (TSS) and alternative 3′ last exon (transcription terminal site)-the last exon splicing (TTS). Besides, there were 292 to 2801 annotated differentially expressed genes (DEGs) in breast muscle and 304 to 1950 annotated DEGs in leg muscle from different databases. It is worth noting that 75 DEGs in breast muscle and 49 DEGs in leg muscle were co-expressed at all developmental points of comparison, respectively. The RNA-Seq data were confirmed to be reliable by qPCR. The identified DEGs, such as CREBL2, RHEB, GDF6, SHISA2, MYLK2, ACTN3, RYR3, and STMN1, were specially highlighted, indicating their strong associations with muscle development in the Hanzhong Ma duck. KEGG pathway analysis suggested that regulation of actin cytoskeleton, oxidative phosphorylation, and focal adhesion were involved in the development of skeletal muscle. The findings from this study can contribute to future investigations of the growth and development mechanism in duck skeletal muscle.

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“…A single miRNA can regulate the expression of multiple genes through post-transcriptional repression and epigenetic regulation, making miRNAs the major regulators of gene expression [ 28 , 29 , 30 , 31 , 32 ]. Several studies have shown the role of miRNAs and their target genes in skeletal muscle growth and development at different prenatal and postnatal stages across different breeds of pigs [ 23 , 33 , 34 , 35 , 36 , 37 , 38 ].…”

Section: Introductionmentioning

confidence: 99%

Prenatal Skeletal Muscle Transcriptome Analysis Reveals Novel MicroRNA-mRNA Networks Associated with Intrauterine Growth Restriction in Pigs

Ali

Muráni

Hadlich

et al. 2021

Cells

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Intrauterine growth restriction (IUGR) occurs in 15–20% of pig neonates and poses huge economic losses to the pig industry. IUGR piglets have reduced skeletal muscle growth, which may persist after birth. Prenatal muscle growth is regulated by complex molecular pathways that are not well understood. MicroRNAs (miRNAs) have emerged as the main regulators of vital pathways and biological processes in the body. This study was designed to identify miRNA–mRNA networks regulating prenatal skeletal muscle development in pigs. We performed an integrative miRNA–mRNA transcriptomic analysis in longissimus dorsi muscle from IUGR fetuses and appropriate for gestational age (AGA) fetuses at 63 days post conception. Our data showed that 47 miRNAs and 3257 mRNAs were significantly upregulated, and six miRNAs and 477 mRNAs were significantly downregulated in IUGR compared to AGA fetuses. Moreover, 47 upregulated miRNAs were negatively correlated and can potentially target 326 downregulated genes, whereas six downregulated miRNAs were negatively correlated and can potentially target 1291 upregulated genes. These miRNA–mRNA networks showed enrichment in biological processes and pathways critical for fetal growth, development, and metabolism. The miRNA–mRNA networks identified in this study can potentially serve as indicators of prenatal fetal growth and development as well as postnatal carcass quality.

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Integrated miRNA–mRNA transcriptomic analysis reveals epigenetic-mediated embryonic muscle growth differences between Wuzhishan and Landrace pigs1

Cited by 15 publications

References 35 publications

In Utero Fetal Weight in Pigs Is Regulated by microRNAs and Their Target Genes

In Utero Fetal Weight in Pigs Is Regulated by microRNAs and Their Target Genes

Skeletal Muscle Transcriptome Analysis of Hanzhong Ma Duck at Different Growth Stages Using RNA-Seq

Prenatal Skeletal Muscle Transcriptome Analysis Reveals Novel MicroRNA-mRNA Networks Associated with Intrauterine Growth Restriction in Pigs

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