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Prenatal skeletal muscle transcriptome analysis reveals novel microRNA-mRNA networks associated with intrauterine growth restriction in pigs

ABSTRACT: Prenatal skeletal muscle transcriptome analysis reveals novel microRNA-mRNA networks associated with intrauterine growth restriction in pigs

PROVIDER: PRJNA715199 | ENA |

REPOSITORIES: ENA

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Prenatal skeletal muscle transcriptome with intrauterine growth restriction in pigs [mRNA]

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Project description:We generated transcriptome profiles of skeletal muscles from Largewhite pigs at 35, 55, and 90 days of gestation (dg), using high-throughput deep sequencing methods. A large number of differentially expressed (DE) genes and miRNAs were identified between stages and dietary treatments. Interestingly, reduced maternal calorie supply led to significant changes in mRNA and miRNA expression patterns. Down-regulation of critical genes and miRNAs associated with increased cell growth and myoblast differentiation at certain stages was found to be responsible for repressed myofiber formation in calorie-restricted pigs. Moreover, an integrative analysis of the miRNA and mRNA using sequence-based target prediction and negative correlation of miRNA-mRNA profiles identified a number of novel miRNA-mRNA interactions that are potentially involved in prenatal myogenesis regulation. Importantly, some critical miRNA-mRNA interactions were validated. And we first proposed a miRNA-TF-mRNA regulatory loop, which significantly increased the number of biologically relevant targets of miRNAs and introduced new mechanisms underlying the nutrient-modulated myogenesis.

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

Project description: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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Prenatal skeletal muscle transcriptome with intrauterine growth restriction in pigs [miRNA]

Project description:Gene expression data of micro RNA from skeletal muscle samples of F2 population based DL and Pi F2 63 days post conception (dpc).

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Prenatal skeletal muscle transcriptome with intrauterine growth restriction in pigs [mRNA]

Project description:47,845 probe-sets were screened, in the first part of this study pig embryos at 63 days post conception (dpc).

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Prenatal skeletal muscle transcriptome analysis reveals novel microRNA-mRNA networks associated with intrauterine growth restriction in pigs

Project description:This SuperSeries is composed of the SubSeries listed below.

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Proteomic analysis of liver proteome affected by intrauterine growth restriction in newborn piglets.

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The proteome landscape of human placentas for monochorionic twins with selective intrauterine growth restriction

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A restricted repertoire of cytosine methylation changes in neonates following intrauterine growth restriction

Project description:Perturbations of the intrauterine environment can affect fetal development during critical periods of plasticity, and can increase susceptibility to a number of age-related diseases (e.g. type 2 diabetes mellitus; T2DM), manifesting sometimes decades later. We hypothesized that this biological memory is mediated by permanent alterations of the epigenome in stem cell populations. Our studies focused specifically on DNA methylation in CD34+ hematopoietic stem and progenitor cells from cord blood, and utilized a two-stage design involving genome-wide discovery followed by quantitative, single-locus validation. We found that changes in cytosine methylation occur in response to intrauterine growth restriction (IUGR), but that they are of a substantially lesser degree and involve many fewer loci than the epigenomic dysregulation observed in cancer. This is consistent with a comparable study of individuals born following maternal starvation during the Dutch famine. We also identify specific loci that are targeted for dysregulation of DNA methylation, in particular the hepatocyte nuclear factor 4Î± (HNF4A) gene, a well-known diabetes candidate gene not previously associated with growth restriction in utero, and other loci encoding HNF4A-interacting proteins. Our results give some insights into the potential contribution of epigenomic dysregulation in mediating the long-term consequences of IUGR, and demonstrate the value of this approach to studies of the fetal origin of adult disease. Direct comparison of DNA methylation in 10 neonatal CD34+ samples isolated from umbilical cord blood belonging to two groups: IUGR (n=5) and their age-matched controls (n=5). Each microarray consists of a two-color comparison of a methylation-sensitive representation of the genome (HpaII) with an internal methylation-insensitive control/reference (MspI).

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