Ontology highlight
ABSTRACT:
PROVIDER: PRJNA699042 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR13615828.fastq.gz | Fastqsanger.gz | |||
| SRR13615829.fastq.gz | Fastqsanger.gz | |||
| SRR13615830.fastq.gz | Fastqsanger.gz | |||
| SRR13615831.fastq.gz | Fastqsanger.gz | |||
| SRR13615835.fastq.gz | Fastqsanger.gz |
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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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Project description:Purpose: MicroRNAs (miRNAs) are non-coding small miRNA ~22 nucleotides in length and play a vital role in muscle development by binding to messenger RNAs (mRNAs). Large White (LW, a lean type pig) and Meishan pigs (MS, a Chinese indigenous obese breed) have significant postnatal phenotype differences in growth rate, muscle mass and meat quality, and theses difference are programmed during prenatal muscle development.To shed directly light on the miRNA transcriptome difference in prenatal muscles between these two distinct pig breeds. Methods: skeletal musle miRNA profiles of Meishan pig and large white pig were generated by deep sequencing, in triplicate, using Illumina Hiseq2000 . The sequence reads that passed quality filters were analyzed at the mature miRNA level . qRT–PCR validation was performed using TaqMan and SYBR Green assays Results: We measure the myofiber phenotypes of LW and MS at developmental stages of 35, 55 and 90 days post-conception (dpc). Results shows that the myogenesis process is more intense in MS than in LW at 35 dpc. To investigate the role of miRNAs involved in regulating muscle development at earlier stages of myogenesis and decipher the miRNAs transcriptome difference between LW and MS, here, the miRNAomes of longissimus dorsi muscle collected at 35 dpc from female LW and MS were analyzed by deep sequencing. Overall, we identified 1147 unique miRNAs comprising 434 known miRNAs, 239 conserved miRNAs and 474 candidate miRNAs. Expression analysis of the 10 most abundant miRANs in every library indicated that functional miRNAome may be smaller and tend to be highly expressed. These set of miRNA may play house keeping roles that were involved in myogenesis. A total of 87 miRNAs were significantly differentially expressed between LW and MS (reads > 1000, P < 0.05). Gene ontology (GO) and KEGG pathway enrichment analysis revealed that the differentially expressed miRNAs (DE miRNAs) were associated mainly with muscle contraction, WNT, mTOR, and MAPK signaling pathways. In addition, the expression patterns of myomiRs (miR-1,-133,-206) at three prenatal stages (35,55 and 90 dpc) were determined using qRT-PCR, Notably, ssc-miR-133 was significantly more highly expressed in LW pig skeletal muscle at all prenatal stages compared with its expression in LW pig skeletal muscle. We concluded that the higher expression levels of miR-133 in MS, possibly regulated by myoD, are potential strategies for improvement of myogenesis in earlier prenatal stages. Conclusions: our results add new information to existing data on porcine miRNAs and be helpful to investigate the dominant (main functional) muscle-related miRNAs sets in different pig breeds. In addition, this study provide a profound knowledge on the role of miRNAs in prenatal muscle development, which could provide great reference value for pork quality improvement.
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