Integrated analysis of miRNA and mRNA paired expression profiling of prenatal skeletal muscle development in three genotype pigs

Abstract

MicroRNAs (miRNAs) play a vital role in muscle development by binding to messenger RNAs (mRNAs). Based on prenatal skeletal muscle at 33, 65 and 90 days post-coitus (dpc) from Landrace, Tongcheng and Wuzhishan pigs, we carried out integrated analysis of miRNA and mRNA expression profiling. We identified 33, 18 and 67 differentially expressed miRNAs and 290, 91 and 502 mRNA targets in Landrace, Tongcheng and Wuzhishan pigs, respectively. Subsequently, 12 mRNAs and 3 miRNAs differentially expressed were validated using quantitative real-time PCR (qPCR), and 5 predicted miRNA targets were confirmed via dual luciferase reporter or western blot assays. We identified a set of miRNAs and mRNA genes differentially expressed in muscle development. Gene ontology (GO) enrichment analysis suggests that the miRNA targets are primarily involved in muscle contraction, muscle development and negative regulation of cell proliferation. Our data indicated that more mRNAs are regulated by miRNAs at earlier stages than at later stages of muscle development. Landrace and Tongcheng pigs also had longer phases of myoblast proliferation than Wuzhishan pigs. This study will be helpful to further explore miRNA-mRNA interactions in myogenesis and aid to uncover the molecular mechanisms of muscle development and phenotype variance in pigs.

Comparative analysis of DNA methylome and transcriptome of skeletal muscle in lean-, obese-, and mini-type pigs

“…The LD vs. WZS comparison yielded more DMRs than were produced by the other comparisons, indicating that the WZS and LD groups had the greatest differences in DNA methylation patterns among the selected breeds. Interestingly, our transcriptome analysis of skeletal muscle identified more differentially expressed mRNAs and miRNAs between the LD and WZS breeds than were identified in the TC vs. LD and TC vs. WZS comparisons, whereas the LD and TC breeds had the most similar gene expression profiles among the three breeds1946. These findings suggest that mini-type and lean-type pigs are less closely related than either breed is to obese-type pigs.…”

“…In particular, TC pigs exhibited a slower muscle growth rate and more complicated molecular changes, while the expression levels of genes associated with increasing cellular growth and myoblast survival were comparatively up-regulated in LD pigs18. Recently, our group integrated miRNA and mRNA expression profiles of prenatal and adult skeletal muscle from TC, LD, and WZS pigs, revealing that the myoblast proliferation phases of LD and TC pigs were longer than that of WZS pigs1920. Zhao et al .…”

“…miRNA, lncRNA, and DNA methylation) regulate gene expression and serve as key regulators of skeletal muscle development, metabolism, and other processes21222324. Genome-wide analyses of miRNAs and lncRNAs have been performed to explore phenotypic variation of skeletal muscle in pigs1920252627. Several miRNAs and lncRNAs associated with muscle development have been identified, including miRNA-1/206, miRNA-133, miRNA-155, miRNA-127, miRNA-148a, Malat1 and H192829303132.…”

Longitudinal epi-transcriptome profiling reveals the crucial role of m6A in prenatal skeletal muscle development of pigs

“…Skeletal muscle development is known to be regulated in a complex spatiotemporal way. Previously identified changes in transcriptional expression and epigenetic modification throughout skeletal muscle development have greatly improved our understanding of the mechanism related to myogenesis [3, 23]. In present study, we hypothesized that m 6 A might also participate in skeletal muscle development, given the role of m 6 A participating in regulation of tissue development, including cerebellum, neural and fat [24–26].…”

miR-206 knockout shows it is critical for myogenesis and directly regulates newly identified target mRNAs

“…Some, but not all, known miR-206 targets were part of this set, including HDAC4 (31), Igfbp5 (19), and Map1a (32). The criterion we used to obtain our list of 130 putative miR-206 targets required a 2-fold or greater enrichment of xOP-seq reads in the differentiated sample.…”