Dataset Information

Pig embryonic muscle iTRAQ analysis

ABSTRACT: Here, we performed the first iTRAQ-based proteomic analysis of early embryonic longissimus dorsi muscle from Landrance (LR) and miniature pig (Wuzhishan WZS) ranging from 21 to 42 days post coitus (dpc). 4431 proteins were identified. In both WZS and LR, the largest amount of differentially expressed proteins (DEPs) were found between 28 and 35 dpc. 252 breed-DEPs were selected by GO analysis, including 8 myofibrillar proteins. Only MYHCⅠ/IIA mRNA were detected due to early embryonic stages, and significantly higher expression of them were found in WZS during these 4 stages. MYHCⅠ was first found in WZS at 28 dpc and expressed in both breeds at later stages, while MYHCII protein was not detected until 35 dpc in both breeds. Thus, 33 myogenic breed-DEPs selected from last two stages were analyzed by STRING, which showed that some myofibrillar proteins (MYH1, TPM4, MYH10, et.al) and functional proteins (CSRP2, CASQ2, OTC, et.al), together with candidate myogenic proteins (H3F3A, HDGFRP2, et.al), probably participate in the regulatory network of myofiber formation. Thus, our study provides new data on myofiber type development during early embryo stages, which contributes to the improved understanding in the regulation mechanism of early myogenesis in agricultural animals.

INSTRUMENT(S): LTQ Orbitrap

ORGANISM(S): Sus Scrofa Domesticus (domestic Pig)

TISSUE(S): Embryo, Early Embryonic Cell

SUBMITTER: Xumeng Zhang

LAB HEAD: Xumeng Zhang

PROVIDER: PXD002481 | Pride | 2016-02-26

REPOSITORIES: Pride

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Publications

iTRAQ-based quantitative proteomic analysis reveals the distinct early embryo myofiber type characteristics involved in landrace and miniature pig.

Zhang Xumeng X Chen Yaosheng Y Pan Jinchun J Liu Xiaohong X Chen Hu H Zhou Xingyu X Yuan Zhuning Z Wang Xilong X Mo Delin D

BMC genomics 20160225

<h4>Background</h4>Pig (Sus scrofa) is a major source of dietary proteins for human consumption and is becoming a valuable model in agricultural and biomedical research. The recently developed isobaric tag for relative and absolute quantitation (iTRAQ) method allows sensitive and accurate protein quantification. Here, we performed the first iTRAQ-based quantitative proteomic analyses of Landrace (LR) and Wuzhishan (WZS) pig longissimus dorsi muscle tissues during early embryonic development.<h4> ...[more]

PMID: 26911206

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Project description:Background : The Blonde Aquitaine (BA) is a French beef breed with enhanced muscularity of unknown genetic origin. Targeted sequencing has shown that the BA is not a carrier of any of the bovine MSTN mutations. At the protein level the BA shows a transition to a faster muscle isoform phenotype with a greater proportion of type IIX and a smaller proportion of type I fibres than comparison Charolais (CH). Associated modifications in the activity of oxidative and glycolytic enzymes were also previously detected. Collectively, these changes are often observed in breeds of production species selected for enhanced growth and efficiency, but the underlying molecular mechanisms are unknown. Method : We examined the transcriptome of the Longissimus thoracis muscle at 4 gestational stages (110, 180, 210, and 260 dpc) in BA and CH foetuses. These time points coincide with primary and secondary myogenesis and functional differentiation. Total RNA was hybridised to the Agilent one-colour microarray platform containing 45,220 probes mapped to 17646 protein coding bovine genes. Following normalisation, we used a combination of differential expression (limma method, Smyth & al 2005) and a network theory method based on differential co-expression analysis (Hudson & al 2009) to compare and contrast the two muscle transcriptomes. Conclusions : In both breeds the most developmentally-regulated genes included: embryonic muscle subunit isoforms (e.g. MYL4) whose expression dropped dramatically prior to birth when they are replaced by the adult isoforms; metabolic enzymes (e.g. the mitochondrially-localised sarcomeric creatine kinase CKMT2) that prepare the foetus for functional independence postpartum, and 1 probe out of 4 representing a gene of unknown function (C13H20ORF194) also previously published as highly developmentally regulated in Wagyu by Hereford longissimus muscle (Hudson & al 2013). In contrasting the breeds, MSTN was the 2nd most differentially expressed muscle gene between the breeds, being approximately 4-fold down-regulated in CH at each of the time points. Given MSTN is a growth inhibitor, this result may reflect either divergent muscle mass or fibre composition in foetuses and could account for the low muscle development of BA calves at birth. Among the most differentially connected transcriptional regulators we prioritised expected molecules like MSTN, but also unexpected ones like PROX1, NMI, MBD1, NRIP2 and TAF12. Although not differentially expressed at the transcript level these molecules are transcriptionally rewired between the breeds and may form attractive new candidates for the development of differential muscle mass and fibre composition in cattle. 2 beef breeds: Blond Aquitaine (BA) and Charolais (CH) ; 4 gestational stages per breed (110, 180, 210, and 260 dpc); 3 animals (biological replicats) per stage and per breed, except for BA 180 dpc, BA 260 dpc and CH 110 dpc (only 2 animals due to technical problem during hybridization).

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.

Dataset Information

Pig embryonic muscle iTRAQ analysis

Publications

iTRAQ-based quantitative proteomic analysis reveals the distinct early embryo myofiber type characteristics involved in landrace and miniature pig.

Similar Datasets

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