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Liver miRNA profiles of newborn male Erhualian and Large White piglets using LC Sciences Pig miRNA Array

ABSTRACT: Erhualian (EHL) is one of the seven strains included in a Chinese indigenous pig breed called Taihu. EHL is famous for its early sexual maturity, large litter size, high adiposity, mild temper, good maternity and high tolerance to roughage and stress. To further investigate the role of miRNAs in different breed-specific metabolic characters, a comparison of miRNA expression profiles in liver of newborn Erhualian (EHL) and Large White (LW) piglets was carried out. Six LC sciences microarrays containing 236 miRNA procine probes based on miRBase Release 16.0 and 100 custom miRNA probes based on the solex deep sequencing results (li et al.,2010) were used. When compaired with LW piglets, 5 down-regulated and 8 up-regulated miRNAs were detected (fold change >1.2 and p value < 0.1) in the liver of EHL among the 236 miRbase probes. When considering the 100 custom miRNA probes, 2 down-regulated and 5 up-regulated miRNAs were observed. These results were further described in the unpublished paper Coordinated miRNA/mRNA expression profiles for understanding breed-specific metabolic characters of liver between Erhualian and Large White pigs.

ORGANISM(S): Sus scrofa

PROVIDER: GSE33523 | GEO | 2012/06/18

SECONDARY ACCESSION(S): PRJNA148807

REPOSITORIES: GEO

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Project description:Erhualian (EHL) is one of the seven strains included in a Chinese indigenous pig breed called Taihu. EHL is famous for its early sexual maturity, large litter size, high adiposity, mild temper, good maternity and high tolerance to roughage and stress.To further investigate the different breed-specific metabolic characters, a comparison of gene expression profile in liver of newborn Erhualian (EHL) and Large White (LW) piglets was carried out. Six niemblegen 135K expression microarrays were used. Among 44,987 pig transcripts investigated, 23,807 transcripts retained for further analysis after removing the probes with poor quality intensities and low dependability.All these qualified transcripts were then annotated by manual blast and by referring to previously developed protein-based annotation for pigs. In total, we observed 9,447 genes expressed in the liver of new born piglets. The microarray data of LW piglets were treated as control in the selection of differentially expressed genes related to EHL piglets. The FDR (False Discovery Rate) and fold change were calculated by SAMR 3.02. With FDR< 5%, after the removal of redundant and unannotated sequences, 53 genes were found to be significantly up-regulated and 200 genes to be significantly down-regulated in the EHL piglets, compared to the LW piglets. With FDR < 10%, 298 genes were found to be significantly up-regulated and 510 genes to be significantly down-regulated in the EHL piglets, compared to the LW piglets. These results were further described in the unpublished paper Coordinated miRNA/mRNA expression profiles for understanding breed-specific metabolic characters of liver between Erhualian and Large White pigs. Six newborn male piglets were sampled from three litters (2 from each litter) of purebred EHL and LW sows and sacrificed. Liver samples were immersed in liquid nitrogen immediately after collection and then stored at -70 M-BM-0C. Total RNA was isolated using the Trizol reagent (Invitrogen, Carlsbad, CA, USA), according to the manufacturerM-bM-^@M-^Ys instructions. Total RNAs of the two littermate piglets were pooled for the microarray analysis. The pooled samples were named as EHL1-3 and LW1-3, representing 3 mixed liver RNA samples each from EHL and LW piglets, respectively. Microarray experiment was performed by a service provider (CapitalBio, Beijing, China). The microarray (Probe length 60-mer, 135K Format) containing 44987 probe sets was provided by Roche-NimbleGen.

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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Liver miRNA profiles of newborn male Erhualian and Large White piglets using LC Sciences Pig miRNA Array

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