MicroRNA Identity and Abundance in Developing Swine Adipose Tissue as Determined by Solexa Sequencing

Laboratory of Animal Fat Deposition and Muscle Development, Northwest A&F University, Yangling, Shaanxi Province 712100, PR China.
Journal of Cellular Biochemistry (Impact Factor: 3.26). 05/2011; 112(5):1318-28. DOI: 10.1002/jcb.23045
Source: PubMed


MicroRNAs (miRNAs) are small ∼22-nt regulatory RNAs that regulate the stability and translation of cognate mRNAs. MiRNAs participate in the regulation of adipogenesis, and identification of the full repertoire of miRNAs expressed in adipose tissue is likely to significantly increase our understanding of adipose tissue growth and development. Here, we adopted a deep sequencing approach to determine the identity and abundance of miRNAs in developing swine adipose tissue. Via this approach, we identified the sequences and relative expression levels of 227 conserved miRNAs (of which 59 were novel) and 66 potential porcine miRNAs. The expression levels displayed a large range, as reflected by the number of sequence reads, which varied from several counts for rare miRNAs to several million reads for the most abundant miRNAs. The abundant miRNAs principally belonged to 32 miRNA gene families, including miR-143, miR-103, let-7, and miR-148. Of the conserved miRNAs, 93 miRNAs were up-regulated and 33 miRNAs were down-regulated in the adult pig adipose tissue. Moreover, we observed sequence variants and seed edits of the miRNAs. KEGG pathway analysis and GO term enrichment suggested that highly expressed miRNAs are involved in adipose tissue development, signal transduction, cell-cell and cell-extracellular matrix communication, neural development and function, and lipid metabolism including carboxylic acid, oxoacid, fatty acid, steroid, glycerolipid, alcohol and phospholipid metabolism. Our results expand the number of known porcine miRNAs and provide a thorough account of the miRNA transcriptome in porcine adipose tissue.

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    • "Distinct sets of miRNAs including miR-122, miR-193b, and miR-483 were reported to be involved in the development of type-2 diabetes mellitus in cats [13]. A large number of miRNAs have been identified in normal tissues of swine and bovine species [14]–[17]. However, information about equine miRNAs and their role in clinical conditions is scarce. "
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    ABSTRACT: The role of microRNAs (miRNAs) as a post-transcriptional gene regulator has been elucidated in a broad range of organisms including domestic animals. Characterization of miRNAs in normal tissues is an important step to investigate the functions of miRNAs in various physiological and pathological conditions. Using Illumina Next Generation Sequencing (NGS) technology, we identified a total of 292 known and 329 novel miRNAs in normal horse tissues including skeletal muscle, colon and liver. Distinct sets of miRNAs were differentially expressed in a tissue-specific manner. The miRNA genes were distributed across all the chromosomes except chromosomes 29 and 31 in the horse reference genome. In some chromosomes, multiple miRNAs were clustered and considered to be polycistronic transcript. A base composition analysis showed that equine miRNAs had a higher frequency of A+U than G+C. Furthermore, U tended to be more frequent at the 5' end of miRNA sequences. This is the first experimental study that identifies and characterizes the global miRNA expression profile in normal horse tissues. The present study enriches the horse miRNA database and provides useful information for further research dissecting biological functions of miRNAs in horse.
    PLoS ONE 04/2014; 9(4):e93662. DOI:10.1371/journal.pone.0093662 · 3.23 Impact Factor
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    • "Another one, miR-130 also inhibits adipogenesis by targeting PPARγ mRNA, and it has been observed that adipose tissue from obese women had lower expression of miR-130 with higher expression of PPARγ mRNA than non-obese women (Lee et al. 2011). But up to now, only a few studies have been conducted to investigate the role of miRNAs on regulation of fat deposition in domestic pigs, and most of them focused on identification of novel miRNAs in porcine adipose tissue (Li et al. 2011b; Chen et al. 2012). Therefore, it is not clear whether testosterone deficiency caused by castration can influence miRNA expression patterns in porcine adipose tissue or not. "
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    ABSTRACT: MicroRNAs (miRNAs) are class of molecular regulators found to participate in numerous biological processes, such as adipogenesis and obesity in mammals. To determine the roles of miRNAs involved in castration-induced body fatness, we investigated the different miRNA expression patterns in subcutaneous adipose tissue between intact and castrated male pigs. Our results showed that castration led to decrease serum testosterone but increase serum Leptin levels (P < 0.01). Moreover, castration also increased adipocyte size, body fat content and backfat thickness in male pigs (P < 0.01). Meanwhile, miRNA expression profiles in adipose tissue were changed by castration, and 18 miRNAs were considered as the differentially expressed candidates between intact and castrated male pigs. Furthermore, functional analysis indicated that the differential expressed miRNAs and their target genes are involved in the regulation of fatty acid metabolism. In brief, our present study provides a comprehensive view on how miRNAs works in subcutaneous adipose tissue with castration. These results suggested that miRNAs might play an important role in the castration-induced fat deposition in male pigs.
    Journal of applied genetics 01/2014; 55(2). DOI:10.1007/s13353-014-0194-0 · 1.48 Impact Factor
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    • "Moreover, it was expressed at a higher level in castrated male pigs than in intact pigs (4.96-fold). This is consistent with ssc-miR-143 being the most highly expressed miRNA (representing 20% of the total miRNA expression) in the backfat of 240 day-old obese Rongchang pigs [30]. In addition, miR-143 was up-regulated after differentiation induction in both human preadipocytes and mouse 3T3-L1 cells. "
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    ABSTRACT: It is widely known that castration has a significant effect on the accumulation of adipose tissue. microRNAs (miRNAs) are known to be involved in fat deposition and to be regulated by the androgen-induced androgen receptor (AR). However, there is little understanding of the relationship between miRNAs and fat deposition after castration. In this study, the high-throughput SOLiD sequencing approach was used to identify and characterize miRNA expression in backfat from intact and castrated full-sib male 23-week-old pigs. The patterns of adipogenesis and fat deposition were compared between castrated and intact male pigs. A total of 366 unique miRNA genes were identified, comprising 174 known pre-miRNAs and 192 novel pre-miRNAs. One hundred and sixty-seven pre-miRNAs were common to both castrated (F3) and intact (F4) male pig small RNA libraries. The novel pre-miRNAs encoded 153 miRNAs/miRNA*s and 141 miRNAs/miRNA*s in the F3 and F4 libraries, respectively. One hundred and seventy-seven miRNAs, including 45 up- and 132 down-regulated, had more than 2-fold differential expression between the castrated and intact male pigs (p-value < 0.001). Thirty-five miRNAs were further selected, based on the expression abundance and differentiation between the two libraries, to predict their targets in KEGG pathways. KEGG pathway analyses suggested that miRNAs differentially expressed between the castrated and intact male pigs are involved in proliferation, apoptosis, differentiation, migration, adipose tissue development and other important biological processes. The expression patterns of eight arbitrarily selected miRNAs were validated by stem-loop reverse-transcription quantitative polymerase chain reaction. These data confirmed the expression tendency observed with SOLiD sequencing. miRNA isomiRs and mirtrons were also investigated in this study. Mirtrons are a recently described category of miRNA relying on splicing rather than processing by the microprocessor complex to generate the RNAi pathway. The functions of miRNAs important for regulating fat deposition were also investigated in this study. This study expands the number of fat-deposition-related miRNAs in pig. The results also indicate that castration can significantly affect the expression patterns of fat-related miRNAs. The differentially expressed miRNAs may play important roles in fat deposition after castration.
    BMC Genomics 01/2014; 15(1):47. DOI:10.1186/1471-2164-15-47 · 3.99 Impact Factor
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