Browse > Article
http://dx.doi.org/10.5187/JAST.2012.54.6.383

Gene Expression Profiling in Hepatic Tissue of two Pig Breeds  

Jang, Gul-Won (Division of Animal Genomics and Bioinformatics, National Institute of Animal Science, Rural Development Administration)
Lee, Kyung-Tai (Division of Animal Genomics and Bioinformatics, National Institute of Animal Science, Rural Development Administration)
Park, Jong Eun (Laboratory of Bioinformatics and Population Genetics, Department of Agricultural Biotechnology, Seoul National University)
Kim, Heebal (Laboratory of Bioinformatics and Population Genetics, Department of Agricultural Biotechnology, Seoul National University)
Kim, Tae-Hun (Division of Animal Genomics and Bioinformatics, National Institute of Animal Science, Rural Development Administration)
Choi, Bong-Hwan (Division of Animal Genomics and Bioinformatics, National Institute of Animal Science, Rural Development Administration)
Kim, Myung Jick (Swine Science Division, National Institute of Animal Science, Rural Development Administration)
Lim, Dajeong (Division of Animal Genomics and Bioinformatics, National Institute of Animal Science, Rural Development Administration)
Publication Information
Journal of Animal Science and Technology / v.54, no.6, 2012 , pp. 383-394 More about this Journal
Abstract
Microarray analyses provide information that can be used to enhance the efficiency of livestock production. For example, microarray profiling can potentially identify the biological processes responsible for the phenotypic characteristics of porcine liver. We performed transcriptome profiling to identify differentially expressed genes (DEGs) in liver of pigs from two breeds, the Korean native pigs (KNP) and Yorkshire pigs. We correctly identified expected DEGs using factor analysis for robust microarray summarization (FARMS) and robust multi-array average (RMA) strategies. We identified 366 DEGs in liver (p<0.05, fold-change>2). We also performed functional analyses, including gene ontology and molecular network analyses. In addition, we identified the regulatory relationship between DEGs and their transcription factors using in silico and qRT-PCR analysis. Our findings suggest that DEGs and their transcription factors may have a potential role in adipogenesis and/or lipid deposition in liver tissues of two pig breeds.
Keywords
Korean native pig; Yorkshire; Microarray; Molecular network; Transcription factor;
Citations & Related Records
연도 인용수 순위
  • Reference
1 Wanders, R. J., Denis, S., Ruiter, J. P., I. J. L and Dacremont, G. 1998. 2,6-Dimethylheptanoyl-CoA is a specific substrate for long-chain acyl-CoA dehydrogenase (LCAD): evidence for a major role of LCAD in branched-chain fatty acid oxidation. Biochim Biophys Acta 1393(1):35-40.   DOI   ScienceOn
2 Zhao, S. H., Kuhar, D., Lunney, J. K., Dawson, H., Guidry, C., Uthe, J. J., Bearson, S. M., Recknor, J., Nettleton, D. and Tuggle, C. K. 2006. Gene expression profiling in Salmonella Choleraesuis-infected porcine lung using a long oligonucleotide microarray. Mamm Genome 17(7):777-789.   DOI   ScienceOn
3 Matsunaga, T., Shintani, S. and Hara, A. 2006. Multiplicity of mammalian reductases for xenobiotic carbonyl compounds. Drug Metab Pharmacokinet 21(1):1-18.   DOI   ScienceOn
4 Matys, V., Fricke, E., Geffers, R., Gossling, E., Haubrock, M., Hehl, R., Hornischer, K., Karas, D., Kel, A. E. and Kel- Margoulis, O. V. 2003. TRANSFAC: transcriptional regulation, from patterns to profiles. Nucleic Acids Res 31(1):374-378.   DOI   ScienceOn
5 Nikitin, A., Egorov, S., Daraselia, N. and Mazo, I. 2003. Pathway studio--the analysis and navigation of molecular networks. Bioinformatics 19(16):2155-2157.   DOI   ScienceOn
6 O'Hea, E. K. and Leveille, G. A. 1969. Significance of adipose tissue and liver as sites of fatty acid synthesis in the pig and the efficiency of utilization of various substrates for lipogenesis. J Nutr 99(3):338-344.   DOI
7 Oppermann, U. 2007. Carbonyl reductases: the complex relationships of mammalian carbonyl- and quinone-reducing enzymes and their role in physiology. Annu Rev Pharmacol Toxicol 47: 293-322.   DOI   ScienceOn
8 Patsouris, D., Mandard, S., Voshol, P. J., Escher, P., Tan, N. S., Havekes, L. M., Koenig, W., Marz, W., Tafuri, S. and Wahli, W. 2004. PPARalpha governs glycerol metabolism. J Clin Invest 114(1):94-103.   DOI
9 Picard, B., Lefaucheur, L., Berri, C. and Duclos, M. J. 2002. Muscle fibre ontogenesis in farm animal species. Reprod Nutr Dev 42(5):415-431.   DOI   ScienceOn
10 Ponsuksili, S., Murani, E., Walz, C., Schwerin, M. and Wimmers, K. 2007. Pre- and postnatal hepatic gene expression profiles of two pig breeds differing in body composition: insight into pathways of metabolic regulation. Physiol Genomics 29(3): 267-279.   DOI   ScienceOn
11 Pothoven, M. A., Beitz, D. C. and Thornton, J. H. 1975. Lipogenesis and lipolysis in adipose tissue of ad libitum and restricted-fed beef cattle during growth. J Anim Sci 40(5): 957-962.   DOI
12 Quilter, C. R., Gilbert, C. L., Oliver, G. L., Jafer, O., Furlong, R. A., Blott, S. C., Wilson, A. E., Sargent, C. A., Mileham, A. and Affara, N. A. 2008. Gene expression profiling in porcine maternal infanticide: a model for puerperal psychosis. Am J Med Genet B Neuropsychiatr Genet 147B(7):1126-1137.   DOI   ScienceOn
13 Rae, F. K., Martinez, G., Gillinder, K. R., Smith, A., Shooter, G., Forrest, A. R., Grimmond, S. M. and Little, M. H. 2004. Anlaysis of complementary expression profiles following WT1 induction versus repression reveals the cholesterol/fatty acid synthetic pathways as a possible major target of WT1. Oncogene 23(17):3067-3079.   DOI   ScienceOn
14 Rakhshandehroo, M., Sanderson, L. M., Matilainen, M., Stienstra, R., Carlberg, C., de Groot, P. J., Muller, M. and Kersten, S. 2007. Comprehensive analysis of PPARalpha-dependent regulation of hepatic lipid metabolism by expression profiling. PPAR Res 2007: 26839.
15 Scott, R. A., Cornelius, S. G. and Mersmann, H. J. 1981. Effects of age on lipogenesis and lipolysis in lean and obese swine. J Anim Sci 52(3):505-511.   DOI
16 Switonski, M., Stachowiak, M., Cieslak, J., Bartz, M. and Grzes, M. 2010. Genetics of fat tissue accumulation in pigs: a comparative approach. J Appl Genet 51(2):153-168.   DOI   ScienceOn
17 Hausman, G. J., Barb, C. R. and Dean. R. G. 2008. Patterns of gene expression in pig adipose tissue: insulin-like growth factor system proteins, neuropeptide Y (NPY), NPY receptors, neurotrophic factors and other secreted factors. Domest Anim Endocrinol 35(1):24-34.   DOI   ScienceOn
18 Hochreiter, S., Clevert, D. A. and Obermayer, K. 2006. A new summarization method for Affymetrix probe level data. Bioinformatics 22(8):943-949.   DOI   ScienceOn
19 Hogan, J. C. and Stephens, J. M. 2001. The identification and characterization of a STAT 1 binding site in the PPARgamma2 promoter. Biochem Biophys Res Commun 287(2):484-492.   DOI   ScienceOn
20 Huang da, W., Sherman, B. T. and Lempicki, R. A. 2009. Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources. Nat Protoc 4(1):44-57.   DOI
21 Irizarry, R. A., Hobbs, B., Collin, F., Beazer-Barclay, Y. D., Antonellis, K. J., Scherf, U. and Speed, T. P. 2003. Exploration, normalization, and summaries of high density oligonucleotide array probe level data. Biostatistics 4(2):249-264.   DOI   ScienceOn
22 Lanthier, F., Lou, Y. and Squires, E. 2007. Skatole metabolism in the intact pre-pubescent male pig: The relationship between hepatic enzyme activity and skatole concentrations in plasma and fat. Livestock Science 106(2-3):145-153.   DOI   ScienceOn
23 Li, J. G., Zhou, J. C., Zhao, H., Lei, X. G., Xia, X. J., Gao, G. and Wang, K. N. 2011. Enhanced water-holding capacity of meat was associated with increased Sepw1 gene expression in pigs fed selenium-enriched yeast. Meat Science 87(2):95-100.   DOI   ScienceOn
24 Li, Z. X. and Guo, Y. A. 2005. Simultaneous determination of trace arsenic, antimony, bismuth and selenium in biological samples by hydride generation-four-channel atomic fluorescence spectrometry. Talanta 65(5):1318-1325.   DOI   ScienceOn
25 Liefooghe, A., T. H. a. V. J.-S. 2006. Large scale matching for Position Weight Matrices Springer Verlag 4009.
26 Liu, W. M., Mei, R., Di, X., Ryder, T. B., Hubbell, E., Dee, S., Webster, T. A., Harrington, C. A., Ho, M. H. and Baid, J. 2002. Analysis of high density expression microarrays with signed-rank call algorithms. Bioinformatics 18(12):1593-1599.   DOI   ScienceOn
27 Lkhagvadorj, S., Qu, L., Cai, W., Couture, O. P., Barb, C. R., Hausman, G. J., Nettleton, D., Anderson, L. L., Dekkers, J. C. and Tuggle, C. K. 2009. Microarray gene expression profiles of fasting induced changes in liver and adipose tissues of pigs expressing the melanocortin-4 receptor D298N variant. Physiol Genomics.
28 Lobjois, V., Liaubet, L., SanCristobal, M., Glenisson, J., Feve, K., Rallieres, J., Le Roy, P., Milan, D., Cherel, P. and Hatey, F. 2008. A muscle transcriptome analysis identifies positional candidate genes for a complex trait in pig. Anim Genet 39(2): 147-162.   DOI   ScienceOn
29 Mash, D. C., ffrench-Mullen, J., Adi, N., Qin, Y., Buck, A. and Pablo, J. 2007. Gene expression in human hippocampus from cocaine abusers identifies genes which regulate extracellular matrix remodeling. PLoS ONE 2(11):e1187.   DOI   ScienceOn
30 Babol, J., Squires, E. J. and Lundstrom, K. 1998. Hepatic metabolism of skatole in pigs by cytochrome P4502E1. Journal of Animal science 76(3):822.   DOI
31 Babol, J., Squires, E. J. and Lundstrom, K. 1998. Relationship between oxidation and conjugation metabolism of skatole in pig liver and concentrations of skatole in fat. Journal of animal science 76(3):829.   DOI
32 Bingham, N. C., Verma-Kurvari, S., Parada, L. F. and Parker, K. L. 2006. Development of a steroidogenic factor 1/Cre transgenic mouse line. Genesis 44(9):419-424.   DOI   ScienceOn
33 Chen, Z., Torrens, J. I., Anand, A., Spiegelman, B. M. and Friedman, J. M. 2005. Krox20 stimulates adipogenesis via C/EBPbeta-dependent and -independent mechanisms. Cell Metab 1(2):93-106.   DOI   ScienceOn
34 Choe, S. E., Boutros, M., Michelson, A. M., Church, G. M. and Halfon, M. S. 2005. Preferred analysis methods for Affymetrix GeneChips revealed by a wholly defined control dataset. Genome Biol 6(2):R16.   DOI
35 Cobanoglu, O., Zaitoun, I., Chang, Y., Shook, G. and Khatib, H. 2006. Effects of the signal transducer and activator of transcription 1 (STAT1) gene on milk production traits in Holstein dairy cattle. Journal of dairy science 89(11):4433-4437.   DOI   ScienceOn
36 Cope, L. M., Irizarry, R. A., Jaffee, H. A., Wu, Z. and Speed, T. P. 2004. A benchmark for Affymetrix GeneChip expression measures. Bioinformatics 20(3):323-331.   DOI   ScienceOn
37 Eguchi, J., Yan, Q. W., Schones, D. E., Kamal, M., Hsu, C. H., Zhang, M. Q., Crawford, G. E. and Rosen, E. D. 2008. Interferon regulatory factors are transcriptional regulators of adipogenesis. Cell metabolism 7(1):86-94.   DOI   ScienceOn
38 Friedman, J. M. 1999. Leptin and the regulation of body weight. Harvey Lect 95:107-136.
39 Gao, B. 2005. Cytokines, STATs and liver disease. Cell Mol Immunol 2(2):92-100.
40 Gervois, P., Kleemann, R., Pilon, A., Percevault, F., Koenig, W., Staels, B. and Kooistra, T. 2004. Global suppression of IL-6-induced acute phase response gene expression after chronic in vivo treatment with the peroxisome proliferatoractivated receptor-alpha activator fenofibrate. J Biol Chem 279(16):16154-16160.   DOI   ScienceOn