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DOI QR Code

Gene Microarray Analysis for Porcine Adipose Tissue: Comparison of Gene Expression between Chinese Xiang Pig and Large White

  • Guo, W. ;
  • Wang, S.H. ;
  • Cao, H.J. ;
  • Xu, K. ;
  • Zhang, J. ;
  • Du, Z.L. ;
  • Lu, W. ;
  • Feng, J.D. ;
  • Li, N. ;
  • Wu, C.H. ;
  • Zhang, L.
  • Received : 2006.04.22
  • Accepted : 2006.11.01
  • Published : 2008.01.01

Abstract

We created a cDNA microarray representing approximately 3,500 pig genes for functional genomic studies. The array elements were selected from 6,494 cDNA clones identified in a large-scale expressed sequence tag (EST) project. These cDNA clones came from normalized and subtracted porcine adipose tissue cDNA libraries. Sequence similarity searches of the 3,426 ESTs represented on the array using BLASTN identified 2,790 (81.4%) as putative human orthologs, with the remainder consisting of "novel" genes or highly divergent orthologs. We used the gene microarray to profile transcripts expressed by adipose tissue of fatty Chinese Xiang pig (XP) and muscley Large White (LW). Microarray analysis of RNA extracted from adipose tissue of fatty XP and muscley LW identified 81 genes that were differently expressed two fold or more. Transcriptional differences of four of these genes, adipocyte fatty acid binding protein (aP2), stearyl-CoA desaturase (SCD), sterol regulatory element binding transcription factor 1 (SREBF1) and lipoprotein lipase (LPL) were confirmed using SYBR Green quantitative RT-PCR technology. Our results showed that high expression of SCD and SREBF1 may be one of the reasons that larger fat deposits are observed in the XP. In addition, our findings also illustrate the potential power of microarrays for understanding the molecular mechanisms of porcine development, disease resistance, nutrition, fertility and production traits.

Keywords

EST (Expressed Sequence Tag);cDNA Microarray;Adipose Tissue;Xiang Pig;Large White;SYBR Green Quantitative RT-PCR

References

  1. Zhang, L., L. Ge, S. Parimoo, K. Stenn and S. M. Prouty. 1999. Human stearoyl-CoA desaturase: alternative transcripts generated from a single gene by usage of tandem polyadenylation sites. Biochem. J. 340:255-264. https://doi.org/10.1042/0264-6021:3400255
  2. White, K. P., S. A. Rifkin, P. Hurban and D. S. Hogness. 1999. Microarray analysis of Drosophila development during metamorphosis. Sci. 286:2179-2184. https://doi.org/10.1126/science.286.5447.2179
  3. Xu, J. M., J. H. Teran-Garcia, Y. Park, M. T. Nakamura and S. D. Clarke. 2001. Polyunsaturated fatty acids suppress hepatic sterol regulatory element-binding protein expression by accelerating transcript decay. J. Biol. Chem. 276:9800-9807. https://doi.org/10.1074/jbc.M008973200
  4. Tabor, D. E., J. B. Kim, B. M. Spiegelman and P. A. Edwards. 1998. Transcriptional activation of the stearoyl-CoA desaturase 2 gene by sterol regulatory element-binding protein/adipocyte determination and differentiation factor 1. J. Biol. Chem. 273(34):22052-22058. https://doi.org/10.1074/jbc.273.34.22052
  5. Tabor, D. E., J. B. Kim, B. M. Spiegelman and P. A. Edwards. 1999. Identification of conserved cis-elements and transcription factors required for sterol-regulated transcription of stearoyl-CoA desaturase 1 and 2. J. Biol. Chem. 274(29):20603-20610. https://doi.org/10.1074/jbc.274.29.20603
  6. Veerkamp, J. H. and H. T. van Moerkerk. 1993. Fatty acidbinding protein and its relation to fatty acid oxidation. Mol Cell Biochem. 123:101-106. https://doi.org/10.1007/BF01076480
  7. Shimomura, I., H. Shimano, B. S. Korn, Y. Bashmakov and J. D. Horton. 1998. Nuclear sterol regulatory element-binding proteins activate genes responsible for the entire program of unsaturated fatty acid biosynthesis in transgenic mouse liver. J. Biol. Chem. 273:35299-35306. https://doi.org/10.1074/jbc.273.52.35299
  8. Spiegelman, B. M. 1998. PPAR-${\gamma}$: adipogenic regulator and thiazolidinedione receptor. Diabetes. 47:507-514. https://doi.org/10.2337/diabetes.47.4.507
  9. Schmittgen, T. D., B. A. Zakrajsek, A. G. Mills, V. Gorn, M. J. Singer and M. W. Reed. 2000. Quantitative reverse transcription-polymerase chain reaction to study mRNA decay: comparison of endpoint and real-time methods. Anal Biochem. 285:194-204. https://doi.org/10.1006/abio.2000.4753
  10. Seo, T. and R. W. St Clair. 1997. Heparan sulfate proteoglycans mediate internalization and degradation of beta-VLDL and promote cholesterol accumulation by pigeon macrophages. J. Lipid Res. 38:765-779.
  11. Shalon, D., S. J. Smith and P. O. Brown. 1996. A DNA microarray system for analyzing complex DNA samples usiong two-color fluorescent probe hybridization. Genome Res. 6:639-645. https://doi.org/10.1101/gr.6.7.639
  12. Shimomura, I.,Y. Bashmakov, S. Ikemoto, J. D. Horton, M. S. Brown and J. L. Goldstein. 1999. Insulin selectively increases SREBP-1c mRNA in the livers of rats with streptozotocininduced diabetes. Proc. Natl. Acad. Sci. USA. 96:13656-13661. https://doi.org/10.1073/pnas.96.24.13656
  13. Osborne, T. F. 2000. Sterol regulatory element-binding proteins (SREBPs): key regulators of nutritional homeostasis and insulin action. J. Biol. Chem. 275:32379-32382. https://doi.org/10.1074/jbc.R000017200
  14. Rump, R., C. Buhlmann, T. Borchers and F. Spener. 1996. Differentiation dependent expression of heart type fatty acidbinding protein in C2C12 muscle cells. Eur. J. Cell Biol. 69:135-142.
  15. Salinelli, S., J. Y. Lo, M. P. Mims, E. Zsigmond, L. C. Smith and L. Chan. 1996. Structure Function Relationship of Lipoprotein Lipase-mediated Enhancement of Very Low Density Lipoprotein Binding and Catabolism by the Low Density Lipoprotein Receptor. J. Biol. Chem. 271:21906-21913. https://doi.org/10.1074/jbc.271.36.21906
  16. Ly, D. H., D. J. Lockhart, R. A. Lerner and P. G. Schultz. 2000. Mitotic misregulation and human aging. Sci. 287:2486-2492. https://doi.org/10.1126/science.287.5462.2486
  17. Miserez, A. R., G. Q. Cao, L. C. Probst and H. H. Hobbs. 1997. Structure of the Human Gene Encoding Sterol Regulatory Element Binding Protein 2 (SREBF2). Genomics. 40(1):31-40. https://doi.org/10.1006/geno.1996.4525
  18. Ntambi, J. M. 1999. Regulation of stearoyl-CoA desaturase by polyunsaturated fatty acids and cholesterol. J. Lipid Res. 40:1549-1558.
  19. Ntambi, J. M., M. Miyazaki, J. P. Stoehr, H. Lan, C. M. Kendziorski, B. S. Yandell, Y. Song, P. Cohen, J. M. Friedman and A. D. Attie. 2002. Loss of stearoyl-CoA desaturase-1 function protects mice against adiposity. Proc. Natl. Acad. Sci. USA. 99(17):11482-11486. https://doi.org/10.1073/pnas.132384699
  20. Kim, H-J., M. Takahashi and O. Ezaki. 1999. Fish oil feeding decreases mature sterol regulatory element-binding protein 1 by down-regulation of SREBP-1c mRNA in mouse liver. A possible mechanism for down-regulation of lipogenic enzyme mRNAs. J. Biol. Chem. 274:25892-25898. https://doi.org/10.1074/jbc.274.36.25892
  21. Kim, J. B. and B. M. Spiegelman. 1996. ADD1/SREBP1 promotes adipocyte differentiation and gene expression linked to fatty acid metabolism. Genes Dev. 10:1096-1107. https://doi.org/10.1101/gad.10.9.1096
  22. Kim, J. B., H. M. Wright, M. Wright and B. M. Spiegelman. 1998. ADD1/SREBP1 activates PPAR gamma through the production of endogenous ligand. Proc. Natl. Acad. Sci. USA. 95:4333-4337. https://doi.org/10.1073/pnas.95.8.4333
  23. Foretz, M., C. Guichard, P. Ferre and F. Foufelle. 1999. Sterol regulatory element binding protein-1c is a major mediator of insulin action on the hepatic expression of glucokinase and lipogenesis-related genes. Proc Natl Acad Sci USA. 96:12737- 12742. https://doi.org/10.1073/pnas.96.22.12737
  24. Glatz, J. F., M. M. York, D. P. Cistola and G. J. van der Vusse. 1993. Cytoplasmic fatty acid binding protein: significance for intracellular transport of fatty acids and putative role on signal transduction pathways. Prostaglandins Leukot Essent Fatty Acids. 48:33-41. https://doi.org/10.1016/0952-3278(93)90007-J
  25. Goldberg, I. J. 1996. Lipoprotein lipase and lipolysis: central roles in lipoprotein metabolism and atherogenesis. J. Lipid Res. 37:693-707.
  26. Gomes, L. I., R. I. Silva, B. S. Stolf, E. B. Cristo, R. Hirata, F. A. Soares, L. F. Reis, E. J. Neves and A. F. Carvalho. 2003. Comparative analysis of amplified and nonamplified RNA for hybridization in cDNA microarray. Anal Biochem. 321(2):244- 251. https://doi.org/10.1016/S0003-2697(03)00466-4
  27. Jing, X., M. T. Nakamura, H. P. Cho and S. D. Clarke. 1999. Sterol regulatory element binding protein-1 expression is suppressed by dietary polyunsaturated fatty acid. J. Biol. Chem. 274:23577-23583. https://doi.org/10.1074/jbc.274.33.23577
  28. Cohen, P., M. Miyazaki, N. D. Socci, A. Hagge-Greenberg, W. Liedtke, A. A. Soukas, R. Sharma, L. C. Hudgins, J. M. Ntambi and J. M. Friedman. 2002. Role for Stearoyl-CoA Desaturase-1 in Leptin-Mediated Weight Loss. Sci. 297:240- 243. https://doi.org/10.1126/science.1071527
  29. Eisenberg, S. 1984. High density lipoprotein metabolism. J. Lipid Res. 25:1017-1058.
  30. Enoch, H. G., A. Catala and P. Strittmatter. 1976. Mechanism of rat liver microsomal stearoyl-CoA desaturase: studies of the substrate specificity, enzyme-substrate interactions and the function of lipid. J. Biol. Chem. 251:5095-5103.
  31. Ewing, B., L. Hillier, M. C. Wendl and P. Green. 1998. Base- Valling of automated sequencer traces using PHRED. I. accuracy assessment. Genome Res. 8:175-185. https://doi.org/10.1101/gr.8.3.175
  32. Brown, P. O. and D. Botstein. 1999. Exploring the new world of the genome with DNA microarrays. Nature Genetics. 21:33-37. https://doi.org/10.1038/4462
  33. Chappell, D. A., G. L. Fry, M. A. Waknitz, L. E. Muhonen, M. W. Pladet, P. H. Iverius and D. K. Strickland. 1993. Lipoprotein lipase induces catabolism of normal triglyceride-rich lipoproteins via the low density lipoprotein receptor-related protein/alpha 2-macroglobulin receptor in vitro. A process facilitated by cell-surface proteoglycans. J. Biol. Chem. 268:14168-14175.
  34. Adams, M. D., J. M. Kelley, J. D. Gocayne, M. Dubnick, M. H. Polymeropoulos, H. Xiao, C. R. Merril, A. Wu, B. Olde, R. F. Moreno, A. R. KerLavage, W. R. McCombie and J. C. Venter. 1991. Complementary DNA sequencing: Expressed sequence Tags and human genome project. Sci. 252:1651-1656. https://doi.org/10.1126/science.2047873
  35. Band, M. R., J. H. Larson, M. Rebiez, C. A. Green, D. W. Heyen, J. Donovan, R. Windish, C. Steining, P. Mahyuddin, J. E. Womack and H. A. Lewin. 2000. An ordered comparative map of the cattle and human genomes. Genome Res. 10:1359-1367. https://doi.org/10.1101/gr.145900
  36. Kim, H. J., M. Miyazaki, W. C. Man and J. M. Ntambi. 2002. Sterol regulatory element-binding proteins (SREBPs) as regulators of lipid metabolism: polyunsaturated fatty acids oppose cholesterol-mediated induction of SREBP-1 maturation. Ann NY Acad Sci. 967:34-42. https://doi.org/10.1111/j.1749-6632.2002.tb04261.x
  37. Schena, M., D. Shalon, R. Heller, A. Chai, P. O. Brown and R. W. Davis. 1996. Parallel human genome analysis: Microarraybased expression monitoring of 1,000 genes. Proc. Natl. Acad. Sci. USA. 93:10614-10619. https://doi.org/10.1073/pnas.93.20.10614
  38. Smith, L., P. Underhill, C. Pritchard, Z. Tymowska-Lalanne, S. Abdul-Hussein, H. Hilton, L. Winchester, D. Williams, T. Freeman, S. Webb and A. Greenfield. 2003. Single primer amplification (SPA) of cDNA for microarray expression analysis. Nucleic Acids Res. 31(3):e9. https://doi.org/10.1093/nar/gng009
  39. Yang, Y. H., S. Dudoit, P. Luu, D. M. Lin, V. Peng, J. Ngai and T. P. Speed. 2002. Normalization for cDNA microarray data: a robust composite method addressing single and multiple slide systematic variation. Nucleic Acids Res. 30(4):e15. https://doi.org/10.1093/nar/30.4.e15

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Acknowledgement

Supported by : National Key Basic Research Development