DOI QR코드

DOI QR Code

In silico Discovery of Genes Expressed in Liver, Kidney, Spleen and Small Intestine of Pigs

  • Pan, Zengxiang (College of Animal Science and Technology, Nanjing Agricultural University) ;
  • Liu, Honglin (College of Animal Science and Technology, Nanjing Agricultural University) ;
  • Chen, Jie (College of Animal Science and Technology, Nanjing Agricultural University) ;
  • Xu, Dan (College of Animal Science and Technology, Nanjing Agricultural University) ;
  • Jiang, Zhihua (Department of Animal Sciences, Washington State University) ;
  • Xie, Zhuang (College of Animal Science and Technology, Nanjing Agricultural University)
  • Received : 2004.04.09
  • Accepted : 2004.08.23
  • Published : 2005.02.01

Abstract

An in silico approach was developed to survey the genes expressed in four internal organs of pig: liver, kidney, spleen and small intestine. The major procedures of the approach included: (1) BLAST searching against GenBank "est_others" database using human cDNA sequences as queries to screen the porcine orthologous expressed sequence tags (ESTs), (2) classifying the porcine ESTs records by resources according to certain criteria and (3) analyzing data for ESTs specifically expressed in each organ. In order to do so, four Java programs were developed. Based on the ESTs available in the GenBank database, it was found that there were at least 2,100 genes expressed in these four organs, including 128 in the liver, 81 in the kidney, 780 in the spleen, and 1,423 in the small intestine respectively (a few genes co-expressed in these tissues). Gene expression patterns, such as co-expressed genes, preferentially expressed genes and basic active genes were also compared and characterized among these organs. This study provides a comprehensive model on how to use the bioinformatics approach and Genbank databases to facilitate the discovery of new genes in livestock species.

Keywords

In silico;Internal Organs;Gene Expression Profiling;Ests;Pig

References

  1. Adams, M. D., J. M. Kelley, J. D. Gocayne, M. Dubnick, M. H. Polymeropoulos, H. Xiao, C. R. Merril, A. Wu, B. Olde and R. F. Moreno. 1991. Complementary DNA sequencing: expressed sequence tags and human genome project. Sci. 252:1651-1656
  2. Balas, A., S. Santos, M. J. Aviles, F. Garcia-Sanchez, R. Lillo and J. L. Vicario. 2000. Identification by sequencing based typing and complete coding region analysis of three new HLA class II alleles: DRB3${\times}$0210, DRB3×0211 and DQB1${\times}$0310. Tissue Antigens. 56:380-384 https://doi.org/10.1034/j.1399-0039.2000.560412.x
  3. Birney, E., M. Clamp and T. Hubbard. 2002. Databases and tools for browsing genomes. Annu. Rev. Genomics Hum. Genet. 3:293-310 https://doi.org/10.1146/annurev.genom.3.030502.101529
  4. Chalasani, N., J. C. Gorski, M. S. Asghar, R. A. Asgha, B. Foresman, S. D. Hall and D. W. Crabb. 2003. Hepatic cytochrome P450 2E1 activity in nondiabetic patients with nonalcoholic steatohepatitis. Hepatology 37:544-550
  5. Esposito, G., L. Vitagliano, R. Santamaria, A. Viola, A. Zagari and F. Salvatore. 2002. Structural and functional analysis of aldolase B mutants related to hereditary fructose intolerance. FEBS Lett. 531:152-156 https://doi.org/10.1016/S0014-5793(02)03451-8
  6. Gill, R. W. and P. Sanseau. 2000. Rapid in silico cloning of genes using expressed sequence tags (ESTs). Biotechnol. Ann. Rev. 5:25-44
  7. Gorinstein, S., A. Caspi, A. Rosen, I. Goshev, M. Zemser, M. Weisz, M. C. Anon, I. Libman, H. T. Lerner and S. Trakhtenberg. 2002. Structure characterization of human serum proteins in solution and dry state. J. Pept. Res. 59:71-78
  8. Ishii, J., H. Adachi, J. Aoki, H. Koizumi, S. Tomita, T. Suzuki, M. Tsujimoto, K. Inoue and H. Arai. 2002. SREC-II, a new member of the scavenger receptor type F family, trans-interacts with SREC-I through its extracellular domain. J. Biol. Chem. 277:39696-39702
  9. Martin, K. J. and A. B. Pardee. 2000. Identifying expressed genes. PNAS. 97:3789-3791
  10. Meijssen, S., H. van Dijk, C. Verseyden, D. W. Erkelens and M. C. Cabezas. 2002. Delayed and exaggerated postprandial complement component 3 response in familial combined hyperlipidemia. Arterioscler. Thromb. Vasc. Biol. 22:811-816 https://doi.org/10.1161/01.ATV.0000014079.98335.72
  11. Moriyama, K. and I. Yahara. 2002. Human CAP1 is a key factor in the recycling of cofilin and actin for rapid actin turnover. J. Cell. Sci. 115:1591-1601
  12. Nieto, N., S. L. Friedman and A. I. Cederbaum. 2002. Cytochrome P450 2E1-derived reactive oxygen species mediate paracrine stimulation of collagen I protein synthesis by hepatic stellate cells. J. Biol. Chem. 277:9853-9864
  13. Pandey, A. and F. Lewitter. 1999. Nucleotide sequence databases: a gold mine for biologists. Trends Biochem. Sci. 24:276-280 https://doi.org/10.1016/S0968-0004(99)01400-0
  14. Rasmussen, T. N., P. Schmidt, S. S. Poulsen and J. J. Holst. 2001a. Localisation and neural control of the release of calcitonin gene-related peptide (CGRP) from the isolated perfused porcine ileum. Regulatory Peptides. 98:137-143
  15. Rasmussen, T. N., P. Schmidt, S. S. Poulsen and J. J. Holst. 2001b. Effect of calcitonin gene-related peptide (CGRP) on motility and on the release of substance P, neurokinin A, somatostatin and gastrin in the isolated perfused porcine antrum. Neurogastroenterol. Mot. 13:353-359
  16. Saito, Y. and K. Takahashi. 2002. Characterization of selenoprotein P as a selenium supply protein. Eur. J. Biochem. 269:5746-5751
  17. Wimmers, K., S. Mekchay, S. Ponsuksili, T. Hardge, M. Yerle and K. Schellander. 2001. Polymorphic sites in exon 15 and 30 of the porcine C3 gene. Animal Genetics 32:40-53
  18. Farber, C. R. and J. F. Medrano. 2003. Putative in silico mapping of DNA sequences to livestock genome maps using SSLP flanking sequences. Animal Genetics 34:11-18
  19. Heaton, J. H., W. M. Dlakic, M. Dlakic and T. D. Gelehrter. 2001. Identification and cDNA cloning of a novel RNA-binding protein that interacts with the cyclic nucleotide-responsive sequence in the Type-1 plasminogen activator inhibitor mRNA. J. Biol. Chem. 276:3341-3347
  20. Narayanan, B. A., N. K. Narayanan, G. G. Re and D. W. Nixon. 2003. Differential expression of genes induced by resveratrol in LNCaP cells: P53-mediated molecular targets. Int. J. Cancer. 104:204-212 https://doi.org/10.1002/ijc.10932
  21. Pittois, K., W. Deleersnijder and J. Merregaert. 1998. cDNA sequence analysis, chromosomal assignment and expression pattern of the gene coding for integral membrane protein 2B. Gene. 217:141-149 https://doi.org/10.1016/S0378-1119(98)00354-0
  22. Austen, B., O. el-Agnaf, S. Nagala, B. Patel, N. Gunasekera, M. Lee and V. Lelyveld. 2002. Properties of neurotoxic peptides related to the BRI gene. Biochem. Soc. Trans. 30:557-559 https://doi.org/10.1042/BST0300557
  23. Lejus, C., A. Fautrel, Y. Malledant and A. Guillouzo. 2002. Inhibition of the cytochrome P450 2E1 by propofol in human and porcine liver microsomes. Biochemical pharmacology. 64:1151-1156
  24. Attwood, T. K. and C. J. Miller. 2002. Progress in bioinformatics and the importance of being earnest. Biotechnol. Annu. Rev. 8:1-54
  25. Buddhikot, M., E. Falkenstein, M. Wehling and S. Meizel. 1999. Recognition of a human sperm surface protein involved in the progesterone-initiated acrosome reaction by antisera against an endomembrane progesterone binding protein from porcine liver. Molecular and Cellular Endocrinology 158:187-193
  26. Campeau, E., L. R. Desviat, D. Leclerc, X. Wu, B. Perez, M. Ugarte and R. A. Gravel. 2001. Structure of the PCCA gene and distribution of mutations causing propionic academia. Mol. Genet. Metab. 74:238-247 https://doi.org/10.1006/mgme.2001.3210
  27. Dumont, P., J. I. Leu, A. C. Della Pietra 3rd, D. L. George and M. Murphy. 2003. The codon 72 polymorphic variants of p53 have markedly different apoptotic potential. Nat. Genet. 33:357-365 https://doi.org/10.1038/ng1093
  28. Guimaraes, D. P. and P. Hainaut. 2002. TP53: a key gene in human cancer. Biochimie. 84:83-93
  29. Scarr, R. B. 2002. PDCD2 is a negative regulator of HCF1 (C1). Oncogene. 21:5245-5254 https://doi.org/10.1038/sj.onc.1205647
  30. Rodriguez-Pombo, P., C. Perez-Cerda, L. R. Desviat, B. Perez and M. Ugarte. 2002. Transfection Screening for Defects in the PCCA and PCCB Genes Encoding Propionyl-CoA Carboxylase Subunits. Mol. Genet. Metab. 75:276-279 https://doi.org/10.1006/mgme.2001.3296
  31. Lynn, D. J., A. T. Lloyd and C. O'Farrelly. 2003. Bioinformatics: implications for medical research and clinical practice. Clin. Invest. Med. 26:70-74
  32. Strausberg, R. L., E. A. Feingold, R. D. Klausner and F. S. Collins. 1999. The Mammalian Gene Collection. Science 286:455-457
  33. Yamada, Y., T. Doi, T. Hamakubo and T. Kodama. 1998. Scavenger receptor family proteins: roles for atherosclerosis, host defence and disorders of the central nervous system. Cell Mol. Life Sci. 54:628-640 https://doi.org/10.1007/s000180050191
  34. Shito, M., N. H. Kim, H. Baskaran, A. W. Tilles, R. G. Tompkins, M. L. Yarmush and M. Toner. 2001. In vitro and in vivo evaluation of the Albumin synthesis rate of porcine hepatocytes in a flat-plate bioreactor. Artificial Organs. 25:571-578 https://doi.org/10.1046/j.1525-1594.2001.025007571.x
  35. Barnes, M. R. 2002. Psychiatric genetics in silico: databases and tools for psychiatric geneticists. Psychiatric Genetics 12:67-73
  36. Gerdes, D., M. Wehling, B. Leube and E. Falkenstein. 1998. Cloning and tissue expression of two putative steroid membrane receptors. Biol. Chem. 379:907-911 https://doi.org/10.1515/bchm.1998.379.7.907
  37. Jiang, Z., M. Zhang, V. D. Wasem, J. J. Michal, H. Zhang and R. W. Wright, Jr. 2003. Census of Genes Expressed in Porcine Embryos and Reproductive Tissues by Mining EST Database Based on the Human Genes. Biol. Reprod. 69:1177-1182
  38. Bedford, M. T., R. Reed and P. Leder. 1998. WW domainmediated interactions reveal a spliceosome-associated protein that binds a third class of proline-rich motif: the proline glycine and methionine-rich motif. Proc. Natl. Acad. Sci. USA 95:10602-10607
  39. Mostert, V. 2000. Selenoprotein P: properties, functions, and regulation. Arch. Biochem. Biophys. 376:433-438 https://doi.org/10.1006/abbi.2000.1735
  40. Pertea, G., X. Huang, F. Liang, V. Antonescu, R. Sultana, S. Karamycheva, Y. Lee, J. White, F. Cheung, B. Parvizi, J. Tsai and J. Quackenbush. 2003. Bioinformatics 19:651-652
  41. Tolan, D. R. and E. E. Penhoet. 1986. Characterization of the human aldolase B gene. Mol. Biol. Med. 3:245-264
  42. Dearden, P. and M. Akam. 2000. Computational biology: Segmentation in silico. Nature 406:131-132
  43. Pruess, M., W. Fleischmann, A. Kanapin, Y. Karavidopoulou, P. Kersey, E. Kriventseva, V. Mittard, N. Mulder, I. Phan, F. Servant and R. Apweiler. 2003. The Proteome Analysis database: a tool for the in silico analysis of whole proteomes. Nucleic Acids Res. 31:414-417 https://doi.org/10.1093/nar/gkg105
  44. Rohrer, G. A., S. C. Fahrenkrug, D. Nonneman, N. Tao and W. C. Warren. 2002. Mapping microsatellite markers identified in porcine EST sequences. Animal Genetics 33:372-376
  45. Skrabanek, L. and F. Campagne. 2001. Tissueinfo: highthroughput identification of tissues expression profiles and specificity. Nucleic Acids Res. 29:21-102
  46. Lee, J. H., C. Moran1 and C. S. Park. 2003. Current Status of Comparative Mapping in Livestock. Asian-Aust. J. Anim. Sci. 16:1411-1420