Molecules and Cells

Korean Society for Molecular and Cellular Biology (한국분자세포생물학회)
권호 표지
DOI QR코드

DOI QR Code

Full-Length Enriched cDNA Library Construction from Tissues Related to Energy Metabolism in Pigs

  • Lee, Kyung-Tai (Division of Animal Genomics and Bioinformatics, National Institute of Animal Science, Rural Development Administration) ;
  • Byun, Mi-Jeong (Division of Animal Genomics and Bioinformatics, National Institute of Animal Science, Rural Development Administration) ;
  • Lim, Dajeong (Division of Animal Genomics and Bioinformatics, National Institute of Animal Science, Rural Development Administration) ;
  • Kang, Kyung-Soo (Department of Agricultural Biotechnology, Seoul National University) ;
  • Kim, Nam-Soon (Laboratory of Human Genomics, Genome Research Center, Korea Research Institute of Bioscience and Biotechnology) ;
  • Oh, Jung-Hwa (Toxicogenomics Team, Korea Institute of Toxicology) ;
  • Chung, Chung-Soo (Department of Animal Science, Chungbuk National University) ;
  • Park, Hae-Suk (Division of Animal Genomics and Bioinformatics, National Institute of Animal Science, Rural Development Administration) ;
  • Shin, Younhee (Bioninformatics Division: Insilicogen, Inc.) ;
  • Kim, Tae-Hun (Division of Animal Genomics and Bioinformatics, National Institute of Animal Science, Rural Development Administration)
  • Received : 2009.06.16
  • Accepted : 2009.09.17
  • Published : 2009.12.31
⟨ Previous Next ⟩

Abstract

Genome sequencing of the pig is being accelerated because of its importance as an evolutionary and biomedical model animal as well as a major livestock animal. However, information on expressed porcine genes is insufficient to allow annotation and use of the genomic information. A series of expressed sequence tags of 5' ends of five full-length enriched cDNA libraries (SUSFLECKs) were functionally characterized. SUSFLECKs were constructed from porcine abdominal fat, induced fat cells, loin muscle, liver, and pituitary gland, and were composed of non-normalized and normalized libraries. A total of 55,658 ESTs that were sequenced once from the 5′ ends of clones were produced and assembled into 17,684 unique sequences with 7,736 contigs and 9,948 singletons. In Gene Ontology analysis, two significant biological process leaf nodes were found: gluconeogenesis and translation elongation. In functional domain analysis based on the Pfam database, the beta transducin repeat domain of WD40 protein was the most frequently occurring domain. Twelve genes, including SLC25A6, EEF1G, EEF1A1, COX1, ACTA1, SLA, and ANXA2, were significantly more abundant in fat tissues than in loin muscle, liver, and pituitary gland in the SUSFLECKs. These characteristics of SUSFLECKs determined by EST analysis can provide important insight to discover the functional pathways in gene networks and to expand our understanding of energy metabolism in the pig.

Keywords

Acknowledgement

Supported by : National Institute of Animal Science

References

  1. Adams, M.D., Kelley, J.M., Gocayne, J.D., Dubnick, M., Polymeropoulos, M.H., Xiao, H., Merril, C.R., Wu, A., Olde, B., Moreno, R.F., et al. (1991). Complementary DNA sequencing: expressed sequence tags and human genome project. Science 252, 1651-1656 https://doi.org/10.1126/science.2047873
  2. Altschul, S.F., Madden, T.L., Schaffer, A.A., Zhang, J., Zhang, Z., Miller, W., and Lipman, D.J. (1997). Gapped BLAST and PSIBLAST: a new generation of protein database search programs. Nucleic Acids Res. 25, 3389-3402 https://doi.org/10.1093/nar/25.17.3389
  3. Ashburner, M., Ball, C.A., Blake, J.A., Botstein, D., Butler, H., Cherry, J.M., Davis, A.P., Dolinski, K., Dwight, S.S., Eppig, J.T., et al. (2000). Gene ontology: tool for the unification of biology. The Gene Ontology Consortium. Nat. Genet. 25, 25-29 https://doi.org/10.1038/75556
  4. Audic, S., and Claverie, J.M. (1997). The significance of digital gene expression profiles. Genome Res. 7, 986-995 https://doi.org/10.1101/gr.7.10.986
  5. Ballard, F.J., Hanson, R.W., and Kronfeld, D.S. (1969). Gluconeogenesis and lipogenesis in tissue from ruminant and nonruminant animals. Fed. Proc. 28, 218-231
  6. Bateman, A., Coin, L., Durbin, R., Finn, R.D., Hollich, V., Griffiths- Jones, S., Khanna, A., Marshall, M., Moxon, S., Sonnhammer, E.L., et al. (2004). The Pfam protein families database. Nucleic Acids Res. 32, D138-141
  7. Bluher, M., Wilson-Fritch, L., Leszyk, J., Laustsen, P.G., Corvera, S., and Kahn, C.R. (2004). Role of insulin action and cell size on protein expression patterns in adipocytes. J. Biol. Chem. 279, 31902-31909 https://doi.org/10.1074/jbc.M404570200
  8. Bonferroni, C.E. (1937). Teoria statistica delle classi e calcolo delle probabilit?, Pubblicazioni del R Istituto Superiore di Scienze Economiche e Commerciali di Firenze 8, 3-62
  9. Bose, A., Guilherme, A., Robida, S.I., Nicoloro, S.M., Zhou, Q.L., Jiang, Z.Y., Pomerleau, D.P., and Czech, M.P. (2002). Glucose transporter recycling in response to insulin is facilitated by myosin Myo1c. Nature 420, 821-824 https://doi.org/10.1038/nature01246
  10. Chen, C.H., Lin, E.C., Cheng, W.T., Sun, H.S., Mersmann, H.J., and Ding, S.T. (2006). Abundantly expressed genes in pig adipose tissue: an expressed sequence tag approach. J. Anim. Sci. 84, 2673-2683 https://doi.org/10.2527/jas.2005-737
  11. Ewing, B., and Green, P. (1998). Base-calling of automated sequencer traces using phred. II. Error probabilities. Genome Res. 8, 186-194 https://doi.org/10.1101/gr.8.3.186
  12. Fang, M., Hu, X., Jiang, T., Braunschweig, M., Hu, L., Du, Z., Feng, J., Zhang, Q., Wu, C., and Li, N. (2005). The phylogeny of Chinese indigenous pig breeds inferred from microsatellite markers. Anim. Genet. 36, 7-13 https://doi.org/10.1111/j.1365-2052.2004.01234.x
  13. Fujisaki, S., Sugiyama, A., Eguchi, T., Watanabe, Y., Hiraiwa, H., Honma, D., Saito, T., and Yasue, H. (2004). Analysis of a fulllength cDNA library constructed from swine olfactory bulb for elucidation of expressed genes and their transcription initiation sites. J. Vet. Med. Sci. 66, 15-23 https://doi.org/10.1292/jvms.66.15
  14. Gilroy, D.W., Colville-Nash, P.R., Willis, D., Chivers, J., Paul-Clark, M.J., and Willoughby, D.A. (1999). Inducible cyclooxygenase may have anti-inflammatory properties. Nat. Med. 5, 698-701 https://doi.org/10.1038/9550
  15. Gordon, D., Abajian, C., and Green, P. (1998). Consed: a graphical tool for sequence finishing. Genome Res. 8, 195-202 https://doi.org/10.1101/gr.8.3.195
  16. Gorodkin, J., Cirera, S., Hedegaard, J., Gilchrist, M.J., Panitz, F., Jorgensen, C., Scheibye-Knudsen, K., Arvin, T., Lumholdt, S., Sawera, M., et al. (2007). Porcine transcriptome analysis based on 97 non-normalized cDNA libraries and assembly of 1,021,891 expressed sequence tags. Genome Biol. 8, R45 https://doi.org/10.1186/gb-2007-8-4-r45
  17. Hajjar, K.A., and Krishnan, S. (1999). Annexin II: a mediator of the plasmin/plasminogen activator system. Trends Cardiovasc. Med. 9, 128-138 https://doi.org/10.1016/S1050-1738(99)00020-1
  18. Harris, M.A., Clark, J., Ireland, A., Lomax, J., Ashburner, M., Foulger, R., Eilbeck, K., Lewis, S., Marshall, B., Mungall, C., et al. (2004). The Gene Ontology (GO) database and informatics resource. Nucleic Acids Res. 32, D258-261 https://doi.org/10.1093/nar/gkh036
  19. Huang, X., and Madan, A. (1999). CAP3: A DNA sequence assembly program. Genome Res. 9, 868-877 https://doi.org/10.1101/gr.9.9.868
  20. Huff-Lonergan, E., Baas, T.J., Malek, M., Dekkers, J.C., Prusa, K., and Rothschild, M.F. (2002). Correlations among selected pork quality traits. J. Anim. Sci. 80, 617-627 https://doi.org/10.2527/2002.803617x
  21. Humphray, S.J., Scott, C.E., Clark, R., Marron, B., Bender, C., Camm, N., Davis, J., Jenks, A., Noon, A., Patel, M., et al. (2007). A high utility integrated map of the pig genome. Genome Biol. 8, R139 https://doi.org/10.1186/gb-2007-8-7-r139
  22. Kato, S., Sekine, S., Oh, S.W., Kim, N.S., Umezawa, Y., Abe, N., Yokoyama-Kobayashi, M., and Aoki, T. (1994). Construction of a human full-length cDNA bank. Gene 150, 243-250 https://doi.org/10.1016/0378-1119(94)90433-2
  23. Kim, T.H., Kim, N.S., Lim, D., Lee, K.T., Oh, J.H., Park, H.S., Jang, G.W., Kim, H.Y., Jeon, M., Choi, B.H., et al. (2006). Generation and analysis of large-scale expressed sequence tags (ESTs) from a full-length enriched cDNA library of porcine backfat tissue. BMC Genomics 7, 36 https://doi.org/10.1186/1471-2164-7-36
  24. Kim, H., Park, T.S., Lee, W.K., Moon, S., Kim, J.N., Shin, J.H., Jung, J.G., Lee, S.D., Park, S.H., Park, K.J., et al. (2007). MPSS profiling of embryonic gonad and primordial germ cells in chicken. Physiol. Genomics 29, 253-259 https://doi.org/10.1152/physiolgenomics.00067.2006
  25. Lee, H.Y., Cui, X.S., Lee, K.A., and Kim, N.H. (2006a). Annealing control primer system identifies differentially expressed genes in blastocyst-stage porcine parthenotes. Zygote 14, 71-80 https://doi.org/10.1017/S0967199406003571
  26. Lee, M.H., Lee, S.H., Kim, H., Jin, J.B., Kim, D.H., and Hwang, I. (2006b). A WD40 repeat protein, Arabidopsis Sec13 homolog 1, may play a role in vacuolar trafficking by controlling the membrane association of AtDRP2A. Mol. Cells 22, 210-219
  27. Lunney, J.K. (2007). Advances in swine biomedical model genomics. Int. J. Biol. Sci. 3, 179-184
  28. Maruyama, K., and Sugano, S. (1994). Oligo-capping: a simple method to replace the cap structure of eukaryotic mRNAs with oligoribonucleotides. Gene 138, 171-174 https://doi.org/10.1016/0378-1119(94)90802-8
  29. Mikawa, A., Suzuki, H., Suzuki, K., Toki, D., Uenishi, H., Awata, T., and Hamasima, N. (2004). Characterization of 298 ESTs from porcine back fat tissue and their assignment to the SSRH radiation hybrid map. Mamm. Genome 15, 315-322
  30. Moon, H.S., and Chung, C.S. (2004). Effect of isomers of conjugated linoleic acid on porcine preadipocyte differentiation. J. Anim. Sci. Technol. 46, 967-974 https://doi.org/10.5187/JAST.2004.46.6.967
  31. Mulder, N.J., Apweiler, R., Attwood, T.K., Bairoch, A., Bateman, A., Binns, D., Bradley, P., Bork, P., Bucher, P., Cerutti, L., et al. (2005). InterPro, progress and status in 2005. Nucleic Acids Res 33, D201-205 https://doi.org/10.1093/nar/gki158
  32. Nafikov, R.A., and Beitz, D.C. (2007). Carbohydrate and lipid metabolism in farm animals. J. Nutr. 137, 702-705 https://doi.org/10.1093/jn/137.3.702
  33. Nygard, A.B., Jorgensen, C.B., Cirera, S., and Fredholm, M. (2007). Selection of reference genes for gene expression studies in pig tissues using SYBR green qPCR. BMC Mol. Biol. 8, 67 https://doi.org/10.1186/1471-2199-8-67
  34. Oh, J.H., Kim, Y.S., and Kim, N.S. (2003). An improved method for constructing a full-length enriched cDNA library using small amounts of total RNA as a starting material. Exp. Mol. Med. 35, 586-590 https://doi.org/10.1038/emm.2003.77
  35. Oh, J.H., Sohn, H.Y., Kim, J.M., Kim, Y.S., and Kim, N.S. (2004). Construction of multi-purpose vectors, pCNS and pCNS-D2, are suitable for collection and functional study of large-scale cDNAs. Plasmid 51, 217-226 https://doi.org/10.1016/j.plasmid.2004.01.001
  36. Palmieri, F. (2004). The mitochondrial transporter family (SLC25): physiological and pathological implications. Pflugers Arch. 447, 689-709 https://doi.org/10.1007/s00424-003-1099-7
  37. Quackenbush, J., Liang, F., Holt, I., Pertea, G., and Upton, J. (2000). The TIGR gene indices: reconstruction and representation of expressed gene sequences. Nucleic Acids Res. 28, 141- 145 https://doi.org/10.1093/nar/28.1.141
  38. Soares, M.B., Bonaldo, M.F., Jelene, P., Su, L., Lawton, L., and Efstratiadis, A. (1994). Construction and characterization of a normalized cDNA library. Proc. Natl. Acad. Sci. USA 91, 9228- 9232 https://doi.org/10.1073/pnas.91.20.9228
  39. Stapleton, M., Carlson, J., Brokstein, P., Yu, C., Champe, M., George, R., Guarin, H., Kronmiller, B., Pacleb, J., Park, S., et al. (2002). A Drosophila full-length cDNA resource. Genome Biol. 3, RESEARCH0080
  40. Stekel, D.J., Git, Y., and Falciani, F. (2000). The comparison of gene expression from multiple cDNA libraries. Genome Res. 10, 2055-2061 https://doi.org/10.1101/gr.GR-1325RR
  41. Suryawan, A., Swanson, L.V., and Hu, C.Y. (1997). Insulin and hydrocortisone, but not triiodothyronine, are required for the differentiation of pig preadipocytes in primary culture. J. Anim. Sci. 75, 105-111 https://doi.org/10.2527/1997.751105x
  42. Suzuki, Y., and Sugano, S. (2001). Construction of full-lengthenriched cDNA libraries. The oligo-capping method. Methods Mol. Biol. 175, 143-153
  43. Tilley, S.L., Coffman, T.M., and Koller, B.H. (2001). Mixed messages: modulation of inflammation and immune responses by prostaglandins and thromboxanes. J. Clin. Invest. 108, 15-23 https://doi.org/10.1172/JCI200113416
  44. Trayhurn, P., and Wood, I.S. (2005). Signalling role of adipose tissue: adipokines and inflammation in obesity. Biochem. Soc. Trans. 33, 1078-1081 https://doi.org/10.1042/BST20051078
  45. Tuggle, C.K., and Schmitz, C.B. (1994). Cloning and characterization of pig muscle cDNAs by an expressed sequence tag approach. Anim. Biotechnol. 5, 1-13
  46. Tuggle, C.K., Green, J.A., Fitzsimmons, C., Woods, R., Prather, R.S., Malchenko, S., Soares, B.M., Kucaba, T., Crouch, K., Smith, C., et al. (2003). EST-based gene discovery in pig: virtual expression patterns and comparative mapping to human. Mamm. Genome 14, 565-579
  47. Uenishi, H., Eguchi, T., Suzuki, K., Sawazaki, T., Toki, D., Shinkai, H., Okumura, N., Hamasima, N., and Awata, T. (2004). PEDE (Pig EST Data Explorer): construction of a database for ESTs derived from porcine full-length cDNA libraries. Nucleic Acids Res. 32, D484-488 https://doi.org/10.1093/nar/gkh037
  48. Uenishi, H., Eguchi-Ogawa, T., Shinkai, H., Okumura, N., Suzuki, K., Toki, D., Hamasima, N., and Awata, T. (2007). PEDE (Pig EST Data Explorer) has been expanded into Pig Expression Data Explorer, including 10 147 porcine full-length cDNA sequences. Nucleic Acids Res. 35, D650-653 https://doi.org/10.1093/nar/gkl954
  49. van Wijk, H.J., Arts, D.J., Matthews, J.O., Webster, M., Ducro, B.J., and Knol, E.F. (2005). Genetic parameters for carcass composition and pork quality estimated in a commercial production chain. J. Anim. Sci. 83, 324-333 https://doi.org/10.2527/2005.832324x
  50. Wang, P., Mariman, E., Keijer, J., Bouwman, F., Noben, J.P., Robben, J., and Renes, J. (2004). Profiling of the secreted proteins during 3T3-L1 adipocyte differentiation leads to the identification of novel adipokines. Cell Mol. Life Sci. 61, 2405-2417
  51. Wernersson, R., Schierup, M.H., Jorgensen, F.G., Gorodkin, J., Panitz, F., Staerfeldt, H.H., Christensen, O.F., Mailund, T., Hornshoj, H., Klein, A., et al. (2005). Pigs in sequence space: a 0.66X coverage pig genome survey based on shotgun sequencing. BMC Genomics 6, 70 https://doi.org/10.1186/1471-2164-6-70
  52. Wintero, A.K., Fredholm, M., and Davies, W. (1996). Evaluation and characterization of a porcine small intestine cDNA library: analysis of 839 clones. Mamm. Genome 7, 509-517
  53. Zhong, S., Storch, K.F., Lipan, O., Kao, M.C., Weitz, C.J., and Wong, W.H. (2004). GoSurfer: a graphical interactive tool for comparative analysis of large gene sets in gene ontology space. Appl. Bioinformatics 3, 261-264 https://doi.org/10.2165/00822942-200403040-00009

Cited by

  1. Elongation Factor 1A-1 Is a Mediator of Hepatocyte Lipotoxicity Partly through Its Canonical Function in Protein Synthesis vol.10, pp.6, 2015, https://doi.org/10.1371/journal.pone.0131269
  2. Treatment with didemnin B, an elongation factor 1A inhibitor, improves hepatic lipotoxicity in obese mice vol.4, pp.17, 2016, https://doi.org/10.14814/phy2.12963