Browse > Article
http://dx.doi.org/10.1007/s10059-009-0147-3

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)
Publication Information
Molecules and Cells / v.28, no.6, 2009 , pp. 529-536 More about this Journal
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
fat; full-length cDNA; gene ontology; pig;
Citations & Related Records
Times Cited By KSCI : 1  (Citation Analysis)
Times Cited By Web Of Science : 1  (Related Records In Web of Science)
연도 인용수 순위
1 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   PUBMED
2 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
3 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
4 Ewing, B., and Green, P. (1998). Base-calling of automated sequencer traces using phred. II. Error probabilities. Genome Res. 8, 186-194   DOI   PUBMED
5 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   DOI   ScienceOn
6 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   DOI
7 Lunney, J.K. (2007). Advances in swine biomedical model genomics. Int. J. Biol. Sci. 3, 179-184   PUBMED
8 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   DOI   PUBMED   ScienceOn
9 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   DOI   ScienceOn
10 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   DOI   ScienceOn
11 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   DOI   PUBMED
12 Palmieri, F. (2004). The mitochondrial transporter family (SLC25): physiological and pathological implications. Pflugers Arch. 447, 689-709   DOI   PUBMED   ScienceOn
13 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   DOI   ScienceOn
14 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   DOI   PUBMED
15 Trayhurn, P., and Wood, I.S. (2005). Signalling role of adipose tissue: adipokines and inflammation in obesity. Biochem. Soc. Trans. 33, 1078-1081   DOI   ScienceOn
16 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   DOI   PUBMED   ScienceOn
17 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   DOI   ScienceOn
18 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   DOI   PUBMED
19 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
20 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
21 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
22 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   DOI   ScienceOn
23 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   DOI   ScienceOn
24 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   DOI   ScienceOn
25 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
26 Gordon, D., Abajian, C., and Green, P. (1998). Consed: a graphical tool for sequence finishing. Genome Res. 8, 195-202   DOI   PUBMED
27 Suzuki, Y., and Sugano, S. (2001). Construction of full-lengthenriched cDNA libraries. The oligo-capping method. Methods Mol. Biol. 175, 143-153
28 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   DOI   ScienceOn
29 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   DOI   ScienceOn
30 Huang, X., and Madan, A. (1999). CAP3: A DNA sequence assembly program. Genome Res. 9, 868-877   DOI   ScienceOn
31 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
32 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   DOI   ScienceOn
33 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   DOI   ScienceOn
34 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   DOI   ScienceOn
35 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   DOI   ScienceOn
36 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   DOI   ScienceOn
37 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   DOI   PUBMED
38 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   DOI   PUBMED
39 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   DOI   ScienceOn
40 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   PUBMED
41 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   DOI   ScienceOn
42 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   DOI   ScienceOn
43 Hajjar, K.A., and Krishnan, S. (1999). Annexin II: a mediator of the plasmin/plasminogen activator system. Trends Cardiovasc. Med. 9, 128-138   DOI   ScienceOn
44 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   DOI   ScienceOn
45 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
46 Stekel, D.J., Git, Y., and Falciani, F. (2000). The comparison of gene expression from multiple cDNA libraries. Genome Res. 10, 2055-2061   DOI   ScienceOn
47 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   DOI
48 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   DOI   ScienceOn
49 Nafikov, R.A., and Beitz, D.C. (2007). Carbohydrate and lipid metabolism in farm animals. J. Nutr. 137, 702-705   DOI   PUBMED
50 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   DOI   PUBMED
51 Audic, S., and Claverie, J.M. (1997). The significance of digital gene expression profiles. Genome Res. 7, 986-995   DOI   PUBMED
52 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   DOI   ScienceOn
53 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   DOI   PUBMED