Systems-wide chicken DNA microarrays, gene expression profiling, and discovery of functional genes

Poultry Science

Volumn 82, Issue 6, 2003, Pages 939-951

  Cogburn, L A ^a   Wang, X ^a   Carre, W ^a   Rejto, L ^a   Porter, T E ^b   Aggrey, S E ^c   Simon, J ^d  

^a UNIVERSITY OF DELAWARE   (United States)

^b UNIVERSITY OF MARYLAND   (United States)

^c UNIVERSITY OF GEORGIA   (United States)

^d STATION DE RECHERCHES AVICOLES   (France)

Author keywords

Chicken gene index; DNA microarray; Expressed sequence tag (EST); Functional genomics; Gene expression profiling

Indexed keywords

AVES; DROSOPHILA MELANOGASTER; EUKARYOTA; GALLUS GALLUS; RODENTIA;

ANIMAL; ANIMAL HUSBANDRY; ARTICLE; CHICKEN; DNA MICROARRAY; GENE EXPRESSION PROFILING; GENE LIBRARY; GENETICS; GENOMICS; PEDIGREE;

ANIMAL HUSBANDRY; ANIMALS; CHICKENS; GENE EXPRESSION PROFILING; GENE LIBRARY; GENOMICS; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; PEDIGREE;

EID: 0041707062     PISSN: 00325791     EISSN: None     Source Type: Journal    
DOI: 10.1093/ps/82.6.939     Document Type: Conference Paper

References (64)

1. Abdrakhmanov, I., D. Lodygin, P. Geroth, H. Arakawa, A. Law, J. Plachy, B. Korn, and J.-M. Buerstedde. 2000. A large database of chicken bursal EST as a resource for the analysis of vertebrate gene function. Genome Res. 10:2062-2069.
2. Altschul S. F., T. L. Madden, A. A. Schaffer, J. Zhang, Z. Zhang, W. Miller, and D. J. Lipman. 1997. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res. 25:3389-3402.
3. Amano, T., K. Leu, K. Yoshizato, and Y. B. Shi. 2002. Thyroid hormone regulation of a transcriptional coactivator in Xenopus laevis: implication for a role in postembryonic tissue remodeling. Dev. Dyn. 223:526-535.
4. Boardman, P. E., J. Sanz-Ezquerro, I. M. Overton, D. W. Burt, E. Bosch, W. T. Fong, C. Tickle, W. R. A. Brown, S. A. Wilson, and S. J. Hubbard. 2002. A Comprehensive collection of chicken cDNA. Curr. Biol. 12:1965-1969.
5. Brown, S. B., M. Maloney, and W. B. Kinlaw. 1997. "Spot 14" protein functions at the pretranslational level in the regulation of hepatic metabolism by thyroid hormone and glucose. J. Biol. Chem. 272:2163-2166.
6. Buerstedde, J.-M., H. Arakawa, A. Watahiki, P. P. Carninci, Y. Y. Hayashizaki, B. Korn, and J. Plachy. 2002. The DT40 web site: Sampling and connecting the genes of a B-cell line. Nucleic Acids Res. 30:230-231.
7. Carre, W., E. Bourneuf, M. Douaire, and C. Diot. 2002a. Differential expression and genetic variation of hepatic messenger RNAs from genetically lean and fat chickens. Gene 299:235-243.
8. Carre, W., C. Diot, V. Fillon, R. P. M. A. Crooijmans, S. Lagarrigue, M. Morrisson, A. Vignal, M. A. M. Groenen, and M. Douaire. 2001. Development of 112 unique expressed sequence tags from chicken liver using an arbitrarily primed reverse transcriptase-polymerase chain reaction and single strand conformation gel purification method. Anim. Genet. 32:289-297.
9. Carre, W., Y. Niu, G. R. Gao, and L. A. Cogburn. 2002b. The chicken gene index: CAP3 sequence assembly and applications for functional genomics. Poult. Sci. 81(Suppl. 1):88. (Abstr.)
10. Chambers, J. R., A. Fortin, D. A. Mackie, and E. Larmond. 1989. Comparison of sensory properties of meat from broilers of modern stocks and experimental strains differing in growth and fatness. Can. Inst. Food Sci. Technol. J. 22:353-358.
11. Chung, S. S., K. C. MacPhee, and A. G. Goodridge. 1999. Effect of the CCAAT/enhancer binding protein on expression of the gene for chicken malic enzyme. Arch. Biochem. Biophys. 364:30-41.
12. Cogburn, L. A. 1991. Endocrine manipulation of body composition in broiler chickens. Crit. Rev. Poult. Biol. 3:283-305.
13. Cogburn, L. A., S. S. Liou, C. P. Alfonso, M. C. McGuinness, and J. P. McMurtry. 1989. Dietary thyrotropin-releasing hormone stimulates growth rate and increases the insulin:glucagon molar ratio of broiler chickens. Proc. Soc. Exp. Biol. Med. 192:127-134.
14. Cogburn, L. A., R. Morgan, and J. Burnside. 2003. Expressed sequence tags, DNA chip technology and gene expression profiling. Pages 629-646 in Poultry Genetics, Breeding & Biotechnology. W. M. Muir and S. E. Aggrey, ed. CABI Publishing, Wallingford, Oxon, UK.
15. Cogburn, L. A., J.-S. Tang, J. Cui, L. Sofer, B. Leclercq, J. Simon, and J. Burnside. 2000. DNA microarray analysis of gene expression in liver of broiler chickens divergently selected for growth rate. Poult. Sci. 79(Suppl.1):72. (Abstr.)
16. de Fatima Bonaldo, M., G. Lennon, and M. B. Soares. 1996. Normalization and subtraction: Two approaches to facilitate gene discovery. Genome Res. 6:791-806.
17. Fahrenkrug, S. C., T. P. L. Smith, B. A. Freking, J. Cho, J. White, J. Vallet, T. Wise, G. Rohrer, G. Pertea, R. Sultana, J. Quackenbush, and J. W. Keele. 2002. Porcine gene discovery by normalized cDNA-library sequencing and EST cluster assembly. Mamm. Genome 13:475-478.
18. Feast, M., R. C. Noble, B. K. Speake, and M. W. J. Ferguson. 1998. The effect of temporary reductions in incubation temperature on growth characteristics and lipid utilisation in the chick embryo. J. Anat. 193:383-390.
19. Feng, X., Y. Jiang, P. Meltzer, and P. M. Yen. 2000. Thyroid hormone regulation of hepatic genes in vivo detected by complementary DNA microarray. Mol. Endocrinol. 14:947-955.
20. Glass, B., X. Wang, W. Carre, L. Rejto, and L. A. Cogburn. 2002. DNA microarray analysis of liver genes during the metabolic jump from choriollantoic to pulmonary respiration. Poult. Sci. 81(Suppl. 1):31. (Abstr.)
21. Goodridge, A. G., D. A. Fantozzi, S. A. Klautky, X. J. Ma, C. Roncero, and L. M. Salati. 1991. Nutritional and hormonal regulation of genes for lipogenic enzymes. Proc. Nutr. Soc. 50:115-122.
22. Goodridge, A. G., A. Garay, and P. Silpananta. 1974. Regulation of lipogenesis and the total activities of lipogenic enzymes in a primary culture of hepatocytes from prenatal and early postnatal chicks. J. Biol. Chem. 249:1469-1475.
23. Grillasca, J. P., M. Gastaldi, H. Khiri, A. Dace, N. Peyrol, P. Reynier, J. Torresani, and R. Planells. 1996. Cloning and initial characterization of human and mouse Spot 14 genes. FEBS Lett. 401:38-42.
24. Horvat, S., L. Bunger, V. M. Falconer, P. Mackay, A. Law, and G. Bulfield. 2000. Mapping of obesity QTLs in a cross between mouse lines divergently selected on fat content. Mamm. Genome 11:2-7.
25. Huang, X., and A. Madan. 1999. CAPS: a DNA sequence assembly program. Genome Res. 9:868-877.
26. Ikeobi, C. O. N., J. A. Woolliams, D. R. Morrice, D. Windsor, D. W. Burt, and P. M. Hocking. 2002. Quantitative trait loci affecting fatness in the chicken. Anim. Genet. 33:428-435.
27. Jump, D. B., A. Bell, and V. Santiago. 1990. Thyroid hormone and dietary carbohydrate interact to regulate rat liver S14 gene transcription and chromatin structure. J. Biol. Chem. 265:3474-3478.
28. Kinlaw, W. B., J. L. Church, J. Harmon, and C. N. Mariash. 1995. Direct evidence for the role of the "Spot 14" protein in the regulation of lipid synthesis. J. Biol. Chem. 270:16615-16618.
29. Lagarrigue, S., F. Pitel, W. Carre, P. Le Roy, A. Neau, Y. Amigues, J. Simon, A. Vignal, B. Leclercq, L. A. Cogburn, and M. Douaire. 2003. An initial QTL scan for abdominal fatness and breast muscle weight in broiler chickens. Proceedings Plant and Animal Genome XI Conference, San Diego. (Abstr.) Available: http://www.intl-pag.org/11/ abstracts/P51_P595_XI.html. Accessed May 2003.
30. Leclercq, B. 1988. Genetic selection of meat-type chickens for high or low abdominal fat content. Pages 25-40 in Leanness in Domestic Birds. B. Leclercq and C. C. Whitehead, ed. Butterworths, London.
31. Leclercq, B., J. C. Blum, and J. P. Boyer. 1980. Selecting broilers for low or high abdominal fat: Initial observations. Br. Poult. Sci. 21:107-113.
32. Liaw, C. W., and H. C. Towle. 1984. Characterization of a thyroid hormone-responsive gene from rat. J. Biol. Chem. 259:7253-7260.
33. Liu, H. C., H. H. Cheng, V. G. Tirunagaru, L. Sofer, and J. Burnside. 2001. A strategy to identify positional candidate genes conferring Marek's disease resistance by integrating DNA microarrays and genetic mapping. Anim. Genet. 32:351-359.
34. Mao, J. N. C., J. Burnside, M. C. Postel-Vinay, J. Chambers, J. Pesek, and L. A. Cogburn. 1998. Ontogeny of growth hormone receptor gene expression in tissue of growth-selected strains of broiler chickens. J. Endocrinol. 156:67-75.
35. Martin, K. J., and A. B. Pardee. 2000. Identifying expressed genes. Proc. Natl. Acad. Sci 97:3789-3791.
36. Moncur, J. T., J. P. Park, V. A. Memoli, T. K. Mohandas, and W. B. Kinlaw. 1998. The "Spot 14" gene resides on the telomeric end of the 11q13 amplicon and is expressed in lipogenic breast cancers: Implications for control of tumor metabolism. Proc. Natl. Acad. Sci. 95:6989-6994.
37. Morgan, R. W., L. Sofer, A. S. Anderson, E. L. Bernberg, J. Cui, and J. Burnside. 2001. Induction of host gene expression following infection of chicken embryo fibroblasts with oncogenic Marek's disease virus. J. Virology 75:533-539.
38. Morris, S. M., L. K. Winberry, J. E. Fisch, D. W. Back, and A. G. Goodridge. 1984. Developmental and nutritional regulation of the messenger RNAs for fatty acid synthase, malic enzyme and albumin in the livers of embryonic and newly hatched chicks. Mol. Cell. Biochem. 64:63-68.
39. Neiman, P. E., A. Ruddell, C. Jasoni, G. Loring, S. J. Thomas, K. A. Brandvold, R. Lee, J. Burnside, and J. Delrow. 2001. Analysis of gene expression during myc oncogene-induced lymphomagenesis in the bursa of Fabricius. Proc. Natl. Acad. Sci. 98:6378-6383.
40. Noy, Y., and D. Sklan. 2001. Yolk and exogenous feed utilization in the posthatch chick. Poult. Sci. 80:1490-1495.
41. Patterson, A. H. 1998. Molecular dissection of complex traits. CRC Press, Boca Raton, FL.
42. Remignon, H., L. Lefaucheur, J. C. Blum, and F. H. Ricard. 1994. Effects of divergent selection for body weight on three skeletal muscles characteristics in the chicken. Br. Poult. Sci. 35:65-76.
43. Ricard, F. H. 1975. Essai de selection sur la forme de la courbe de croissance chez le poulet. Ann. Genet. Sel. Anim. 7:427-443.
44. Sabour, M. P., J. R. Chambers, A. A. Grunder, U. Kuhnlein, and J. S. Gavora. 1992. Endogenous viral gene distribution in populations of meat-type chickens. Poult. Sci. 71:1259-1270.
45. Salati, L. M., X. J. Ma, C. C. McCormick, S. R. Stapleton, and A. G. Goodridge. 1991. Triiodothyronine stimulates and cyclic AMP inhibits transcription of the gene for malic enzyme in chick embryo hepatocytes in culture. J. Biol. Chem. 266:4010-4016.
46. 3). Endocrinology 110:671-673.
47. Seelig, S., C. Liaw, H. C. Towle, and J. H. Oppenheimer. 1981. Thyroid hormone attenuates and augments hepatic gene expression at a pretranslational level. Proc. Natl. Acad. Sci. 78:4733-4737.
48. Sewalem, A., D. M. Morrice, A. Law, D. Windsor, C. S. Haley, C. O. N. Ikeobi, D. W. Burt, and P. M. Hocking. 2002. Mapping of quantitative trait loci for body weight at three, six and nine weeks of age in a broiler layer cross. Poult. Sci. 81:1775-1781.
49. Smith, T. P. L., W. M. Grosse, B. A. Freking, A. J. Roberts, R. T. Stone, E. Casas, J. E. Wray, J. White, J. Cho, S. C. Fahrenkrug, G. L. Bennet, M. P. Heaton, W. W. Laegreid, G. A. Rohrer, C. G. Chitko-McKown, G. Pertea, I. Holt, S. Karamycheva, F. Liang, J. Quackenbush, and J. W. Keele. 2001. Sequence evaluation of four poole-tissue normalized bovine cDNA libraries and construction of a gene index for cattle. Genome Res. 11:626-630.
50. Speake, B. K., A. M. B. Murray, and R. C. Noble. 1998. Transport and transformations of yolk lipids during development of the avian embryo. Prog. Lipid Res. 37:1-32.
51. Stapleton, S. R., D. A. Mitchell, L. M. Salati, and A. G. Goodridge. 1990. Triiodothyronine stimulates transcription of the fatty acid synthase gene in chick embryo hepatocytes in culture. J. Biol. Chem. 265:18442-18446.
52. Swierczynski, J., D. A. Mitchell, D. S. Reinhold, L. M. Salati, S. R. Stapleton, S. A. Klautky, A. E. Struve, and A. G. Goodridge. 1991. Triiodothyronine-induced accumulations of malic enzyme, fatty acid synthase, acetyl-coenzyme A carboxylase, and their mRNAs are blocked by protein kinase inhibitors. J. Biol. Chem. 266:17459-17466.
53. Tamayo, P., D. Slonim, J. Mesirov, Q. Zhu, S. Kitareewan, E. Dmitrovsky, E. S. Lander, and T. R. Golub. 1999. Interpreting patterns of gene expression with self-organizing maps: Methods and application to hematopoietic differentiation. Proc. Natl. Acad. Sci. 96:2907-2912.
54. Tarte-Deckert, S., C. Chavey, M.-N. Monthouel, N. Gautier, and E. van Obberghen. 2001. The matricellular protein SPARC/osteonectin as a newly identified factor up-regulated in obesity. J. Biol. Chem. 276:22231-22237.
55. 2 family. Br. Poult. Sci. 42:333-337.
56. Tirunagaru, V. G., L. Sofer, J. Cui, and J. Burnside. 2000. An expressed sequence tag database of T-cell-enriched activated splenocytes: Sequence analysis of 5251 clones. Genomics 66:144-151.
57. Toronen, P., M. Kolehmainen, G. Wong, and E. Castren. 1999. Analysis of gene expression data using self-organizing maps. FEBS Lett. 451:142-146.
58. Van Kaam, J. B. C. H. M., M. A. M. Groenen, H. Bovenhuis, A. Veenendaal, A. L. J. Vereijken, and J. A. M. Van Arendonk. 1999. Whole genome scan in chickens for quantitative trait loci affecting carcass traits. Poult. Sci. 78:1091-1099.
59. Van Kaam, J. B. C. H. M., J. A. M. Van Arendonk, M. A. M. Groenen, H. Bovenhuis, A. L. J. Vereijken, R. P. M. A. Crooijmans, J. J. van der Poel, and A. Veenendal. 1998. Whole genome scan for quantitative trait loci affecting body weight in chickens using a three generation design. Livest. Prod. Sci. 54:133-150.
60. Wang, X., W. Carre, L. Rejto, and L. A. Cogburn. 2002. Global gene expression profiling in liver of thyroid manipulated and/or growth hormone (GH) injected broiler chickens. Poult. Sci. 81(Suppl. 1):63. (Abstr.)
61. Weldon, S. L., A. Rando, A. S. Matathias, Y. Hod, P. A. Kalonick, S. Savon, J. S. Cook, and R. W. Hanson. 1990. Mitochondrial phosphoenolpyruvate carboxykinase from the chicken: Comparison of the cDNA and protein sequences with the cytosolic isozyme. J. Biol. Chem. 265:7308-7317.
62. West, K. L., Y. Ito, Y. Birger, Y. Postnikov, H. Shirakawa, and M. Bustin. 2001. HMGN3a and HMGN3b, two protein isoforms with a tissue-specific expression pattern, expand the cellular repertoire of nucleosome-binding proteins. J. Biol. Chem. 276:25959-25969.
63. Wilson, S. B., D. W. Back, S. M. Morris, Jr., J. Swierczynski, and A. G. Goodridge. 1986. Hormonal regulation of lipogenic enzymes in chick embryo hepatocytes in culture. J. Biol. Chem. 261:15179-15182.
64. Zhu, Q., A. Mariash, M. R. Margosian, S. Gopinath, M. T. Fareed, G. W. Anderson, and C. N. Mariash. 2001. Spot 14 gene deletion increases hepatic de novo lipogenesis. Endocrinology 142:4363-4370.