A Comparative Assessment of the Pig, Mouse and Human Genomes Structural and Functional Analysis of Genes Involved in Immunity and Inflammation

The Minipig in Biomedical Research

Volumn , Issue , 2011, Pages 323-342

  Dawson, Harry D ^a  

^a and Immunology Laboratory   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

EID: 85137916412     PISSN: None     EISSN: None     Source Type: Book    
DOI: 10.1201/b11356-26     Document Type: Chapter

References (204)

1. Vasquez, Y.R. and D. Spina, What have transgenic and knockout animals taught us about respiratory disease? Respir Res, 2000. 1(2):82-6.
2. Kips, J.C. et al., Murine models of asthma. Eur Respir J, 2003. 22(2):374-82.
3. Finkelman, F.D. et al., Cytokine regulation of host defense against parasitic gastrointestinal nematodes: Lessons from studies with rodent models. Annu Rev Immunol, 1997. 15:505-33.
4. Mestas, J. and C.C. Hughes, Of mice and not men: Differences between mouse and human immunology. J Immunol, 2004. 172(5):2731-8.
5. Farrar, J.D. et al., Recruitment of Stat4 to the human interferon-alpha/beta receptor requires activated Stat2. J Biol Chem, 2000. 275(4):2693-7.
6. Kinet, J.P., The high-affinity IgE receptor (Fc epsilon RI): From physiology to pathology. Annu Rev Immunol, 1999. 17:931-72.
7. Andrews, R. et al., Reconstitution of a functional human type II IL-4/IL-13 receptor in mouse B cells: Demonstration of species specificity. J Immunol, 2001. 166(3):1716-22.
8. Greenfeder, S. et al., Th2 cytokines and asthma. The role of interleukin-5 in allergic eosinophilic disease. Respir Res, 2001. 2(2):71-9.
9. Cooper, D.A. et al., Nutritional status of pigs fed olestra with and without increased dietary levels of vitamins A and E in long-term studies. J Nutr, 1997. 127(8 Suppl): 1609S-1635S.
10. Phelps, C.J. et al., Production of alpha 1, 3-galactosyltransferase-deficient pigs. Science, 2003. 299(5605):411-14.
11. Uenishi, H. and H. Shinkai, Porcine Toll-like receptors: The front line of pathogen monitoring and possible implications for disease resistance. Dev Comp Immunol, 2009. 33(3): 353-61.
12. Gerner, W., T. Kaser, and A. Saalmuller, Porcine T lymphocytes and NK cells-An update. Dev Comp Immunol, 2009. 33(3):310-20.
13. Butler, J.E. et al., The piglet as a model for B cell and immune system development. Vet Immunol Immunopathol, 2009. 128(1-3):147-70.
14. Alving, K., R. Matran, and J.M. Lundberg, The possible role of prostaglandin D2 in the long-lasting airways vasodilatation induced by allergen in the sensitized pig. Acta Physiol Scand, 1991. 143(1):93-103.
15. Fornhem, C. et al., Allergen-induced late-phase airways obstruction in the pig: Mediator release and eosinophil recruitment. Eur Respir J, 1995. 8(7):1100-9.
16. Boes, J. and A.B. Helwigh, Animal models of intestinal nematode infections of humans. Parasitology, 2000. 121 (Suppl): S97-111.
17. Hein, W.R. and P.J. Griebel, A road less travelled: Large animal models in immunological research. Nat Rev Immunol, 2003. 3(1):79-84.
18. Brooks, D.L., P.C. Tillman, and S.M. Niemi, Ungulates as Laboratory Animals, in Fox, J.G., B.J. Cohen, and F.M. Loew (eds), Laboratory Animal Medicine, 2002, Academic Press: New York, NY.
19. Bendixen, E. et al., Advances in porcine genomics and proteomics-A toolbox for developing the pig as a model organism for molecular biomedical research. Brief Funct Genomics, 2010. 9(3):208-19.
20. Entrican, G. et al., A current perspective on availability of tools, resources and networks for veterinary immunology. Vet Immunol Immunopathol, 2009. 128(1-3):24-9.
21. Archibald, A.L. et al., Pig genome sequence-Analysis and publication strategy. BMC Genomics, 2010. 11:438.
22. Lander, E.S. et al., Initial sequencing and analysis of the human genome. Nature, 2001. 409(6822):860-921.
23. Venter, J.C. et al., The sequence of the human genome. Science, 2001. 291(5507):1304-51.
24. Waterston, R.H. et al., Initial sequencing and comparative analysis of the mouse genome. Nature, 2002. 420(6915):520-62.
25. Chen, K. et al., Genetic resources, genome mapping and evolutionary genomics of the pig (Sus scrofa). Int J Biol Sci, 2007. 3(3):153-65.
26. Wernersson, R. et al., Pigs in sequence space: A 0.66X coverage pig genome survey based on shotgun sequencing. BMC Genomics, 2005. 6(1):70.
27. Kapranov, P. et al., RNA maps reveal new RNA classes and a possible function for pervasive transcription. Science, 2007. 316(5830):1484-8.
28. Cordaux, R. and M.A. Batzer, The impact of retrotransposons on human genome evolution. Nat Rev Genet, 2009. 10(10):691-703.
29. Piriyapongsa, J. et al., Exonization of the LTR transposable elements in human genome. BMC Genomics, 2007. 8:291.
30. Sironen, A. et al., An intronic insertion in KPL2 results in aberrant splicing and causes the immotile short-tail sperm defect in the pig. Proc Natl Acad Sci U S A, 2006. 103(13): 5006-11.
31. Wiedmann, R.T., D.J. Nonneman, and J.W. Keele, Novel porcine repetitive elements. BMC Genomics, 2006. 7:304.
32. Ostertag, E.M. and H.H. Kazazian, Jr., Biology of mammalian L1 retrotransposons. Annu Rev Genet, 2001. 35:501-38.
33. Goodier, J.L. et al., A novel active L1 retrotransposon subfamily in the mouse. Genome Res, 2001. 11(10):1677-85.
34. Thomsen, P.D. and J.R. Miller, Pig genome analysis: Differential distribution of SINE and LINE sequences is less pronounced than in the human and mouse genomes. Mamm Genome, 1996. 7(1):42-6.
35. Kim, D.S. et al., LINE FUSION GENES: A database of LINE expression in human genes. BMC Genomics, 2006. 7:139.
36. Yamamoto, R. et al., Porcine TCR CD3zeta-chain and eta-chain. Mol Immunol, 2005. 42(12):1485-93.
37. Donnelly, S.R., T.E. Hawkins, and S.E. Moss, A conserved nuclear element with a role in mammalian gene regulation. Hum Mol Genet, 1999. 8(9):1723-8.
38. Mancini, G., S.H. Kan, and G. Gallagher, A novel insertion variant of the human IL-23 receptor-alpha chain transcript. Genes Immun, 2008. 9(6):566-9.
39. Crow, M.K., Long interspersed nuclear elements (LINE-1): Potential triggers of systemic autoimmune disease. Autoimmunity, 2010. 43(1):7-16.
40. Ponicsan, S.L., J.F. Kugel, and J.A. Goodrich, Genomic gems: SINE RNAs regulate mRNA production. Curr Opin Genet Dev, 2010. 20(2):149-55.
41. Shimamura, M. et al., Genealogy of families of SINEs in cetaceans and artiodactyls: The presence of a huge superfamily of tRNA(Glu)-derived families of SINEs. Mol Biol Evol, 1999. 16(8):1046-60.
42. Belshaw, R. et al., Long-term reinfection of the human genome by endogenous retroviruses. Proc Natl Acad Sci U S A, 2004. 101(14):4894-9.
43. Benarafa, C. et al., Characterization of four murine homologs of the human ov-serpin monocyte neutrophil elastase inhibitor MNEI (SERPINB1). J Biol Chem, 2002. 277(44):42028-33.
44. Balada, E., M. Vilardell-Tarres, and J. Ordi-Ros, Implication of human endogenous retroviruses in the development of autoimmune diseases. Int Rev Immunol, 2010. 29(4): 351-70.
45. Jung, W.Y. et al., Comparison of PERV genomic locations between Asian and European pigs. Anim Genet, 2010. 41(1):89-92.
46. Scobie, L. and Y. Takeuchi, Porcine endogenous retrovirus and other viruses in xenotransplantation. Curr Opin Organ Transpl, 2009. 14(2):175-9.
47. Valdes-Gonzalez, R. et al., No evidence of porcine endogenous retrovirus in patients with type 1 diabetes after long-term porcine islet xenotransplantation. J Med Virol, 2010. 82(2):331-4.
48. Dorrschuck, E., C. Munk, and R.R. Tonjes, APOBEC3 proteins and porcine endogenous retroviruses. Transpl Proc, 2008. 40(4):959-61.
49. Seemann, S.E. et al., Detection of RNA structures in porcine EST data and related mammals. BMC Genomics, 2007. 8:316.
50. Xiao, B. et al., Identification, bioinformatic analysis and expression profiling of candidate mRNA-like non-coding RNAs in Sus scrofa. J Genet Genomics, 2009. 36(12): 695-702.
51. Fedorova, N. and A. Fedorov, Puzzles of the human genome: Why do we need our introns? Current Genomics, 2005. 6:589-595.
52. Christov, C.P. et al., Functional requirement of noncoding Y RNAs for human chromosomal DNA replication. Mol Cell Biol, 2006. 26(18):6993-7004.
53. Kelly, K.M. et al., “Endogenous adjuvant” activity of the RNA components of lupus autoantigens Sm/RNP and Ro 60. Arthritis Rheum, 2006. 54(5):1557-67.
54. Perreault, J., J.P. Perreault, and G. Boire, Ro-associated Y RNAs in metazoans: Evolution and diversification. Mol Biol Evol, 2007. 24(8):1678-89.
55. Pruijn, G.J. et al., Ro RNP associated Y RNAs are highly conserved among mammals. Biochim Biophys Acta, 1993. 1216(3):395-401.
56. Berezikov, E. et al., Many novel mammalian microRNA candidates identified by extensive cloning and RAKE analysis. Genome Res, 2006. 16(10):1289-98.
57. Lu, M. et al., An analysis of human microRNA and disease associations. PLoS ONE, 2008. 3(10):e3420.
58. O’Connell, R.M. et al., Physiological and pathological roles for microRNAs in the immune system. Nat Rev Immunol, 2010. 10(2):111-22.
59. Jones, M.R. et al., Zcchc11-dependent uridylation of microRNA directs cytokine expression. Nat Cell Biol, 2009. 11(9):1157-63.
60. Federico, C. et al., The pig genome: Compositional analysis and identification of the gene-richest regions in chromosomes and nuclei. Gene, 2004. 343(2):245-51.
61. Varriale, A. and G. Bernardi, Distribution of DNA methylation, CpGs, and CpG islands in human isochores. Genomics, 2010. 95(1):25-8.
62. Tuller, T. et al., Translation efficiency is determined by both codon bias and folding energy. Proc Natl Acad Sci U S A, 2010. 107(8):3645-50.
63. Kosiol, C. et al., Patterns of positive selection in six Mammalian genomes. PLoS Genet, 2008. 4(8): e1000144.
64. Rodriguez-Manzanet, R. et al., The costimulatory role of TIM molecules. Immunol Rev, 2009. 229(1):259-70.
65. Hwang, D.G. and P. Green, Bayesian Markov chain Monte Carlo sequence analysis reveals varying neutral substitution patterns in mammalian evolution. Proc Natl Acad Sci U S A, 2004. 101(39):13994-4001.
66. Wang, W. et al., Origin and evolution of new exons in rodents. Genome Res, 2005. 15(9):1258-64.
67. Zhu, J. et al., Comparative genomics search for losses of long-established genes on the human lineage. PLoS Comput Biol, 2007. 3(12):e247.
68. Murphy, W.J. et al., Dynamics of mammalian chromosome evolution inferred from multispecies comparative maps. Science, 2005. 309(5734):613-17.
69. Tanaka, M. et al., Genomic structure and gene order of swine chromosome 7q1.1- > q1.2. Anim Genet, 2006. 37(1):10-6.
70. Petersen, C.B. et al., Cloning, characterization and mapping of porcine CD14 reveals a high conservation of mammalian CD14 structure, expression and locus organization. Dev Comp Immunol, 2007. 31(7):729-37.
71. Wimmers, K. et al., Molecular characterization of the pig C3 gene and its association with complement activity. Immunogenetics, 2003. 54(10):714-24.
72. Harraghy, N. and T.J. Mitchell, Isolation and characterization of the promoter and partial enhancer region of the porcine inter-alpha-trypsin inhibitor heavy chain 4 gene. Clin Diagn Lab Immunol, 2005. 12(11):1336-9.
73. Yang, J. et al., Molecular characterization of miniature porcine RANTES and its chemotactic effect on human mononuclear cells. Transplantation, 2006. 82(9):1229-33.
74. Yang, J. et al., Molecular characterization of cDNA encoding porcine IP-10 and induction of porcine endothelial IP-10 in response to human TNF-alpha. Vet Immunol Immunopathol, 2007. 117(1-2):124-8.
75. Uenishi, H. et al., Genomic organization and assignment of the interleukin 7 gene (IL7) to porcine chromosome 4q11- > q13 by FISH and by analysis of radiation hybrid panels. Cytogenet Cell Genet, 2001. 93(1-2):65-72.
76. Wimmers, K. et al., Porcine IL12A and IL12B gene mapping, variation and evidence of association with lytic complement and blood leucocyte proliferation traits. Int J Immunogenet, 2008. 35(1):75-85.
77. Kuhnert, P. et al., The porcine tumor necrosis factor-encoding genes: Sequence and comparative analysis. Gene, 1991. 102(2):171-8.
78. Honma, D. et al., Cloning and characterization of porcine common gamma chain gene. J Interferon Cytokine Res, 2003. 23(2):101-11.
79. Chen, K. et al., Isolation and molecular characterization of the porcine transforming growth factor beta type I receptor (TGFBR1) gene. Gene, 2006. 384:62-72.
80. Tennant, L.M. et al., Regulation of porcine classical and nonclassical MHC class I expression. Immunogenetics, 2007. 59(5):377-89.
81. Thomas, A.V. et al., Genomic structure, promoter analysis and expression of the porcine (Sus scrofa) TLR4 gene. Mol Immunol, 2006. 43(6):653-9.
82. Rupec, R.A. et al., Structural analysis, expression, and chromosomal localization of the mouse ikba gene. Immunogenetics, 1999. 49(5):395-403.
83. Tungtrakoolsub, P. et al., Polymorphisms in the promoter region of the porcine antiviral MX1 and MX2 genes. Anim Genet, 2008. 39(1):22-7.
84. Baena, A. et al., Primate TNF promoters reveal markers of phylogeny and evolution of innate immunity. PLoS ONE, 2007. 2(7):e621.
85. Godwin, J.W. et al., Towards endothelial cell-specific transgene expression in pigs: Characterization of the pig ICAM-2 promoter. Xenotransplantation, 2006. 13(6):514-21.
86. Willson, T.A., D. Metcalf, and N.M. Gough, Cross-species comparison of the sequence of the leukaemia inhibitory factor gene and its protein. Eur J Biochem, 1992. 204(1):21-30.
87. Rehli, M., Of mice and men: Species variations of Toll-like receptor expression. Trends Immunol, 2002. 23(8):375-8.
88. Raymond, C.R. and B.N. Wilkie, Toll-like receptor, MHC II, B7 and cytokine expression by porcine monocytes and monocyte-derived dendritic cells in response to microbial pathogen-associated molecular patterns. Vet Immunol Immunopathol, 2005. 107(3-4):235-47.
89. Ben-Asouli, Y. et al., Human interferon-gamma mRNA autoregulates its translation through a pseudoknot that activates the interferon-inducible protein kinase PKR. Cell, 2002. 108(2):221-32.
90. Cahen-Kramer, Y., I.L. Martensson, and F. Melchers, The structure of an alternate form of complement C3 that displays costimulatory growth factor activity for B lymphocytes. J Exp Med, 1994. 180(6):2079-88.
91. Rogatcheva, M.B. et al., Characterization of the porcine ATM gene: Towards the generation of a novel non-murine animal model for Ataxia-Telangiectasia. Gene, 2007. 405(1-2): 27-35.
92. Halees, A.S., R. El-Badrawi, and K.S. Khabar, ARED Organism: Expansion of ARED reveals AU-rich element cluster variations between human and mouse. Nucleic Acids Res, 2008. 36(Database issue):D137-40.
93. Hel, Z., S. Di Marco, and D. Radzioch, Characterization of the RNA binding proteins forming complexes with a novel putative regulatory region in the 3'-UTR of TNF-alpha mRNA. Nucleic Acids Res, 1998. 26(11):2803-12.
94. Beutler, B. and T. Brown, Polymorphism of the mouse TNF-alpha locus: Sequence studies of the 3'-untranslated region and first intron. Gene, 1993. 129(2):279-83.
95. Stoecklin, G. et al., A novel mechanism of tumor suppression by destabilizing AU-rich growth factor mRNA. Oncogene, 2003. 22(23):3554-61.
96. Osman, F. et al., A cis-acting element in the 3'-untranslated region of human TNF-alpha mRNA renders splicing dependent on the activation of protein kinase PKR. Genes Dev, 1999. 13(24):3280-93.
97. Nygard, A.B. et al., A study of alternative splicing in the pig. BMC Res Notes, 2010. 3:123.
98. Haines, B.P. et al., Complex conserved organization of the mammalian leukemia inhibitory factor gene: Regulated expression of intracellular and extracellular cytokines. J Immunol, 1999. 162(8):4637-46.
99. Gurney, A.L. et al., Genomic structure, chromosomal localization, and conserved alternative splice forms of thrombopoietin. Blood, 1995. 85(4):981-8.
100. Straubinger, A.F., M.M. Viveiros, and R.K. Straubinger, Identification of two transcripts of canine, feline, and porcine interleukin-1 alpha. Gene, 1999. 236(2):273-80.
101. Ye, L. et al., Identification and characterization of an alternatively spliced variant of the MHC class I-related porcine neonatal Fc receptor for IgG. Dev Comp Immunol, 2008. 32(8):966-79.
102. Church, D.M. et al., Lineage-specific biology revealed by a finished genome assembly of the mouse. PLoS Biol, 2009. 7(5):e1000112.
103. Puente, X.S. et al., Human and mouse proteases: A comparative genomic approach. Nat Rev Genet, 2003. 4(7): 544-58.
104. Kaiserman, D. et al., The major human and mouse granzymes are structurally and functionally divergent. J Cell Biol, 2006. 175(4):619-30.
105. Kelley, J., L. Walter, and J. Trowsdale, Comparative genomics of natural killer cell receptor gene clusters. PLoS Genet, 2005. 1(2):129-39.
106. Zhao, X. et al., Characterization and virus-induced expression profiles of the porcine interferon-omega multigene family. J Interferon Cytokine Res, 2009. 29(10):687-93.
107. Zhang, J., K.D. Dyer, and H.F. Rosenberg, Evolution of the rodent eosinophil-associated RNase gene family by rapid gene sorting and positive selection. Proc Natl Acad Sci U S A, 2000. 97(9):4701-6.
108. Barreiro, L.B. and L. Quintana-Murci, From evolutionary genetics to human immunology: How selection shapes host defence genes. Nat Rev Genet, 2010. 11(1):17-30.
109. den Dunnen, J., S.I. Gringhuis, and T.B. Geijtenbeek, Innate signaling by the C-type lectin DC-SIGN dictates immune responses. Cancer Immunol Immunother, 2009. 58(7):1149-57.
110. Svajger, U. et al., C-type lectin DC-SIGN: An adhesion, signalling and antigen-uptake molecule that guides dendritic cells in immunity. Cell Signal, 2010. 22(10):1397-405.
111. Tailleux, L. et al., DC-SIGN induction in alveolar macrophages defines privileged target host cells for mycobacteria in patients with tuberculosis. PLoS Med, 2005. 2(12):e381.
112. Caminschi, I. et al., Functional comparison of mouse CIRE/mouse DC-SIGN and human DC-SIGN. Int Immunol, 2006. 18(5):741-53.
113. Huang, Y.W. et al., Porcine DC-SIGN: Molecular cloning, gene structure, tissue distribution and binding characteristics. Dev Comp Immunol, 2009. 33(4):464-80.
114. Powlesland, A.S. et al., Widely divergent biochemical properties of the complete set of mouse DC-SIGN-related proteins. J Biol Chem, 2006. 281(29):20440-9.
115. Gramberg, T. et al., Evidence that multiple defects in murine DC-SIGN inhibit a functional interaction with pathogens. Virology, 2006. 345(2):482-91.
116. Mosmann, T.R. et al., Species-specificity of T cell stimulating activities of IL 2 and BSF-1 (IL 4): Comparison of normal and recombinant, mouse and human IL 2 and BSF-1 (IL 4). J Immunol, 1987. 138(6):1813-16.
117. Collins, R.A. et al., Cloning and expression of bovine and porcine interleukin-2 in baculovirus and analysis of species cross-reactivity. Vet Immunol Immunopathol, 1994. 40(4):313-24.
118. Farrar, J.D. et al., Selective loss of type I interferon-induced STAT4 activation caused by a minisatellite insertion in mouse Stat2. Nat Immunol, 2000. 1(1):65-9.
119. Persky, M.E., K.M. Murphy, and J.D. Farrar, IL-12, but not IFN-alpha, promotes STAT4 activation and Th1 development in murine CD4+ T cells expressing a chimeric murine/human Stat2 gene. J Immunol, 2005. 174(1):294-301.
120. Parisien, J.P. et al., Selective STAT protein degradation induced by paramyxoviruses requires both STAT1 and STAT2 but is independent of alpha/beta interferon signal transduction. J Virol, 2002. 76(9):4190-8.
121. Chatziandreou, N. et al., Relationships and host range of human, canine, simian and porcine isolates of simian virus 5 (parainfluenza virus 5). J Gen Virol, 2004. 85(Pt 10):3007-16.
122. Dawson, H. et al., Localized Th1-, Th2-, T regulatory cell-, and inflammation-associated hepatic and pulmonary immune responses in Ascaris suum-infected swine are increased by retinoic acid. Infect Immun, 2009. 77(6):2576-87.
123. Blanchard, C. et al., Eotaxin-3 and a uniquely conserved gene-expression profile in eosinophilic esophagitis. J Clin Invest, 2006. 116(2):536-47.
124. Pope, S.M. et al., Identification of a cooperative mechanism involving interleukin-13 and eotaxin-2 in experimental allergic lung inflammation. J Biol Chem, 2005. 280(14):13952-61.
125. Petkovic, V. et al., Eotaxin-3/CCL26 is a natural antagonist for CC chemokine receptors 1 and 5. A human chemokine with a regulatory role. J Biol Chem, 2004. 279(22):23357-63.
126. Shinkai, A. et al., N-terminal domain of eotaxin-3 is important for activation of CC chemokine receptor 3. Protein Eng, 2002. 15(11):923-9.
127. Weaver, B.K. et al., ABIN-3: A molecular basis for species divergence in interleukin-10-induced anti-inflammatory actions. Mol Cell Biol, 2007. 27(13):4603-16.
128. Vaughan, A.N. et al., Porcine CTLA4-Ig lacks a MYPPPY motif, binds inefficiently to human B7 and specifically suppresses human CD4+ T cell responses costimulated by pig but not human B7. J Immunol, 2000. 165(6):3175-81.
129. Jonsson, S.R. et al., Evolutionarily conserved and non-conserved retrovirus restriction activities of artiodactyl APOBEC3F proteins. Nucleic Acids Res, 2006. 34(19):5683-94.
130. Puttagunta, R. et al., Comparative maps of human 19p13.3 and mouse chromosome 10 allow identification of sequences at evolutionary breakpoints. Genome Res, 2000. 10(9):1369-80.
131. Hillarp, A. et al., Molecular cloning of rat C4b binding protein alpha- and beta-chains: Structural and functional relationships among human, bovine, rabbit, mouse, and rat proteins. J Immunol, 1997. 158(3):1315-23.
132. Lamkanfi, M. et al., INCA, a novel human caspase recruitment domain protein that inhibits interleukin-1beta generation. J Biol Chem, 2004. 279(50):51729-38.
133. Eckhart, L. et al., Identification and characterization of a novel mammalian caspase with proapoptotic activity. J Biol Chem, 2005. 280(42):35077-80.
134. Zlotnik, A., O. Yoshie, and H. Nomiyama, The chemokine and chemokine receptor superfamilies and their molecular evolution. Genome Biol, 2006. 7(12):243.
135. Eguchi-Ogawa, T. et al., Analysis of the genomic structure of the porcine CD1 gene cluster. Genomics, 2007. 89(2):248-61.
136. Brossay, A. et al., Porcine CD58: cDNA cloning and molecular dissection of the porcine CD58-human CD2 interface. Biochem Biophys Res Commun, 2003. 309(4):992-8.
137. Bussink, A.P. et al., Evolution of mammalian chitinase(-like) members of family 18 glycosyl hydrolases. Genetics, 2007. 177(2): 959-70.
138. Plog, S. et al., Genomic, tissue expression and protein characterization of pCLCA1, a putative modulator of cystic fibrosis in the pig. J Histochem Cytochem, 2009. 57(12):1169-81.
139. Fitzgerald, J. and J.F. Bateman, Why mice have lost genes for COL21A1, STK17A, GPR145 and AHRI: Evidence for gene deletion at evolutionary breakpoints in the rodent lineage. Trends Genet, 2004. 20(9):408-12.
140. Sol-Church, K. et al., Evolution of placentally expressed cathepsins. Biochem Biophys Res Commun, 2002. 293(1):23-9.
141. Hagemann, S. et al., The human cysteine protease cathepsin V can compensate for murine cathepsin L in mouse epidermis and hair follicles. Eur J Cell Biol, 2004. 83(11-12): 775-80.
142. Patil, A.A. et al., Cross-species analysis of the mammalian beta-defensin gene family: Presence of syntenic gene clusters and preferential expression in the male reproductive tract. Physiol Genomics, 2005. 23(1):5-17.
143. Bjarnadottir, T.K. et al., The human and mouse repertoire of the adhesion family of G-protein-coupled receptors. Genomics, 2004. 84(1):23-33.
144. Hamann, J. et al., Inactivation of the EGF-TM7 receptor EMR4 after the Pan-Homo divergence. Eur J Immunol, 2003. 33(5):1365-71.
145. Endo, Y. et al., Identification of the mouse H-ficolin gene as a pseudogene and orthology between mouse ficolins A/B and human L-/M-ficolins. Genomics, 2004. 84(4):737-44.
146. Davis, R.S., Fc receptor-like molecules. Annu Rev Immunol, 2007. 25:525-60.
147. Huang, H. et al., Evolutionary conservation and selection of human disease gene orthologs in the rat and mouse genomes. Genome Biol, 2004. 5(7):R47.
148. Krucken, J. et al., Comparative analysis of the human gimap gene cluster encoding a novel GTPase family. Gene, 2004. 341:291-304.
149. Endsley, J.J. et al., Characterization of bovine homologues of granulysin and NK-lysin. J Immunol, 2004. 173(4):2607-14.
150. Rompler, H. et al., The rise and fall of the chemoattractant receptor GPR33. J Biol Chem, 2005. 280(35):31068-75.
151. MacIvor, D.M., C.T. Pham, and T.J. Ley, The 5' flanking region of the human granzyme H gene directs expression to T/natural killer cell progenitors and lymphokine-activated killer cells in transgenic mice. Blood, 1999. 93(3):963-73.
152. Renard, C. et al., The genomic sequence and analysis of the swine major histocompatibility complex. Genomics, 2006. 88(1):96-110.
153. Arimura, Y. et al., Mouse HLA-DPA homologue H2-Pa: A pseudogene that maps between H2-Pb and H2-Oa. Immunogenetics, 1996. 43(3):152-5.
154. Leeb, T. and M. Muller, Comparative human-mouse-rat sequence analysis of the ICAM gene cluster on HSA 19p13.2 and a 185-kb porcine region from SSC 2q. Gene, 2004. 343(2):239-44.
155. Parker, N. and A.C. Porter, Identification of a novel gene family that includes the interferon-inducible human genes 6-16 and ISG12. BMC Genomics, 2004. 5(1):8.
156. Bufler, P. et al., A complex of the IL-1 homologue IL-1F7b and IL-18-binding protein reduces IL-18 activity. Proc Natl Acad Sci U S A, 2002. 99(21):13723-8.
157. Fickenscher, H. and H. Pirzer, Interleukin-26. Int Immunopharmacol, 2004. 4(5):609-13.
158. Fox, B.A., P.O. Sheppard, and P.J. O’Hara, The role of genomic data in the discovery, annotation and evolutionary interpretation of the interferon-lambda family. PLoS ONE, 2009. 4(3):e4933.
159. Shimanuki, S., E. Kobayashi, and T. Awata, Genomic structure of the porcine Interleukin 8 gene and development of a microsatellite marker within intron 1. Anim Genet, 2002. 33(6):470-1.
160. Bjornholm, M. et al., Absence of functional insulin receptor substrate-3 (IRS-3) gene in humans. Diabetologia, 2002. 45(12):1697-702.
161. Carlyle, J.R. et al., Evolution of the Ly49 and Nkrp1 recognition systems. Semin Immunol, 2008. 20(6):321-30.
162. Yokoyama, W.M. and B.F. Plougastel, Immune functions encoded by the natural killer gene complex. Nat Rev Immunol, 2003. 3(4):304-16.
163. Seyfarth, J., P. Garred, and H.O. Madsen, The ‘involution’ of mannose-binding lectin. Hum Mol Genet, 2005. 14(19):2859-69.
164. Liang, Y. et al., Structural organization of the human MS4A gene cluster on Chromosome 11q12. Immunogenetics, 2001. 53(5):357-68.
165. Biesbrock, A.R., L.A. Bobek, and M.J. Levine, MUC7 gene expression and genetic polymorphism. Glycoconj J, 1997. 14(4):415-22.
166. Hollyoake, M., R.D. Campbell, and B. Aguado, NKp30 (NCR3) is a pseudogene in 12 inbred and wild mouse strains, but an expressed gene in Mus caroli. Mol Biol Evol, 2005. 22(8):1661-72.
167. Tian, X., G. Pascal, and P. Monget, Evolution and functional divergence of NLRP genes in mammalian reproductive systems. BMC Evol Biol, 2009. 9:202.
168. Geiszt, M., NADPH oxidases: New kids on the block. Cardiovasc Res, 2006. 71(2):289-99.
169. Perelygin, A.A. et al., The Mammalian 2'-5' Oligoadenylate Synthetase Gene Family: Evidence for Concerted Evolution of Paralogous Oas1 Genes in Rodentia and Artiodactyla. J Mol Evol, 2006. 63(4):562-76.
170. Cousin, W. et al., Cloning of hOST-PTP: The only example of a protein-tyrosine-phosphatase the function of which has been lost between rodent and human. Biochem Biophys Res Commun, 2004. 321(1):259-65.
171. Yang, R.Z. et al., Comparative studies of resistin expression and phylogenomics in human and mouse. Biochem Biophys Res Commun, 2003. 310(3):927-35.
172. Fuellen, G. et al., Computational searches for missing orthologs: The case of S100A12 in mice. Omics, 2004. 8(4): 334-40.
173. Wolf, R. et al., The mouse S100A15 ortholog parallels genomic organization, structure, gene expression, and protein-processing pattern of the human S100A7/A15 subfamily during epidermal maturation. J Invest Dermatol, 2006. 126(7):1600-8.
174. Larson, M.A. et al., Induction of human mammary-associated serum amyloid A3 expression by prolactin or lipopolysaccharide. Biochem Biophys Res Commun, 2003. 301(4):1030-7.
175. Angata, T. et al., Cloning and characterization of human Siglec-11. A recently evolved signaling that can interact with SHP-1 and SHP-2 and is expressed by tissue macrophages, including brain microglia. J Biol Chem, 2002. 277(27):24466-74.
176. Tateno, H., P.R. Crocker, and J.C. Paulson, Mouse Siglec-F and human Siglec-8 are functionally convergent paralogs that are selectively expressed on eosinophils and recognize 6'-sulfo-sialyl Lewis X as a preferred glycan ligand. Glycobiology, 2005. 15(11):1125-35.
177. Ellison, J.W. et al., Rapid evolution of human pseudoautosomal genes and their mouse homologs. Mamm Genome, 1996. 7(1):25-30.
178. Leavenworth, J.W. et al., SUMO conjugation contributes to immune deviation in nonobese diabetic mice by suppressing c-Maf transactivation of IL-4. J Immunol, 2009. 183(2):1110-19.
179. Eguchi-Ogawa, T., D. Toki, and H. Uenishi, Genomic structure of the whole D-J-C clusters and the upstream region coding V segments of the TRB locus in pig. Dev Comp Immunol, 2009. 33(10):1111-19.
180. Hasan, U. et al., Human TLR10 is a functional receptor, expressed by B cells and plasmacytoid dendritic cells, which activates gene transcription through MyD88. J Immunol, 2005. 174(5):2942-50.
181. Shinkai, H. et al., Porcine Toll-like receptor 1, 6, and 10 genes: Complete sequencing of genomic region and expression analysis. Mol Immunol, 2006. 43(9):1474-80.
182. Reed, J.C. et al., Comparative analysis of apoptosis and inflammation genes of mice and humans. Genome Res, 2003. 13(6B):1376-88.
183. Plog, S. et al., Genomic, tissue expression, and protein characterization of pCLCA1, a putative modulator of cystic fibrosis in the pig. J Histochem Cytochem, 2009. 57(12):1169-81.
184. Grossman, W.J. et al., The orphan granzymes of humans and mice. Curr Opin Immunol, 2003. 15(5):544-52.
185. Cheng, G. et al., Characterization of the porcine alpha interferon multigene family. Gene, 2006. 382:28-38.
186. Layton, D.S. et al., Development of an anti-porcine CD34 monoclonal antibody that identifies hematopoietic stem cells. Exp Hematol, 2007. 35(1):171-8.
187. Perez de la Lastra, J.M. et al., Pigs express multiple forms of decay-accelerating factor (CD55), all of which contain only three short consensus repeats. J Immunol, 2000. 165(5):2563-73.
188. Yim, D. et al., Molecular cloning, expression pattern and chromosomal mapping of pig CD69. Immunogenetics, 2002. 54(4):276-81.
189. Bie Petersen, C. et al., Various domains of the B-cell regulatory molecule CD72 has diverged at different rates in mammals: Cloning, transcription and mapping of porcine CD72. Dev Comp Immunol, 2006. 31(5):530-8.
190. Yamanishi, Y. et al., Analysis of mouse LMIR5/CLM-7 as an activating receptor: Differential regulation of LMIR5/CLM-7 in mouse versus human cells. Blood, 2008. 111(2):688-98.
191. Deiuliis, J.A. et al., Alternative splicing of delta-like 1 homolog (DLK1) in the pig and human. Comp Biochem Physiol B Biochem Mol Biol, 2006. 145(1):50-9.
192. Haase, B. et al., Molecular characterization of the porcine deleted in malignant brain tumors 1 gene (DMBT1). Gene, 2006. 376(2):184-91.
193. Yim, D. et al., Molecular cloning and characterization of pig immunoreceptor DAP10 and NKG2D. Immunogenetics, 2001. 53(3):243-9.
194. Muller, M., E.L. Winnacker, and G. Brem, Molecular cloning of porcine Mx cDNAs: New members of a family of interferon-inducible proteins with homology to GTP-binding proteins. J Interferon Res, 1992. 12(2):119-29.
195. Gatphayak, K. et al., Structural and expression analysis of the porcine FUS2 gene. Gene, 2004. 337:105-11.
196. Matesanz, F. and A. Alcina, Glutamine and tetrapeptide repeat variations affect the biological activity of different mouse interleukin-2 alleles. Eur J Immunol, 1996. 26(8): 1675-82.
197. Alvarez, B. et al., Molecular cloning characterization and expression of porcine immunoreceptor SIRPalpha. Dev Comp Immunol, 2007. 31(3):307-18.
198. Liu, Y. et al., SIRPbeta1 is expressed as a disulfide-linked homodimer in leukocytes and positively regulates neutrophil transepithelial migration. J Biol Chem, 2005. 280(43): 36132-40.
199. Tohno, M. et al., Molecular cloning and functional characterization of porcine nucleotide-binding oligomerization domain-2 (NOD2). Mol Immunol, 2007. 45(1):194-203.
200. Tsang, Y.T. et al., Porcine E-selectin: Cloning and functional characterization. Immunology, 1995. 85(1):140-5.
201. Goureau, A. et al., Conserved synteny and gene order difference between human chromosome 12 and pig chromosome 5. Cytogenet Cell Genet, 2001. 94(1-2):49-54.
202. Tsang, Y.T., D.O. Haskard, and M.K. Robinson, Cloning and expression kinetics of porcine vascular cell adhesion molecule. Biochem Biophys Res Commun, 1994. 201(2): 805-12.
203. Vogt, L., et al., VSIG4, a B7 family-related protein, is a negative regulator of T cell activation. J Clin Invest, 2006. 116(10): 2817-26.
204. Xie, L., et al., Molecular cloning and functional characterization of porcine DNA-dependent activator of IFN-regulatory factors (DAI). Dev Comp Immunol, 2010. 34(3):293-9.