Comparative analysis of genome sequences of the Th2 cytokine region of rabbit (Oryctolagus cuniculus) with those of nine different species

Immunology and Immunogenetics Insights

Volumn 3, Issue 1, 2011, Pages 59-82

  Michael Gertz, E ^a   Agarwala, Richa ^a   Mage, Rose G ^b   Schäffer, Alejandro A ^a  

^a NATIONAL INSTITUTES OF HEALTH   (United States)

^b NATIONAL INSTITUTE OF ALLERGY AND INFECTIOUS DISEASES   (United States)

Author keywords

Genomic assembly; IL13; IL4; Rabbit; Th2 cytokines; Tuberculosis

Indexed keywords

MAMMALIA; ORYCTOLAGUS CUNICULUS; VERMES;

EID: 84861976770     PISSN: None     EISSN: 11786345     Source Type: Journal    
DOI: 10.4137/III.S7236     Document Type: Article

References (48)

1. ENCODE Project Consortium. The ENCODE (ENCyclopedia Of DNA Elements) Project. Science. 2004;306:636-40.
2. Dorman SE, Hatem CL, Tyagi S, et al. Susceptibility to tuberculosis: clues from studies with inbred and outbred New Zealand White rabbits. Infect Immun. 2004;72:1700-5.
3. Seah GT, Scott GM, Rook GAW. Type 2 cytokine gene activation and its relationship to extent of disease in patients with tuberculosis. J Infect Dis. 2000;18:385-9.
4. Dheda K, Chang J-S, Huggett JF, et al. The stability of mRNA encoding IL-4 is increased in pulmonary tuberculosis, while stability of mRNA encoding the antagonistic splice variant, IL-4 2, is not. Tuberculosis. 2007;87:237-41.
5. Rook GA. Th2 cytokines in susceptibility to tuberculosis. Current Molecular Medicine. 2007;7:327-37.
6. Paul WE, Zhu J. How are TH2-type immune responses initiated and amplified? Nat Rev Immunol. 2010;10:225-35.
7. Zhu J, Yamane H, Paul WE. Differentiation of effector CD4 T cell populations. Annu Rev Immunol. 2010;28:445-89.
8. Loots GG, Locksley RM, Blankespoor CM, et al. Identification of a coordinate regulator of interleukins 4, 13, and 5 by cross-species sequence comparisons. Science. 2000;288:136-40.
9. Strempel JM, Grenningloh R, Ho I-C, Vercelli D. Phylogenetic and functional analysis identifies Ets-1 as a novel regulator of the Th2 cytokine gene locus. J Immunol. 2010;184:1309-16.
10. Agarwal S, Avni O, Rao A. Cell-type-restricted binding of the transcription factor NFAT to a distal IL-4 enhancer in vivo. Immunity. 2000;12: 643-52.
11. Yamashita M, Ukai-Tadenuma M, Kimura M, et al. Identification of a conserved GATA3 response element upstream proximal from the interleukin-13 gene locus. J Biol Chem. 2002;277:42399-408.
12. Kim JI, Ho I-C, Grusby MJ, Glimcher LH. The transcription factor c-Maf controls the production of interleukin-4 but not other Th2 cytokines. Immunity. 1999;10:745-51.
13. Amsen D, Blander JM, Lee GR, Tanigaki K, Honjo T, Flavell RA. Instruction of distinct CD4 T helper cell fates by different Notch ligands on antigen-presenting cells. Cell. 2004;117:515-26.
14. Djuretic IM, Levanon D, Negreanu V, Groner Y, Rao A, Ansel KM. Transcription factors T-bet and Runx3 cooperate to activate Ifng and silence Il4 in T helper type 1 cells. Nat Immunol. 2007;8:145-53.
15. Hu C-M, Jang SY, Fanzo JC, Pernis AB. Modulation of T cell cytokine production by interferon regulatory factor-4. J Biol Chem. 2002;277: 49238-46.
16. Li B, Tournier C, Davis RJ, Flavell RA. Regulation of IL-4 expression by the transcription factor JunB during T helper cell differentiation. EMBO J. 1999;18:420-32.
17. Lee DU, Rao A. Molecular analysis of a locus control region in the T helper 2 cytokine gene cluster: a target for STAT6 but not GATA3. Proc Natl Acad Sci U S A. 2004;101:16010-5.
18. Zhu J, Cote-Sierra J, Guo L, Paul WE. Stat5 activation plays a critical role in Th2 differentiation. Immunity. 2003;19:739-48.
19. Avery S, Rothwell L, Degen WD, et al. Characterization of the first nonmammalian T2 cytokine gene cluster: the cluster contains functional single-copy genes for IL-3, IL-4, IL-13, and GM-CSF, a gene for IL-5 that appears to be a pseudogene, and a gene encoding another cytokinelike transcript, KK34. J Interferon Cytokine Res. 2004;24:600-10.
20. Altschul SF, Madden TL, Schäffer AA, et al. Gapped BLAST and PSIBLAST: a new generation of protein database search programs. Nucleic Acids Res. 1997;25:3389-402.
21. Ovcharenko I, Loots GG, Giardine BM, et al. Mulan: multiple-sequence local alignment and visualization for studying function and evolution. Genome Res. 2005;15:184-94.
22. Lee GR, Fields PE, Griffin TJ IV, Flavell RA. Regulation of the Th2 cytokine locus by a locus control region. Immunity. 2003;19:145-53.
23. Fields PE, Lee GR, Kim ST, Bartsevich VV, Flavell RA. Th2-specific chromatin remodeling and enhancer activity in the Th2 cytokine locus control region. Immunity. 2004;21:865-76.
24. Spilianakis CG, Flavell RA. Long-range intrachromosomal interactions in the T helper type 2 cytokine locus. Nat Immunol. 2004;5:1017-27.
25. Spilianakis CG, Lalioti MD, Town T, Lee GR, Flavell RA. Interchromosomal associations between alternatively expressed loci. Nature. 2005; 435:637-45.
26. Rowell E, Merkenschlager M, Wilson CB. Long-range regulation of cytokine gene expression. Curr Opin Immunol. 2008;20:272-80.
27. Wilson CB, Rowell E, Sekimata M. Epigenetic control of T-helper-cell differentiation. Nat Rev Immunol. 2009;9:91-105.
28. Göndör A, Ohlsson R. Transcription in the loop. Nature Genetics 2006;38: 1229-30.
29. Galande S, Purbey PK, Notani D, Kumar PP. The third dimension of gene regulation: organization of dynamic chromatin loopscape by SATB1. Curr Opin Genet Dev. 2007;17:408-14.
30. Cai S, Lee CC, Kohwi-Shigematsu T. SATB1 packages densely looped, transcriptionally active chromatin for coordinated expression of cytokine genes. Nat Genet. 2006;38:1278-88.
31. Ribeiro de Almeida C, Heath H, Krpic S, et al. Critical role for the transcription regulator CCCTC-binding factor in the control of Th2 cytokine expression. J Immunol. 2009;182:999-1010.
32. Ridruechai C, Mahasirimongkol S, Phromjai J, et al. Association analysis of susceptibility candidate region on chromosome 5q31 for tuberculosis. Genes Immun. 2010;11:416-22.
33. Sorg RV, Enczmann J, Sorg UR, Schneider EM, Wernet P. Identification of an alternatively spliced transcript of human interleukin-4 lacking the sequence encoded by exon 2. Exp Hematol. 1993;21:560-3.
34. Perkins HD, van Leeuwen BH, Hardy CM, Kerr PJ. The complete cDNA sequences of IL-2, IL-4, IL-6 and IL-10 from the European rabbit (Oryctolagus cuniculus). Cytokine. 2000;12:555-65.
35. Gautherot I, Burdin N, Seguin D, Aujame L, Sodoyer R. Cloning of interleukin-4 delta2 splice variant (IL-4 2) in chimpanzee and cynomolgus macaque: phylogenetic analysis of 2 splice variant appearance, and implications for the study of IL-4-driven immune processes. Immunogenetics. 2002;54:635-44.
36. Yatsenko OP, Filipenko ML, Voronina EN, Khrapov E, Sennikov SV, Kozlov VA. Alternative splicing of murine Interleukin-4 mRNA. Bull Exp Biol Med. 2004;137:179-81.
37. Mazzarella G, Bianco A, Perna F, et al. T lymphocyte phenotypic profile in lung segments affected by cavitary and non-cavitary tuberculosis. Clin Exp Immunol. 2003;132:283-8.
38. van Crevel R, Karyadi E, Preyers F, et al. Increased production of interleukin 4 by CD4and CD8T cells from patients with tuberculosis is related to the presence of pulmonary cavities. J Infect Dis. 2000;181:1194-7.
39. Luzina IG, Lockatell V, Todd NW, Keegan AD, Hasday JD, Atamas SP. Splice isoforms of human interleukin-4 are functionally active in mice in vivo. Immunology. 2011;132:385-93.
40. Luzina IG, Lockatell V, Todd NW, et al. Alternatively spliced variants of interleukin-4 promote inflammation differentially. J Leukoc Biol. 2011, in press, doi: 10.1189/jlb.0510271.
41. Via LE, Lin PL, Ray SM, et al. Tuberculous granulomas are hypoxic in guinea pigs, rabbits, and nonhuman primates. Infect Immun. 2008;76:2333-40.
42. Mendez S, Hatem CL, Kesavan AK, et al. Susceptibility to tuberculosis: composition of tuberculous granulomas in Thorbecke and outbred New Zealand White rabbits. Vet Immunol Immunopathol. 2008;122:167-74.
43. Kapustin Y, Souvourov A, Tatusova T, Lipman D. Splign: algorithms for computing spliced alignments with identification of paralogs. Biol Direct. 2008;3:20.
44. Gertz EM, Yu Y-K, Agarwala R, Schäffer AA, Altschul SF. Compositionbased statistics and translated nucleotide searches: Improving the TBLASTN module of BLAST. BMC Biology. 2006;4:41.
45. Allen JE, Salzberg SL. JIGSAW: integration of multiple sources of evidence for gene prediction. Bioinformatics. 2005; 21: 3596-603.
46. LaPorte SL, Juo ZS, Vaclavikova J, et al. Molecular and structural basis of cytokine receptor pleiotropy in the interleukin-4/13 system. Cell. 2008; 132:259-72.
47. Papadopoulos JS, Agarwala R. COBALT: constraint-based alignment tool for multiple protein sequences. Bioinformatics. 2007;23:1073-9.
48. The PyMol Molecular Graphics System, Schrödinger, LLC.