Genome-wide analysis of interferon regulatory factor I binding in primary human monocytes

Gene

Volumn 487, Issue 1, 2011, Pages 21-28

  Shi, Lihua ^a   Perin, Juan C ^b   Leipzig, Jeremy ^b   Zhang, Zhe ^b   Sullivan, Kathleen E ^a  

^a UNIVERSITY OF PENNSYLVANIA   (United States)

^b CHILDREN S HOSPITAL OF PHILADELPHIA   (United States)

Author keywords

Chromatin immunoprecipitation; Inflammation; Interferon; IRF E; IRF1; Lupus

Indexed keywords

INTERFERON REGULATORY FACTOR 1;

ARTICLE; BINDING SITE; GENE EXPRESSION; GENE FUNCTION; GENE IDENTIFICATION; GENE TARGETING; GENETIC ANALYSIS; GENETIC ASSOCIATION; GENETIC TRANSFECTION; HUMAN; HUMAN CELL; IN VIVO STUDY; MONOCYTE; PRIORITY JOURNAL;

BASE SEQUENCE; BINDING SITES; CARRIER PROTEINS; CELLS, CULTURED; CHROMATIN IMMUNOPRECIPITATION; GENE EXPRESSION; GENE EXPRESSION PROFILING; GENOME, HUMAN; HUMANS; INTERFERON REGULATORY FACTOR-1; INTERFERONS; INTERLEUKIN-4; INTRACELLULAR SIGNALING PEPTIDES AND PROTEINS; MONOCYTES; PROTEIN BINDING; PROTEINS; SEQUENCE ANALYSIS, DNA;

EID: 80052321986     PISSN: 03781119     EISSN: 18790038     Source Type: Journal    
DOI: 10.1016/j.gene.2011.07.004     Document Type: Article

References (49)

1. Baechler E.C., et al. Interferon-inducible gene expression signature in peripheral blood cells of patients with severe lupus. Proc. Natl. Acad. Sci. U. S. A. 2003, 100:2610-2615.
2. Bennett L., et al. Interferon and granulopoiesis signatures in systemic lupus erythematosus blood. J. Exp. Med. 2003, 197:711-723.
3. Chang C.H., Hammer J., Loh J.E., Fodor W.L., Flavell R.A. The activation of major histocompatibility complex class I genes by interferon regulatory factor-1 (IRF-1). Immunogenetics 1992, 35:378-384.
4. Decker T., Muller M., Stockinger S. The yin and yang of type I interferon activity in bacterial infection. Nat. Rev. Immunol. 2005, 5:675-687.
5. Denny M.F., et al. Accelerated macrophage apoptosis induces autoantibody formation and organ damage in systemic lupus erythematosus. J. Immunol. 2006, 176:2095-2104.
6. Digweed M., Gunthert U., Schneider R., Seyschab H., Friedl R., Sperling K. Irreversible repression of DNA synthesis in Fanconi anemia cells is alleviated by the product of a novel cyclin-related gene. Mol. Cell. Biol. 1995, 15:305-314.
7. Escalante C.R., Yie J., Thanos D., Aggarwal A.K. Expression, purification, and co-crystallization of IRF-I bound to the interferon-beta element PRDI. FEBS Lett. 1997, 414:219-220.
8. Frontini M., Vijayakumar M., Garvin A., Clarke N. A ChIP-chip approach reveals a novel role for transcription factor IRF1 in the DNA damage response. Nucleic Acids Res. 2009, 37:1073-1085.
9. Fujii Y., Shimizu T., Kusumoto M., Kyogoku Y., Taniguchi T., Hakoshima T. Crystal structure of an IRF-DNA complex reveals novel DNA recognition and cooperative binding to a tandem repeat of core sequences. EMBO J. 1999, 18:5028-5041.
10. Gabriele L., et al. IRF-1 deficiency skews the differentiation of dendritic cells toward plasmacytoid and tolerogenic features. J. Leukoc. Biol. 2006, 80:1500-1511.
11. Graham R.R., et al. A common haplotype of interferon regulatory factor 5 (IRF5) regulates splicing and expression and is associated with increased risk of systemic lupus erythematosus. Nat. Genet. 2006, 38:550-555.
12. Harada H., et al. Structurally similar but functionally distinct factors, IRF-1 and IRF-2, bind to the same regulatory elements of IFN and IFN-inducible genes. Cell 1989, 58:729-739.
13. Honda K., Taniguchi T. IRFs: master regulators of signalling by Toll-like receptors and cytosolic pattern-recognition receptors. Nat. Rev. Immunol. 2006, 6:644-658.
14. Kashiwaba M., Tamura G., Ishida M. Aberrations of the APC gene in primary breast carcinoma. J. Cancer Res. Clin. Oncol. 1994, 120:727-731.
15. Kim P.K., et al. IRF-1 expression induces apoptosis and inhibits tumor growth in mouse mammary cancer cells in vitro and in vivo. Oncogene 2004, 23:1125-1135.
16. Kimura T., et al. Involvement of the IRF-1 transcription factor in antiviral responses to interferons. Science 1994, 264:1921-1924.
17. Ko J., Gendron-Fitzpatrick A., Splitter G.A. Susceptibility of IFN regulatory factor-1 and IFN consensus sequence binding protein-deficient mice to brucellosis. J. Immunol. 2002, 168:2433-2440.
18. Kroger A., et al. Growth suppression of the hepatocellular carcinoma cell line Hepa1-6 by an activatable interferon regulatory factor-1 in mice. Cancer Res. 2001, 61:2609-2617.
19. Kroger A., Dallugge A., Kirchhoff S., Hauser H. IRF-1 reverts the transformed phenotype of oncogenically transformed cells in vitro and in vivo. Oncogene 2003, 22:1045-1056.
20. Lee J.H., et al. Syndecan-2 regulates the migratory potential of melanoma cells. J. Biol. Chem. 2009, 284:27167-27175.
21. Li L. GADEM: a genetic algorithm guided formation of spaced dyads coupled with an EM algorithm for motif discovery. J. Comput. Biol. 2009, 16:317-329.
22. Miyamoto M., et al. Regulated expression of a gene encoding a nuclear factor, IRF-1, that specifically binds to IFN-beta gene regulatory elements. Cell 1988, 54:903-913.
23. Morin P., et al. Preferential binding sites for interferon regulatory factors 3 and 7 involved in interferon - a gene transcription. J. Mol. Biol. 2002, 316:1009-1022.
24. Muse G.W., et al. RNA polymerase is poised for activation across the genome. Nat. Genet. 2007, 39:1507-1511.
25. Naf D., Hardin S.E., Weissmann C. Multimerization of AAGTGA and GAAAGT generates sequences that mediate virus inducibility by mimicking an interferon promoter element. Proc. Natl. Acad. Sci. U. S. A. 1991, 88:1369-1373.
26. Nishizaki T., et al. Genetic alterations in lobular breast cancer by comparative genomic hybridization. Int. J. Cancer 1997, 74:513-517.
27. O'Connell P., Pekkel V., Fuqua S.A., Osborne C.K., Clark G.M., Allred D.C. Analysis of loss of heterozygosity in 399 premalignant breast lesions at 15 genetic loci. J. Natl. Cancer Inst. 1998, 90:697-703.
28. Ogasawara K., et al. Requirement for IRF-1 in the microenvironment supporting development of natural killer cells. Nature 1998, 391:700-703.
29. Ohteki T., Yoshida H., Matsuyama T., Duncan G.S., Mak T.W., Ohashi P.S. The transcription factor interferon regulatory factor 1 (IRF-1) is important during the maturation of natural killer 1.1+ T cell receptor-alpha/beta+(NK1+ T) cells, natural killer cells, and intestinal intraepithelial T cells. J. Exp. Med. 1998, 187:967-972.
30. Penninger J.M., et al. The interferon regulatory transcription factor IRF-1 controls positive and negative selection of CD8+ thymocytes. Immunity 1997, 7:243-254.
31. Pine R. Constitutive expression of an ISGF2/IRF1 transgene leads to interferon-independent activation of interferon-inducible genes and resistance to virus infection. J. Virol. 1992, 66:4470-4478.
32. Platanias L.C. Mechanisms of type-I- and type-II-interferon-mediated signalling. Nat. Rev. Immunol. 2005, 5:375-386.
33. Romeo G., Fiorucci G., Chiantore M.V., Percario Z.A., Vannucchi S., Affabris E. IRF-1 as a negative regulator of cell proliferation. J. Interferon Cytokine Res. 2002, 22:39-47.
34. Siegrist F., Ebeling M., Certa U. The small interferon-induced transmembrane genes and proteins. J. Interferon Cytokine Res. 2011, 31:183-197.
35. Skaar T.C., Prasad S.C., Sharareh S., Lippman M.E., Brunner N., Clarke R. Two-dimensional gel electrophoresis analyses identify nucleophosmin as an estrogen regulated protein associated with acquired estrogen-independence in human breast cancer cells. J. Steroid Biochem. Mol. Biol. 1998, 67:391-402.
36. Taki S., et al. Multistage regulation of Th1-type immune responses by the transcription factor IRF-1. Immunity 1997, 6:673-679.
37. Tamura T., et al. An IRF-1-dependent pathway of DNA damage-induced apoptosis in mitogen-activated T lymphocytes. Nature 1995, 376:596-599.
38. Tanaka N., Kawakami T., Taniguchi T. Recognition DNA sequences of interferon regulatory factor 1 (IRF-1) and IRF-2, regulators of cell growth and the interferon system. Mol. Cell. Biol. 1993, 13:4531-4538.
39. Tanaka N., et al. Cellular commitment to oncogene-induced transformation or apoptosis is dependent on the transcription factor IRF-1. Cell 1994, 77:829-839.
40. Tanaka N., et al. Cooperation of the tumour suppressors IRF-1 and p53 in response to DNA damage. Nature 1996, 382:816-818.
41. Taniguchi T., Ogasawara K., Takaoka A., Tanaka N. IRF family of transcription factors as regulators of host defense. Annu. Rev. Immunol. 2001, 19:623-655.
42. Testa U., et al. Impaired myelopoiesis in mice devoid of interferon regulatory factor 1. Leukemia 2004, 18:1864-1871.
43. Tirkkonen M., Tanner M., Karhu R., Kallioniemi A., Isola J., Kallioniemi O.P. Molecular cytogenetics of primary breast cancer by CGH. Genes Chromosomes Cancer 1998, 21:177-184.
44. Troyanovsky B., Levchenko T., Mansson G., Matvijenko O., Holmgren L. Angiomotin: an angiostatin binding protein that regulates endothelial cell migration and tube formation. J. Cell Biol. 2001, 152:1247-1254.
45. Urschel J.D., Bertsch D.J., Takita H. Thoracic packing for postoperative hemorrhage. J. Cardiovasc. Surg. (Torino) 1997, 38:673-675.
46. Waddell S.J., et al. Dissecting interferon-induced transcriptional programs in human peripheral blood cells. PLoS One 2010, 5:e9753.
47. Yim J.H., Wu S.J., Casey M.J., Norton J.A., Doherty G.M. IFN regulatory factor-1 gene transfer into an aggressive, nonimmunogenic sarcoma suppresses the malignant phenotype and enhances immunogenicity in syngeneic mice. J. Immunol. 1997, 158:1284-1292.
48. Zhang Z., Maurer K., Perin J.C., Song L., Sullivan K.E. Cytokine-induced monocyte characteristics in SLE. J. Biomed. Biotechnol. 2010, 2010:507475.
49. Zhang Z., Song L., Maurer K., Petri M.A., Sullivan K.E. Global H4 acetylation analysis by ChIP-chip in systemic lupus erythematosus monocytes. Genes Immun. 2010, 11:124-133.