DNA methylation profile of Aire-deficient mouse medullary thymic epithelial cells

BMC Immunology

Volumn 13, Issue , 2012, Pages

  Wu, Guoying ^a   Hirabayashi, Keiji ^a   Sato, Shinya ^a   Akiyama, Nobuko ^b   Akiyama, Taishin ^b   Shiota, Kunio ^a   Yagi, Shintaro ^a  

^a UNIVERSITY OF TOKYO   (Japan)

^b UNIVERSITY OF TOKYO   (Japan)

Author keywords

Aire; Medullary thymic epithelial cells; T DMR

Indexed keywords

AUTOIMMUNE REGULATOR PROTEIN; B7 ANTIGEN; DNA; PROTEIN; RECEPTOR ACTIVATOR OF NUCLEAR FACTOR KAPPA B; TRP63 PROTEIN; UNCLASSIFIED DRUG;

ANIMAL EXPERIMENT; ARTICLE; BRAIN; CONTROLLED STUDY; DNA METHYLATION; EMBRYONIC STEM CELL; EPITHELIUM CELL; GENE EXPRESSION PROFILING; GENETIC ANALYSIS; GENETIC ASSOCIATION; LIVER; MEDULLARY THYMIC EPITHELIUM CELL; MOUSE; NONHUMAN; SIGNAL TRANSDUCTION; THYMUS;

ANIMALS; ANTIGENS, CD45; BIOLOGICAL MARKERS; CELL SEPARATION; DNA METHYLATION; EPITHELIAL CELLS; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION; MICE; MICE, INBRED C57BL; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; ORGAN SPECIFICITY; STROMAL CELLS; THYMUS GLAND; TRANSCRIPTION FACTORS; TRANSCRIPTION INITIATION SITE;

EID: 84868261972     PISSN: None     EISSN: 14712172     Source Type: Journal    
DOI: 10.1186/1471-2172-13-58     Document Type: Article

References (36)

1. Kyewski B, Klein L. A central role for central tolerance. Annu Rev Immunol 2006, 24:571-606. 10.1146/annurev.immunol.23.021704.115601, 16551260.
2. Mathis D, Benoist C. Aire. Annu Rev Immunol 2009, 27:287-312. 10.1146/annurev.immunol.25.022106.141532, 19302042.
3. Derbinski J, Gäbler J, Brors B, Tierling S, Jonnakuty S, Hergenhahn M, Peltonen L, Walter J, Kyewski B. Promiscuous gene expression in thymic epithelial cells is regulated at multiple levels. J Exp Med 2005, 202(1):33-45. 10.1084/jem.20050471, 2212909, 15983066.
4. Johnnidis JB, Venanzi ES, Taxman DJ, Ting JP, Benoist CO, Mathis DJ. Chromosomal clustering of genes controlled by the aire transcription factor. Proc Natl Acad Sci U S A 2005, 102(20):7233-7238. 10.1073/pnas.0502670102, 1129145, 15883360.
5. Derbinski J, Pinto S, Rösch S, Hexel K, Kyewski B. Promiscuous gene expression patterns in single medullary thymic epithelial cells argue for a stochastic mechanism. Proc Natl Acad Sci U S A 2008, 105(2):657-662. 10.1073/pnas.0707486105, 2206592, 18180458.
6. Gillard GO, Farr AG. Features of medullary thymic epithelium implicate postnatal development in maintaining epithelial heterogeneity and tissue-restricted antigen expression. J Immunol 2006, 176(10):5815-5824.
7. Dooley J, Erickson M, Farr AG. Alterations of the medullary epithelial compartment in the Aire-deficient thymus: implications for programs of thymic epithelial differentiation. J Immunol 2008, 181(8):5225-5232. 2677919, 18832676.
8. Senoo M, Pinto F, Crum CP, McKeon F. p63 Is essential for the proliferative potential of stem cells in stratified epithelia. Cell 2007, 129(3):523-536. 10.1016/j.cell.2007.02.045, 17482546.
9. Yano M, Kuroda N, Han H, Meguro-Horike M, Nishikawa Y, Kiyonari H, Maemura K, Yanagawa Y, Obata K, Takahashi S, et al. Aire controls the differentiation program of thymic epithelial cells in the medulla for the establishment of self-tolerance. J Exp Med 2008, 205(12):2827-2838. 10.1084/jem.20080046, 2585853, 19015306.
10. Matsumoto M. Contrasting models for the roles of Aire in the differentiation program of epithelial cells in the thymic medulla. Eur J Immunol 2011, 41(1):12-17. 10.1002/eji.201041024, 21182071.
11. Hikosaka Y, Nitta T, Ohigashi I, Yano K, Ishimaru N, Hayashi Y, Matsumoto M, Matsuo K, Penninger JM, Takayanagi H, et al. The cytokine RANKL produced by positively selected thymocytes fosters medullary thymic epithelial cells that express autoimmune regulator. Immunity 2008, 29(3):438-450. 10.1016/j.immuni.2008.06.018, 18799150.
12. Akiyama T, Shimo Y, Yanai H, Qin J, Ohshima D, Maruyama Y, Asaumi Y, Kitazawa J, Takayanagi H, Penninger JM, et al. The tumor necrosis factor family receptors RANK and CD40 cooperatively establish the thymic medullary microenvironment and self-tolerance. Immunity 2008, 29(3):423-437. 10.1016/j.immuni.2008.06.015, 18799149.
13. Shiota K, Kogo Y, Ohgane J, Imamura T, Urano A, Nishino K, Tanaka S, Hattori N. Epigenetic marks by DNA methylation specific to stem, germ and somatic cells in mice. Genes Cells 2002, 7(9):961-969. 10.1046/j.1365-2443.2002.00574.x, 12296826.
14. Sakamoto H, Suzuki M, Abe T, Hosoyama T, Himeno E, Tanaka S, Greally JM, Hattori N, Yagi S, Shiota K. Cell type-specific methylation profiles occurring disproportionately in CpG-less regions that delineate developmental similarity. Genes Cells 2007, 12(10):1123-1132. 10.1111/j.1365-2443.2007.01120.x, 17903172.
15. Sakamoto H, Kogo Y, Ohgane J, Hattori N, Yagi S, Tanaka S, Shiota K. Sequential changes in genome-wide DNA methylation status during adipocyte differentiation. Biochem Biophys Res Commun 2008, 366(2):360-366. 10.1016/j.bbrc.2007.11.137, 18062916.
16. Yagi S, Hirabayashi K, Sato S, Li W, Takahashi Y, Hirakawa T, Wu G, Hattori N, Ohgane J, Tanaka S, et al. DNA methylation profile of tissue-dependent and differentially methylated regions (T-DMRs) in mouse promoter regions demonstrating tissue-specific gene expression. Genome Res 2008, 18(12):1969-1978. 10.1101/gr.074070.107, 2593572, 18971312.
17. Sato S, Yagi S, Arai Y, Hirabayashi K, Hattori N, Iwatani M, Okita K, Ohgane J, Tanaka S, Wakayama T, et al. Genome-wide DNA methylation profile of tissue-dependent and differentially methylated regions (T-DMRs) residing in mouse pluripotent stem cells. Genes Cells 2010, 15(6):607-618. 10.1111/j.1365-2443.2010.01404.x, 20477876.
18. Kikuchi R, Yagi S, Kusuhara H, Imai S, Sugiyama Y, Shiota K. Genome-wide analysis of epigenetic signatures for kidney-specific transporters. Kidney Int 2010, 78(6):569-577. 10.1038/ki.2010.176, 20555317.
19. Murumägi A, Vähämurto P, Peterson P. Characterization of regulatory elements and methylation pattern of the autoimmune regulator (AIRE) promoter. J Biol Chem 2003, 278(22):19784-19790. 10.1074/jbc.M210437200, 12651856.
20. Kont V, Murumägi A, Tykocinski LO, Kinkel SA, Webster KE, Kisand K, Tserel L, Pihlap M, Ströbel P, Scott HS, et al. DNA methylation signatures of the AIRE promoter in thymic epithelial cells, thymomas and normal tissues. Mol Immunol 2011, 49(3):518-526. 10.1016/j.molimm.2011.09.022, 22036612.
21. Tykocinski LO, Sinemus A, Rezavandy E, Weiland Y, Baddeley D, Cremer C, Sonntag S, Willecke K, Derbinski J, Kyewski B. Epigenetic regulation of promiscuous gene expression in thymic medullary epithelial cells. Proc Natl Acad Sci U S A 2010, 107(45):19426-19431. 10.1073/pnas.1009265107, 2984162, 20966351.
22. Anderson MS, Venanzi ES, Klein L, Chen Z, Berzins SP, Turley SJ, von Boehmer H, Bronson R, Dierich A, Benoist C, et al. Projection of an immunological self shadow within the thymus by the aire protein. Science 2002, 298(5597):1395-1401. 10.1126/science.1075958, 12376594.
23. Rodewald HR. Thymus organogenesis. Annu Rev Immunol 2008, 26:355-388. 10.1146/annurev.immunol.26.021607.090408, 18304000.
24. Nishikawa Y, Hirota F, Yano M, Kitajima H, Miyazaki J, Kawamoto H, Mouri Y, Matsumoto M. Biphasic Aire expression in early embryos and in medullary thymic epithelial cells before end-stage terminal differentiation. J Exp Med 2010, 207(5):963-971. 10.1084/jem.20092144, 2867289, 20404099.
25. Candi E, Rufini A, Terrinoni A, Giamboi-Miraglia A, Lena AM, Mantovani R, Knight R, Melino G. DeltaNp63 regulates thymic development through enhanced expression of FgfR2 and Jag2. Proc Natl Acad Sci U S A 2007, 104(29):11999-12004. 10.1073/pnas.0703458104, 1924561, 17626181.
26. Rossi SW, Kim MY, Leibbrandt A, Parnell SM, Jenkinson WE, Glanville SH, McConnell FM, Scott HS, Penninger JM, Jenkinson EJ, et al. RANK signals from CD4(+)3(-) inducer cells regulate development of Aire-expressing epithelial cells in the thymic medulla. J Exp Med 2007, 204(6):1267-1272. 10.1084/jem.20062497, 2118623, 17502664.
27. Russell HI, York IA, Rock KL, Monaco JJ. Class II antigen processing defects in two H2d mouse cell lines are caused by point mutations in the H2-DMa gene. Eur J Immunol 1999, 29(3):905-911. 10.1002/(SICI)1521-4141(199903)29:03<905::AID-IMMU905>3.0.CO;2-8, 10092094.
28. Zuklys S, Balciunaite G, Agarwal A, Fasler-Kan E, Palmer E, Holländer GA. Normal thymic architecture and negative selection are associated with Aire expression, the gene defective in the autoimmune-polyendocrinopathy-candidiasis-ectodermal dystrophy (APECED). J Immunol 2000, 165(4):1976-1983.
29. Van Vliet E, Jenkinson EJ, Kingston R, Owen JJ, Van Ewijk W. Stromal cell types in the developing thymus of the normal and nude mouse embryo. Eur J Immunol 1985, 15(7):675-681. 10.1002/eji.1830150707, 4007044.
30. Gray DH, Chidgey AP, Boyd RL. Analysis of thymic stromal cell populations using flow cytometry. J Immunol Methods 2002, 260(1-2):15-28.
31. Johnson WE, Li W, Meyer CA, Gottardo R, Carroll JS, Brown M, Liu XS. Model-based analysis of tiling-arrays for ChIP-chip. Proc Natl Acad Sci U S A 2006, 103(33):12457-12462. 10.1073/pnas.0601180103, 1567901, 16895995.
32. Goecks J, Nekrutenko A, Taylor J, Team G. Galaxy: a comprehensive approach for supporting accessible, reproducible, and transparent computational research in the life sciences. Genome Biol 2010, 11(8):R86. 10.1186/gb-2010-11-8-r86, 2945788, 20738864.
33. Ihaka R, Gentleman R. R: a language for data analysis and graphics. J. Comp. Graph. Stat 1996, 5(3):299-314.
34. Edgar R, Domrachev M, Lash AE. Gene Expression Omnibus: NCBI gene expression and hybridization array data repository. Nucleic Acids Res 2002, 30(1):207-210. 10.1093/nar/30.1.207, 99122, 11752295.
35. Wu ZJ, Irizarry RA, Gentleman R, Martinez-Murillo F, Spencer R. A model-based background adjustment for oligonucleotide expression arrays. J Am Stat Assoc 2004, 99:909-917.
36. Haider S, Ballester B, Smedley D, Zhang J, Rice P, Kasprzyk A. BioMart Central Portal-unified access to biological data. Nucleic Acids Res 2009, 37(Web Server issue):W23-W27. 2703988, 19420058.