Methods for analyzing the role of DNA methylation and chromatin structure in regulating T lymphocyte gene expression

Biological Procedures Online

Volumn 6, Issue 1, 2004, Pages 189-203

  Lu, Qianjin ^a,b,c   Richardson, Bruce ^a,b  

^a UNIVERSITY OF MICHIGAN MEDICAL SCHOOL   (United States)

^b CENTRAL SOUTH UNIVERSITY   (China)

^c NONE   (United States)

Author keywords

DNA methylation; Gene expression regulation; T lymphocytes

Indexed keywords

BISULFITE; CD4 ANTIGEN; CD8 ANTIGEN; DEOXYRIBONUCLEASE I; DNA; DNA METHYLTRANSFERASE; LYMPHOCYTE FUNCTION ASSOCIATED ANTIGEN 1; PERFORIN;

ANALYTIC METHOD; ANTIGEN DETECTION; ARTICLE; CELL FUNCTION; CHROMATIN STRUCTURE; CONTROLLED STUDY; DNA FLANKING REGION; DNA METHYLATION; ENZYME INHIBITION; FIBROBLAST; GENE EXPRESSION REGULATION; GENE SEQUENCE; HUMAN; HUMAN CELL; HUMAN EXPERIMENT; NORMAL HUMAN; PROMOTER REGION; SENSITIVITY ANALYSIS; SEQUENCE ANALYSIS; T LYMPHOCYTE;

EID: 18644366081     PISSN: 14809222     EISSN: None     Source Type: Journal    
DOI: 10.1251/bpo89     Document Type: Article

References (22)

1. Bird AP, Wolffe AP. Methylation-induced repression - belts, braces, and chromatin. Cell 1999; 99:451-454.
2. Attwood JT, Yung RL, Richardson BC. DNA methylation and the regulation of gene transcription. Cell Mol Life Sci 2002; 59:241-257.
3. Richardson BC. Role of DNA methylation in the regulation of cell function: autoimmunity, aging and cancer. J Nutr 2002; 132(8 Suppl):2401S-2405S.
4. Nguyen CT, Gonzales FA, Jones PA. Altered chromatin structure associated with methylation-induced gene silencing in cancer cells: correlation of accessibility, methylation, MeCP2 binding and acetylation. Nucleic Acids Res 2001; 29:4598-4606.
5. Fraga MF, Esteller M. DNA methylation: a profile of methods and applications. Biotechniques 2002; 33(3):632, 634, 636-649.
6. Clark SJ, Harrison J, Paul CL, Frommer M. High sensitivity mapping of methylated cytosines. Nucleic Acids Res 1994; 22:2990-2997.
7. Lu Q, Wu A, Ray D, Deng C, Attwood J, Hanash S, Pipkin M, Lichtenheld M, Richardson B. DNA methylation and chromatin structure regulate T cell perforin gene expression. J Immunol 2003; 170:5124-5132.
8. Oelke K, Lu Q, Richardson D, Wu A, Deng C, Hanash S, Richardson B. Overexpression of CD70 and overstimulation of IgG synthesis by lupus T cells and T cells treated with DNA methylation inhibitors. Arthritis Rheum 2004; 50:1850-1860.
9. Cornacchia E, Golbus J, Maybaum J, Strahler J, Hanash S, Richardson B. Hydralazine and procainamide inhibit T cell DNA methylation and induce autoreactivity. J Immunol 1988;140:2197-2200.
10. Lu Q, Kaplan M, Ray D, Zacharek S, Gutsch D, Richardson B. Demethylation of ITGAL (CD11a) regulatory sequences in systemic lupus erythematosus. Arthritis Rheum 2002; 46:1282-1291.
11. Lu Q, Ray D, Gutsch D, Richardson B. Effect of DNA methylation and chromatin structure on ITGAL expression. Blood 2002; 99:4503-4508.
12. Cornwell RD, Gollahon KA, Hickstein DD. Description of the leukocyte function-associated antigen 1 (LFA-1 or CD11a) promoter. Proc Natl Acad Sci USA 1993; 90:4221-4225.
13. Yoder JA, Walsh CP, Bestor TH. Cytosine methylation and the ecology of intragenomic parasites. Trends Genet 1997; 13:335-340.
14. Lichtenheld MG, Podack ER. Structure of the human perforin gene. A simple gene organization with interesting potential regulatory sequences. J Immunol 1989; 143:4267-4274.
15. Zhang J, Scordi I, Smyth MJ, Lichtenheld MG. Interleukin 2 receptor signaling regulates the perforin gene through signal transducer and activator of transcription (Stat)5 activation of two enhancers. J Exp Med 1999; 190:1297-1308.
16. Jones PA. Gene activation by 5-azacytidine. In: Razin A, Cedar H, Riggs A, editors. DNA Methylation. Biochemistry and Biological Significance. New York: Springer-Verlag; 1984. p 165-187.
17. Lu Q, Richardson B. DNaseI hypersensitivity analysis of chromatin structure. In: T T, editor. Methods in Molecular Biology. Volume 287. Totowa NJ: Humana Press; 2004. p 77-86.
18. Macnab JC, Adams RL, Rinaldi A, Orr A, Clark L. Hypomethylation of host cell DNA synthesized after infection or transformation of cells by herpes simplex virus. Mol Cell Biol 1988; 8:1443-1448.
19. Javed A, Zaidi SK, Gutierrez SE, Lengner CJ, Harrington KS, Hovhannisyan H, Cho BC, Pratap J, Pockwinse SM, Montecino M et al. Chromatin immunoprecipitation. Methods Mol Biol 2004; 285:41-44.
20. Bird A. The essentials of DNA methylation. Cell 1992; 70:5-8.
21. Cihak A. Biological effects of 5-azacytidine in eukaryotes. Oncology 1974; 30: 405-422.
22. Nyce J, Liu L, Jones PA. Variable effects of DNA-synthesis inhibitors upon DNA methylation in mammalian cells. Nucleic Acids Res 1986; 14:4353-4367.