MethPrimer: Designing primers for methylation PCRs

Bioinformatics

Volumn 18, Issue 11, 2002, Pages 1427-1431

  Li, Long Cheng ^a   Dahiya, Rajvir ^a  

^a UNIVERSITY OF CALIFORNIA   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

BISULFITE; PRIMER DNA; ESTROGEN RECEPTOR; ESTROGEN RECEPTOR BETA;

ARTICLE; COMPUTER GRAPHICS; COMPUTER PROGRAM; COMPUTER SYSTEM; CONTROLLED STUDY; CPG ISLAND; DNA METHYLATION; DNA SEQUENCE; GENE MAPPING; HUMAN COMPUTER INTERACTION; INTERNET; POLYMERASE CHAIN REACTION; PREDICTION; PRIORITY JOURNAL; SEQUENCE ANALYSIS; CHEMISTRY; CLASSIFICATION; COMPUTER AIDED DESIGN; COMPUTER INTERFACE; EQUIPMENT DESIGN; EVALUATION; GENETICS; HUMAN; INSTRUMENTATION; METHODOLOGY; MOLECULAR GENETICS; MULTIMEDIA; NUCLEOTIDE SEQUENCE; PILOT STUDY; QUALITY CONTROL; SENSITIVITY AND SPECIFICITY; SEQUENCE ALIGNMENT;

BASE SEQUENCE; COMPUTER-AIDED DESIGN; CPG ISLANDS; DNA METHYLATION; DNA PRIMERS; EQUIPMENT DESIGN; ESTROGEN RECEPTOR BETA; HUMANS; INTERNET; MOLECULAR SEQUENCE DATA; MULTIMEDIA; PILOT PROJECTS; POLYMERASE CHAIN REACTION; QUALITY CONTROL; RECEPTORS, ESTROGEN; SENSITIVITY AND SPECIFICITY; SEQUENCE ALIGNMENT; SEQUENCE ANALYSIS, DNA; SOFTWARE; USER-COMPUTER INTERFACE;

EID: 0036856355     PISSN: 13674803     EISSN: 13674811     Source Type: Journal    
DOI: 10.1093/bioinformatics/18.11.1427     Document Type: Article

References (22)

1. Antequera,F. and Bird,A. (1993) CpG islands. Exs, 64, 169-185.
2. Baylin,S.B., Herman,J.G., Graff,J.R., Vertino,P.M. and Issa,J.P. (1998) Alterations in DNA methylation: a fundamental aspect of neoplasia. Adv. Cancer. Res., 72, 141-196.
3. Clark,S.J., Harrison,J., Paul,C.L. and Frommer,M. (1994) High sensitivity mapping of methylated cytosines. Nucleic. Acids Res., 22, 2990-2997.
4. Frommer,M., McDonald,L.E., Millar,D.S., Collis,C.M., Watt,F., Grigg,G.W., Molloy,P.L. and Paul,C.L. (1992) A genomic sequencing protocol that yields a positive display of 5-methylcytosine residues in individual DNA strands. Proc Natl Acad. Sci. USA, 89, 1827-1831.
5. Gardiner-Garden,M. and Frommer,M. (1987) CpG islands in vertebrate genomes. J. Mol. Biol., 196, 261-282.
6. Gonzalgo,M.L. and Jones,P.A. (1997) Rapid quantitation of methylation differences at specific sites using methylation-sensitive single nucleotide primer extension (Ms-SNuPE). Nucleic Acids Res., 25, 2529-2531.
7. Graff,J.R., Herman,J.G., Myohanen,S., Baylin,S.B. and Vertino,P.M. (1997) Mapping patterns of CpG island methylation in normal and neoplastic cells implicates both upstream and downstream regions in de novo methylation. J. Biol. Chem., 272, 22322-22329.
8. Hayatsu,H., Wataya,Y., Kai,K. and Iida,S. (1970) Reaction of sodium bisulfite with uracil, cytosine, and their derivatives. Biochemistry, 9, 2858-2865.
9. Herman,J.G., Graff,J.R., Myohanen,S., Nelkin,B.D. and Baylin,S.B. (1996) Methylation-specific PCR: a novel PCR assay for methylation status of CpG islands. Proc Natl Acad. Sci. USA, 93, 9821-9826.
10. Larsen,F., Gundersen,G., Lopez,R. and Prydz,H. (1992) CpG islands as gene markers in the human genome. Genomics, 13, 1095-1107.
11. Li,E., Beard,C. and Jaenisch,R. (1993) Role for DNA methylation in genomic imprinting. Nature, 366, 362-365.
12. Li,L.C., Chui,R., Nakajima,K., Oh,B.R., Au,H.C. and Dahiya,R. (2000a) Frequent methylation of estrogen receptor in prostate cancer: correlation with tumor progression. Cancer Res., 60, 702-706.
13. Li,L.C., Yeh,C.C., Nojima,D. and Dahiya,R. (2000b) Cloning and characterization of human estrogen receptor beta promoter. Biochem. Biophys. Res. Commun., 275, 682-689.
14. Li,L.C., Zhao,H., Nakajima,K., Oh,B.R., Filho,L.A., Carroll,P. and Dahiya,R. (2001) Methylation of the E-cadherin gene promoter correlates with progression of prostate cancer. J. Urol., 166, 705-709.
15. Monk,M., Boubelik,M. and Lehnert,S. (1987) Temporal and regional changes in DNA methylation in the embryonic, extraembryonic and germ cell lineages during mouse embryo development. Development, 99, 371-382.
16. Nojima,D., Nakajima,K., Li,L.C., Franks,J., Ribeiro-Filho,L., Ishii,N. and Dahiya,R. (2001) CpG methylation of promoter region inactivates E-cadherin gene in renal cell carcinoma. Mol. Carcinog., 32, 19-27.
17. Paulsen,M. and Ferguson-Smith,A.C. (2001) DNA methylation in genomic imprinting, development, and disease. J. Pathol., 195, 97-110.
18. Rozen,S. and Skaletsky,H. (2000) Primer3 on the WWW for general users and for biologist programmers. Methods Mol. Biol., 132, 365-386.
19. Rychlik,W. (2000) Primer selection and design for polymerase chain reaction. In Rapley,R. (ed.), The Nucleic Acid Protocols Handbook. Humana Press, Totowa, NJ, pp. 581-588.
20. Shapiro,R. and Weisgras,J.M. (1970) Bisulfite-catalyzed transamination of cytosine and cytidine. Biochem. Biophys. Res. Commun., 40, 839-843.
21. Singer-Sam,J. and Riggs,A.D. (1993) X chromosome inactivation and DNA methylation. Exs, 64, 358-384.
22. Xiong,Z. and Laird,P.W. (1997) COBRA: a sensitive and quantitative DNA methylation assay. Nucleic. Acids Res., 25, 2532-2534.