Restriction site-specific methylation studies of imprinted genes with quantitative real-time PCR

Clinical Chemistry

Volumn 54, Issue 3, 2008, Pages 491-499

  Bruce, Sara ^a,b,e   Hannula Jouppi, Katariina ^b   Lindgren, Cecilia M ^c,d   Lipsanen Nyman, Marita ^b   Kere, Juha ^a,b  

^a KAROLINSKA INSTITUTE   (Sweden)

^b UNIVERSITY OF HELSINKI   (Finland)

^c UNIVERSITY OF OXFORD   (United Kingdom)

^d UNIVERSITY OF OXFORD   (United Kingdom)

^e Department of Biosciences and Nutrition ^*  (Sweden)

Author keywords

[No Author keywords available]

Indexed keywords

DNA; GENOMIC DNA; POTASSIUM CHANNEL KCNQ1; RESTRICTION ENDONUCLEASE;

ARTICLE; BECKWITH WIEDEMANN SYNDROME; CHROMOSOME 11; CHROMOSOME 7; CLINICAL ARTICLE; CONTROLLED STUDY; DIAGNOSTIC ACCURACY; DIGESTION; DNA METHYLATION; FATHER; FEMALE; GENE LOCUS; GENETIC SCREENING; GENOME IMPRINTING; HUMAN; MALE; MOTHER; POLYMERASE CHAIN REACTION; QUANTITATIVE GENETICS; RESTRICTION SITE; REVERSE TRANSCRIPTION POLYMERASE CHAIN REACTION; SILVER RUSSELL SYNDROME; UNIPARENTAL DISOMY; VALIDATION PROCESS;

CHROMOSOMES, HUMAN, PAIR 11; CHROMOSOMES, HUMAN, PAIR 7; DNA METHYLATION; FEMALE; GENETIC DISEASES, INBORN; GENOMIC IMPRINTING; HUMANS; MALE; POLYMERASE CHAIN REACTION; UNIPARENTAL DISOMY;

EID: 40449105358     PISSN: 00099147     EISSN: None     Source Type: Journal    
DOI: 10.1373/clinchem.2007.098491     Document Type: Article

References (30)

1. Costello JF, Plass C. Methylation matters. J Med Genet 2001;38:285-303.
2. Morison IM, Ramsay JP, Spencer HG. A census of mammalian imprinting. Trends Genet 2005;21:457-65.
3. Horsthemke B, Buiting K. Imprinting defects on human chromosome 15. Cytogenet Genome Res 2006;113:292-9.
4. Smith AC, Choufani S, Ferreira JC, Weksberg R. Growth regulation, imprinted genes, and chromosome 11p15.5. Pediatr Res 2007;61:43R-7R.
5. Fraga MF, Esteller M. DNA methylation: a profile of methods and applications. Biotechniques 2002;33:632.
6. Sandovici I, Leppert M, Hawk PR, Suarez A, Linares Y, Sapienza C. Familial aggregation of abnormal methylation of parental alleles at the IGF2/H19 and IGF2R differentially methylated regions. Hum Mol Genet 2003;12:1569-78.
7. Cooper WN, Luharia A, Evans GA, Raza H, Haire AC, Grundy R, et al. Molecular subtypes and phenotypic expression of Beckwith-Wiedemann syndrome. Eur J Hum Genet 2005;13:1025-32.
8. Cottrell SE, Distler J, Goodman NS, Mooney SH, Kluth A, Olek A, et al. A real-time PCR assay for DNA-methylation using methylation-specific blockers. Nucleic Acids Res 2004;32:e10.
9. Thomassin H, Kress C, Grange T. MethylQuant: a sensitive method for quantifying methylation of specific cytosines within the genome. Nucleic Acids Res 2004;32:e168.
10. Trinh BN, Long TI, Laird PW. DNA methylation analysis by MethyLight technology. Methods 2001;25:456-62.
11. Bliek J, Maas SM, Ruijter JM, Hennekam RC, Alders M, Westerveld A, Mannens MM. Increased tumour risk for BWS patients correlates with aberrant H19 and not KCNQ1OT1 methylation: occurrence of KCNQ1OT1 hypomethylation in familial cases of BWS. Hum Mol Genet 2001;10:467-76.
12. Ehrich M, Nelson MR, Stanssens P, Zabeau M, Liloglou T, Xinarianos G, et al. Quantitative high-throughput analysis of DNA methylation patterns by base-specific cleavage and mass spectrometry. Proc Natl Acad Sci U S A 2005;102:15785-90.
13. Gicquel C, Rossignol S, Cabrol S, Houang M, Steunou V, Barbu V, et al. Epimutation of the telomeric imprinting center region on chromosome 11p15 in Silver-Russell syndrome. Nat Genet 2005;37:1003-7.
14. Xiong Z, Laird PW. COBRA: a sensitive and quantitative DNA methylation assay. Nucleic Acids Res 1997;25:2532-4.
15. Arnaud P, Monk D, Hitchins M, Gordon E, Dean W, Beechey CV, et al. Conserved methylation imprints in the human and mouse GRB10 genes with divergent allelic expression suggests differential reading of the same mark. Hum Mol Genet 2003;12:1005-19.
16. Frevel MA, Sowerby SJ, Petersen GB, Reeve AE. Methylation sequencing analysis refines the region of H19 epimutation in Wilms tumor. J Biol Chem 1999;274:29331-40.
17. Kerjean A, Dupont JM, Vasseur C, Le Tessier D, Cuisset L, Paldi A, et al. Establishment of the paternal methylation imprint of the human H19 and MEST/PEG1 genes during spermatogenesis. Hum Mol Genet 2000;9:2183-7.
18. Smilinich NJ, Day CD, Fitzpatrick GV, Caldwell GM, Lossie AC, Cooper PR, et al. A maternally methylated CpG island in KvLQT1 is associated with an antisense paternal transcript and loss of imprinting in Beckwith-Wiedemann syndrome. Proc Natl Acad Sci U S A 1999;96:8064-9.
19. Bruce S, Leinonen R, Lindgren CM, Kivinen K, Dahlman-Wright K, Lipsanen-Nyman M, et al. Global analysis of uniparental disomy using high density genotyping arrays. J Med Genet 2005;42:847-51.
20. Hannula K, Kere J, Pirinen S, Holmberg C, Lipsanen-Nyman M. Do patients with maternal uniparental disomy for chromosome 7 have a distinct mild Silver-Russell phenotype? J Med Genet 2001;38:273-8.
21. Hannula K, Lipsanen-Nyman M, Kontiokari T, Kere J. A narrow segment of maternal uniparental disomy of chromosome 7q31-qter in Silver-Russell syndrome delimits a candidate gene region. Am J Hum Genet 2001;68:247-53.
22. Hannula K, Lipsanen-Nyman M, Kristo P, Kaitila I, Simola KO, Lenko HL, et al. Genetic screening for maternal uniparental disomy of chromosome 7 in prenatal and postnatal growth retardation of unknown cause. Pediatrics 2002;109:441-8.
23. Hoglund P, Holmberg C, de la Chapelle A, Kere J. Paternal isodisomy for chromosome 7 is compatible with normal growth and development in a patient with congenital chloride diarrhea. Am J Hum Genet 1994;55:747-52.
24. Rozen S, Skaletsky H. Primer3 on the WWW for general users and for biologist programmers. Methods Mol Biol 2000;132:365-86.
25. Bookout AL, Mangelsdorf DJ. Quantitative real-time PCR protocol for analysis of nuclear receptor signaling pathways. Nucl Recept Signal 2003;1:e012.
26. R Development Core Team. R: A language and environment for statistical computing. Vienna, Austria: R Foundation for Statistical Computing, 2005.
27. Reik W, Brown KW, Slatter RE, Sartori P, Elliott M, Maher ER. Allelic methylation of H19 and IGF2 in the Beckwith-Wiedemann syndrome. Hum Mol Genet 1994;3:1297-301.
28. Schonherr N, Meyer E, Eggermann K, Ranke MB, Wollmann HA, Eggermann T. (Epi)mutations in 11p15 significantly contribute to Silver-Russell syndrome: but are they generally involved in growth retardation? Eur J Med Genet 2006;49:414-8.
29. Cui H, Cruz-Correa M, Giardiello FM, Hutcheon DF, Kafonek DR, Brandenburg S, et al. Loss of IGF2 imprinting: a potential marker of colorectal cancer risk. Science 2003;299:1753-5.
30. Heijmans BT, Kremer D, Tobi EW, Boomsma DI, Slagboom PE. Heritable rather than age-related environmental and stochastic factors dominate variation in DNA methylation of the human IGF2/H19 locus. Hum Mol Genet 2007;16:547-54.