Whole-genome methylation scan in ICF syndrome: Hypomethylation of non-satellite DNA repeats D4Z4 and NBL2

Human Molecular Genetics

Volumn 9, Issue 4, 2000, Pages 597-604

  Kondo, Tadashi ^a   Bobek, Miroslav P ^a   Kuick, Rork ^a   Lamb, Barbara ^a   Zhu, Xiaoxiang ^a   Narayan, Ajita ^b   Bourc'his, Déborah ^c   Viegas Péquignot, Evani ^c   Ehrlich, Melanie ^b   Hanash, Samir M ^a  

^a UNIVERSITY OF MICHIGAN   (United States)

^b TULANE UNIVERSITY SCHOOL OF MEDICINE   (United States)

^c HÔPITAL NECKER ENFANTS MALADES   (France)

Author keywords

[No Author keywords available]

Indexed keywords

MITOGENIC AGENT; REPETITIVE DNA; RESTRICTION ENDONUCLEASE;

ARTICLE; B LYMPHOCYTE; CASE REPORT; CENTROMERE; CONTROLLED STUDY; CPG ISLAND; DNA METHYLATION; FACE MALFORMATION; FACIOSCAPULOHUMERAL MUSCULAR DYSTROPHY; FEMALE; GENE MUTATION; GENETIC STABILITY; GENOME; HETEROCHROMATIN; HUMAN; HUMAN CELL; IMMUNE DEFICIENCY; LYMPHOCYTE; MALE; NONHUMAN; NUCLEOTIDE SEQUENCE; PRIORITY JOURNAL; RECESSIVE INHERITANCE; TWO DIMENSIONAL GEL ELECTROPHORESIS;

EID: 0034162852     PISSN: 09646906     EISSN: None     Source Type: Journal    
DOI: 10.1093/hmg/9.4.597     Document Type: Article

References (46)

1. Hulten, M. (1978) Selective somatic pairing and fragility at 1q12 in a boy with common variable immunodeficiency: a new syndrome. Clin. Genet., 14, 294-295.
2. Tiepolo, L., Maraschio, P., Gimelli, G., Cuoco, C., Gargani, G. and Romano, C. (1979) Multibranched chromosomes 1, 9, and 16 in a patient with combined IgA and IgE deficiency. Hum. Genet., 51, 127-137.
3. Smeets, D.F.C.M., Moog, U., Weemaes, C.M.R., Vaes-Peeters, G., Merkx, G.F.M., Niehof, J.P. and Hamers, G. (1997) ICF syndrome: a new case and review of the literature. Hum. Genet., 94, 240-246.
4. Sawyer, J.R., Swanson, C.M., Wheeler, G. and Cunniff, C. (1995) Chromosome instability in ICF syndrome: formation of micronuclei from multibranched chromosomes 1 demonstrated by fluorescence in situ hybridization. Am. J. Med. Genet., 56, 203-209.
5. Ji, W., Hernandez, R., Zhang, X.-Y., Qu, G., Frady, A., Varela, M. and Ehrlich, M. (1997) DNA demethylation and pericentromeric rearrangements of chromosome 1. Mutat. Res., 379, 33-41.
6. Jeanpierre, M., Turleau, C., Aurias, A., Prieur, M., Ledeist, F., Fischer, A. and Viegas-Péquignot, E. (1993) An embryonic-like methylation pattern of classical satellite DNA is observed in ICF syndrome. Hum. Mol. Genet., 2, 731-735.
7. Schuffenhauer, S., Bartsch, O., Stumm, M., Buchholz, T., Petropoulou, T., Kraft, S., Belohradsky, B., Hinkel, G.K., Meitinger, T. and Wegner, R.D. (1995) DNA, FISH and complementation studies in ICF syndrome; DNA hypomethylation of repetitive and single copy loci and evidence for a trans acting factor. Hum. Genet., 96, 562-571.
8. Hernandez, R., Frady, A., Zhang, X.-Y., Varela, M. and Ehrlich, M. (1997) Preferential induction of chromosome 1 multibranched figures and whole-arm deletions in a human pro-B cell line treated with 5-azacytidine or 5-azadeoxycytidine. Cytogenet. Cell Genet., 76, 196-201.
9. Kokalj-Vokac, N., Almeida, A., Viegas-Pequignot, E., Jeanpierre, M., Malfoy, B. and Dutrillaux, B. (1993) Specific induction of uncoiling and recombination by azacytidine in classical satellite-containing constitutive heterochromatin. Cytogenet. Cell Genet., 63, 11-15.
10. Miniou, P., Jeanpierre, M., Blanquet, V., Sibella, V., Bonneau, D., Herbelin, C., Fischer, A., Niveleau, A. and Viegas-Péquignot, E. (1994) Abnormal methylation pattern in constitutive and facultative (X inactive chromosome) heterochromatin of ICF patients. Hum. Mol. Genet., 3, 2093-2102.
11. Xie, S., Wang, Z., Okano, M., Nogami, M., Li, Y., He, W.W., Okumura, K. and Li, E. (1999) Cloning, expression and chromosome locations of the human DNMT3 gene family. Gene, 236, 87-95.
12. Xu, G., Bestor, T.H., Bourc'his, D., Hsieh, C., Tommerup, N., Bugge, M., Hulten, M., Zu, X., Russo, J.J. and Viegas-Péquignot, E. (1999) Chromosome instability and immunodeficiency syndrome caused by mutations in a DNA methyltransferase gene. Nature, 402, 187-191.
13. Okano, M., Bell, D.W., Haber, D.A. and Li, E. (1999) DNA methyltransferases Dnmt3a and Dnmt3b are essential for de novo methylation and mammalian development. Cell, 99, 247-257.
14. Hansen, R.S., Wijmenga, C., Luo, P., Stanek, A.M., Canfield, T.K., Weemaes, C.M.R. and Gartler, S.M. (1999) The DNMT3B DNA methyltransferase gene is mutated in the ICF immunodeficiency syndrome. Proc. Natl Acad. Sci. USA, 96, 14412-14417.
15. Aijmenga, C., van den Heuvel, L.P.W.J., Strengman, E. and Luyten, J.A.F.M. (1998) Localization of the ICF syndrome to chromosome 20 by homozygosity mapping. Am. J. Hum. Genet., 63, 803-809.
16. Miniou, P., Jeanpierre, M., Bourc'his, D., Coutinho Barbosa, A.C., Blanquet, V. and Viegas-Péquignot, E. (1997) α-Satellite DNA methylation in normal individuals and in ICF patients: heterogeneous methylation of constitutive heterochromatin in adult and fetal tissues. Hum. Genet., 99, 738-745.
17. Miniou, P., Bourc'his, D., Gomes, D.M., Jeanpierre, M. and Viegas-Péquignot, E. (1997) Undermethylation of Alu sequences in ICF syndrome: molecular and in situ analysis. Cytogenet. Cell Genet., 77, 308-313.
18. Bourc'his, D., Miniou, P., Jeanpierre, M., Gomes, D.M., Dupont, J.M., de Saint-Basile, G., Maraschio, P., Tiepolo, L. and Viegas-Péquignot, E. (1999) Abnormal methylation does not prevent X inactivation in ICF patients. Cytogenet. Cell Genet., 82, 245-252.
19. Asakawa, J., Kuick, R., Neel, J.V., Kodaira, M., Satoh, C. and Hanash, S.M. (1995) Quantitative and qualitative genetic variation in two-dimensional DNA gels of human lymphocytoid cell lines. Electrophoresis, 16, 241-252.
20. Kuick, R., Asakawa, J., Neel, J.V., Satoh, C. and Hanash, S.M. (1995) High yield of restriction fragment length polymorphisms in two-dimensional separations of human genomic DNA. Genomics, 25, 345-353.
21. Thoraval, D., Asakawa, J., Wimmer, K., Kuick, R., Lamb, B., Richardson, B., Ambros, P., Glover, T. and Hanash, S. (1996) Demethylation of repetitive DNA sequences in neuroblastoma. Genet Chromosomes Cancer, 17, 234-244.
22. Hughes, S.J., Glover, T.W., Zhu, X.-X., Kuick, R., Thoraval, D., Orringer, M.B., Beer, D.G. and Hanash, S. (1998) A novel amplicon at 8p22-23 results in overexpression of cathepsin B in esophageal adenocarcinoma. Proc. Natl Acad. Sci. USA, 98, 12410-12415.
23. Wimmer, K., Zhu, X.X., Lamb, B.J., Kuick, R., Ambros, P.F., Kovar, H., Thoraval, D., Motyka, S., Alberts, J.R. and Hanash, S.M. (1999) Co-amplification of a novel gene, NAG, with the N-myc gene in neuroblastoma. Oncogene, 18, 233-238.
24. Hatada, I., Hayashizaki, Y., Hirotsune, S. and Komatsubara, H. (1991) A genomic scanning method for higher organisms using restriction sites as landmarks. Proc. Natl Acad. Sci. USA, 88, 9523-9527.
25. Zhu, X., Deng, C., Kuick, R., Yung, R., Lamb, B., Neel, J.V., Richardson, B. and Hanash, S. (1999) Analysis of human peripheral blood T cells and single-cell-derived T cell clones uncovers extensive clonal CpG island methylation heterogeneity throughout the genome. Proc. Natl Acad. Sci. USA, 96, 8058-8063.
26. van Deutekon, J.C.T., Wijmenga, C., van Tienhoven, E.A.E., Gruter, A.M., Hewitt, J.E., Padbert, G.W., van Ommen, G.J.B., Hofker, M.H. and Fants, R.R. (1993) FSHD associated DNA rearrangements are due to deletions of integral copies of a 3.2 kb tandem repeated unit. Hum. Mol. Genet., 12, 2037-2042.
27. van Deutekom, J.C., Bakker, E., Lemmers, R.J., van der Wielen, M.J., Bik, E., Hofker, M.H., Padberg, G.W. and Frants, R.R. (1996) Evidence for subtelomeric exchange of 3.3 kb tandemly repeated units between chromosomes 4q35 and 10q26: implications for genetic counselling and etiology of FSHD1. Hum. Mol. Genet., 5, 1997-2003.
28. Gabriels, J., Beckers, M.C., Ding, H., De Vriese, A., Plaisance, S., van der Maarel, S.M., Padberg, G.W., Frants, R.R., Hewitt, J.E., Collen, D. and Belayew, A. (1999) Nucleotide sequence of the partially deleted D4Z4 locus in a patient with FHSD identifies a putative gene within each 3.3 kb element. Gene, 236, 25-32.
29. Bakker, E., Wijmenga, C., Vossen, R.H., Padberg, G.W., Hewitt, J., van der Wielen, M., Rasmussen, K. and Frants, R.R. (1995) The FSHD-linked locus D4F104S1 (p13E-11) on 4q35 has a homologue on 10qter. Muscle Nerve, 2, 39-44.
30. Hewitt, J.E., Lyle, R., Clark, L.N., Valleley, E.M., Wright, T.J., Wijimenga, C., van Deutekom, J.C.T., Francis, F., Sharpe, P.T., Hofker, M. et al. (1994) Analysis of the tandem repeat locus D4Z4 associated with facioscapulohumeral muscular dystrophy. Hum. Mol. Genet., 3, 1287-1295.
31. Wijmenga, C., Hewitt, J.E., Sandkuijl, L.A., Clark, L.N., Wright, T.J., Dauwerse, H.G., Gruter, A.M. Hofker, M.H., Moerer, P., Williamson, R. et al. (1992) Chromosome 4q DNA rearrangements associated with facioscapulohumeral muscular dystrophy. Nature Genet., 2, 26-30.
32. Lemmers, R.J.L.F., van der Maarel, S.M., van Deutekom, J.C.T., van der Wielen, M.J.R., Deidda, G., Dauwerse, H.G., Hewitt, J., Hofker, M., Bakker, E., Padberg, G.W. and Frants, R.R. (1998) Inter-and intrachromosomal sub-telomeric rearrangements on 4q35: implications for facioscapulohumeral muscular dystrophy (FSHD) aetiology and diagnosis. Hum. Mol. Genet., 7, 1207-1214.
33. Lunt, P.W., Jardine, P.E., Koch, M.C., Maynard, J., Osborn, M., Williams, M., Harper, P.S. and Upadhyaya, M. (1995) Correlation between fragment size at D4F104S1 and age at onset or at wheelchair use, with a possible generational effect, accounts for much phenotypic variation in 4q35-facioscapulohumeral muscular dystrophy. Hum. Mol. Genet., 4, 951-958.
34. Viegas-Péquignot, E. and Dutrillaux, B. (1976) Segmentation of human chromosomes induced by 5-ACR (5-azacytidine). Hum. Genet., 34, 247-254.
35. Giacalone, J., Friedes, J. and Francke, U. (1992) A novel GC-rich human macrosatellite VNTR in Xq24 is differentially methylated on active and inactive X chromosomes. Nature Genet., 1, 137-143.
36. Okano, M., Xie, S. and Li, E. (1998) Cloning and characterization of a family of novel mammalian DNA (cytosine-5) methyltransferases. Nature Genet., 19, 219-220.
37. Qu, G.Z., Grundy, P.E., Narayan, A. and Ehrlich, M. (1999) Frequent hypomethylation in Wilms tumors of pericentromeric DNA in chromosomes 1 and 16. Cancer Genet. Cytogenet., 109, 34-39.
38. Brown, C.J., Ballabio, A., Rupert, J.L., Lafreniére, R.G., Grompe, M., Tonlorenzi, R. and Willard, H.F. (1991) A gene from the region of the human X inactivation center is expressed exclusively from the inactive chromosome. Nature, 349, 38-44.
39. Bartolomei, M.S., Zemel, S. and Tilghman, S.M. (1991) Parental imprinting of the mouse H19 gene. Nature, 351, 153-155.
40. Wutz, A., Smrzka, O.W., Schweifer, N., Schellander, K., Wagner, E.F. and Barlow, D.P. (1997) Imprinted expression of the IGf2r gene depends on an intronic CpG island. Nature, 389, 745-759.
41. Falls, J.G., Pulford, D.J., Wylie, A.A. and Lirtle, R.L. (1999) Genomic imprinting: implication for human disease. Am. J. Pathol., 154, 634-647.
42. Funakoshi, M., Goto, K. and Arahata, K. (1998) Epilepsy and mental retardation in a subset of early onset 4q35-facioscapulohumeral muscular dystrophy. Neurology, 50, 1791-1794.
43. Meneveri, R., Agresti, A., Marozzi, A., Saccone, S., Rocchi, M., Archidiacono, N., Coreneo, G., Valle, G.D. and Ginelli, E. (1993) Molecular organization and chromosomal location of human GC-rich heterochromatic blocks. Gene, 123, 227-234.
44. Meneveri, R., Agresti, A., Valle, G.D., Talarico, D., Siccardi, A.G. and Ginelli, E. (1985) Identification of a human clustered G + C-rich DNA family of repeat (Sau3A family). J. Mol. Biol., 186, 483-489.
45. Zhang, X., Loflin, P.T., Gehrke, C.W., Andrews, P.A. and Ehrlich, M. (1987) Hypermethylation of human DNA sequences in embryonal carcinoma cells and somatic tissues but not in sperm. Nucleic Acids Res., 15, 9429-9449.
46. Carpenter, N.J., Filipovich, A., Blaese, R.M., Carey, T.L. and Berkel, A. (1988) Variable immunodeficiency with abnormal condensation of the heterochromatin of chromosomes 1, 9, and 16. J. Pediatr., 112, 757-760.