Perturbations of chromatin structure in human genetic disease: Recent advances

Human Molecular Genetics

Volumn 12, Issue REV. ISS. 2, 2003, Pages

  Bickmore, Wendy A ^a   van der Maarel, Silvère M ^b  

^a UNIVERSITY OF EDINBURGH   (United Kingdom)

^b LEIDEN UNIVERSITY MEDICAL CENTER   (Netherlands)

Author keywords

[No Author keywords available]

Indexed keywords

BINDING PROTEIN; COMPLEMENTARY RNA; DNA METHYLTRANSFERASE;

ALPHA THALASSEMIA; CHROMATIN STRUCTURE; CHROMOSOME ABERRATION; CPG ISLAND; DNA METHYLATION; FACIOSCAPULOHUMERAL MUSCULAR DYSTROPHY; GENE ACTIVATION; GENE DELETION; GENE EXPRESSION; GENE INACTIVATION; GENE MUTATION; GENE REPRESSION; GENE SEQUENCE; GENETIC CODE; GENETIC DISORDER; GENETIC TRANSCRIPTION; HUMAN; ICF SYNDROME; MOLECULAR MECHANICS; MOUSE; NONHUMAN; OPEN READING FRAME; PRIORITY JOURNAL; REVIEW; SEQUENCE HOMOLOGY; TRANSCRIPTION INITIATION;

EUKARYOTA; MAMMALIA;

EID: 0141994824     PISSN: 09646906     EISSN: None     Source Type: Journal    
DOI: 10.1093/hmg/ddg260     Document Type: Review

References (59)

1. Hendrich, B. and Bickmore, W. (2001) Human diseases with underlying defects in chromatin structure and modification. Hum. Mol. Genet., 10, 2233-2242.
2. Weiler, K.S. and Wakimoto, B.T. (1995) Heterochromatin and gene expression in Drosophila. Ann. Rev. Genet., 29, 577-605.
3. Kleinjan, D.J. and van Heyningen, V. (1998) Position effect in human genetic disease. Hum. Mol. Genet., 7, 1611-1618.
4. 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.
5. Xu, G.-L., Bestor, T.H., Bourc'his, D., Hsieh, C.-L., Tommerup, N., Bugge, M., Hulten, M., Qu, 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.
6. Smeets, D.F., Moog, U., Weemaes, C.M., Vaes-Peeters, G., Merkx, G.F., Niehof, J.P. and Hamers, G. (1994) ICT syndrome: a new case and review of the literature. Hum. Genet., 94, 240-246.
7. Schmid, M., Haaf, T. and Grunert, D. (1984) 5-Azacytidine-induced undercondensations in human chromosomes. Hum. Genet., 67, 257-263.
8. 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.
9. 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.
10. 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.
11. Wijmenga, C., Hansen, R.S., Gimelli, G., Bjorck, E.J., Davies, E.G., Valentine, D., Belohradsky, B.H., van Dongen, J.J., Smeets, D.F., van den Heuvel, L.P. et al. (2000) Genetic variation in ICF syndrome: evidence for genetic heterogeneity. Hum. Mutat., 16, 509-517.
12. Gowher, H. and Jeltsch, A. (2002). Molecular enzymology of the catalytic domains of the Dnmt3a and Dnmt3b DNA methyltransferases. J. Biol. Chem., 277, 20409-20414.
13. Tao, Q., Huang, H., Geiman, T.M., Lim, C.Y., Fu, L., Qiu, G.H. and Robertson, K.D. (2002). Defective de novo methylation of viral and cellular DNA sequences in ICF syndrome cells. Hum. Mol. Genet., 11, 2091-2102.
14. Kondo, T., Bobek, M.P., Kuick, R., Lamb, B., Zhu, X., Narayan, A., Bourc'his, D., Viegas-Pequignot, E., Ehrlich, M. and Hanash, S.M. (2000) Whole-genome methylation scan in ICT syndrome: hypomethylation of non-satellite DNA repeats D4Z4 and NBL2. Hum. Mol. Genet., 9, 597-604.
15. Jeanpierre, M., Turleau, C., Aurias, A., Prieur, M., Ledeist, F., Fischer, A. and Viegas-Pequignot, E. (1993) An embryonic-like methylation pattern of classical satellite DNA is observed in ICF syndrome. Hum. Mol. Genet., 2, 731-735.
16. Miniou, P., Jeanpierre, M., Blanquet, V., Sibella, V., Bonneau, D., Herbelin, C., Fischer, A., Niveleau, A. and Viegas-Pequignot, E. (1994) Abnormal methylation pattern in constitutive and facultative (X inactive chromosome) heterochromatin of ICF patients. Hum. Mol. Genet., 3, 2093-2102.
17. Bourc'his, D., Miniou, P., Jeanpierre, M., Molina Gomes, D., Dupont, J., De Saint-Basile, G., Maraschio, P., Tiepolo, L. and Viegas-Pequignot, E. (1999) Abnormal methylation does not prevent X inactivation in ICT patients. Cytogenet. Cell Genet., 84, 245-252.
18. Hansen, R.S., Stoger, R., Wijmenga, C., Stanek, A.M., Canfield, T.K., Luo, P., Matarazzo, M.R., D'Esposito, M., Feil, R., Gimelli, G. et al. (2000) Escape from gene silencing in ICF syndrome: evidence for advanced replication time as a major determinant. Hum. Mol. Genet., 9, 2575-2587.
19. Bachman, K.E., Rountree, M.R. and Baylin, S.B. (2001) Dnmt3a and Dnmt3b are transcriptional repressors that exhibit unique localization properties to heterochromatin. J. Biol. Chem., 276, 32282-32287.
20. Qiu, C., Sawada, K., Zhang, X. and Cheng, X. (2002) The PWWP domain of mammalian DNA methyltransferase Dnmt3b defines a new family of DNA-binding folds. Nat. Struct. Biol., 9, 217-224.
21. Maurer-Stroh, S., Dickens, N.J., Hughes-Davies, L., Kouzarides, T., Eisenhaber, F. and Ponting, C.P. (2003) The Tudor domain 'Royal Family': tudor, plant Agenet, Chromo, PWWP and MBT domains. Trends Biochem. Sci., 28, 69-74.
22. Shirohzu, H., Kubota, T., Kumazawa, A., Sado, T., Chijiwa, T. Inagaki, K., Suetake, I., Tajima, S., Wakui, K., Miki, Y et al. (2002) Three novel DNMT3B mutations in Japanese patients with ICF syndrome. Am. J. Med. Genet.. 112, 31-37.
23. Ehrlich, M., Buchanan, K.L., Tsien, F., Jiang, G., Sun, B., Uicker, W., Weemaes, C.M., Smeets, D., Sperling, K., Belohradsky, B.H. et al. (2001) DNA methyltransferase 3B mutations linked to the ICF syndrome cause dysregulation of lymphogenesis genes. Hum. Mol. Genet., 10, 2917-2931.
24. Wade, P.A. (2001) Methyl CpG-binding proteins and transcriptional repression. Bioessays, 23, 1131-1137.
25. Fuks, F., Hurd, P.J., Wolf, D., Nan, X., Bird, A.P. and Kouzarides, T. (2003) The methyl-CpG-binding protein MeCP2 links DNA methylation to histone methylation. J. Biol. Chem., 278, 4035-4040.
26. Brown, K.E., Baxter, J., Graf, D., Merkenschlager, M. and Fisher, A.G. (1999) Dynamic repositioning of genes in the nucleus of lymphocytes preparing for cell division. Mol. Cell, 3, 207-217.
27. Skok, J.A., Brown, K.E., Azuara, V., Caparros, M.L., Baxter, J., Takacs, K., Dillon, N., Gray, D., Perry, R.P., Merkenschlager, M. and Fisher, A.G. (2001) Nonequivalent nuclear location of immunoglobulin alleles in B lymphocytes. Nat. Immunol., 2, 848-854.
28. Lettice, L.A., Horikoshi, T., Heaney, S.J., van Baren, M.J., van der Linde, H.C., Breedveld, G.J., Joosse, M., Akarsu, N., Oostra, B.A., Endo, N. et al. (2002) Disruption of a long-range cis-acting regulator for Shh causes preaxial polydactyly. Proc. Natl Acad. Sci. USA, 995 7548-7553.
29. 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. Nat. Genet, 2, 26-30.
30. van Deutekom, J.C., Wijmenga, C., van Tienhoven, E.A., Gruter, A.M., Hewitt, J.E., Padberg, G.W., van Ommen, G.J., Hofker, M.H. and Frants, R.R. (1993) FSHD associated DNA rearrangements are due to deletions of integral copies of a 3.2 kb tandemly repeated unit. Hum. Mol. Genet., 2, 2037-2042.
31. 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 (FSHD). Hum. Mol. Genet., 4, 951-958.
32. Tawil, R., Forrester, J., Griggs, R.C., Mendell, J., Kissel, J., McDermott, M., King, W., Weiffenbach, B. and Figlewicz, D. (1996). Evidence for anticipation and association of deletion size with severity in facioscapulohumeral muscular dystrophy. The FSH-DY Group. Ann. Neurol., 39, 744-748.
33. Ricci, E., Galluzzi, G., Deidda, G., Cacurri, S., Colantoni, L., Merico, B., Piazzo, N., Servidei, S., Vigneti, E. et al. (1999). Progress in the molecular diagnosis of facioscapulohumeral muscular dystrophy and correlation between the number, of KpnI repeats at the 4q35 locus and clinical phenotype. Ann. Neurol., 45, 751-757.
34. Tupler, R., Berardinelli, A., Barbierato, L., Frants, R., Hewitt, J.E., Lanzi, G., Maraschio, P. and Tiepolo, L. (1996). Monosomy of distal 4q does not cause facioscapulohumeral muscular dystrophy. J. Med. Genet., 33, 366-370.
35. van Geel, M., Dickso, M.C., Beck, A.F., Bolland, D.J., Frants, R.R., van der Maarel, S.M., de Jong, P.J. and Hewitt, J.E. (2002) Genomic analysis of human chromosome 10q and 4q telomeres suggests a common origin. Genomics, 79, 210-217.
36. Waye, J.S. and Willard, H.F. (1989) Human beta satellite DNA: genomic organization and sequence definition of a class of highly repetitive tandem DNA. Proc. Natl Acad. Sci. USA, 86, 6250-6254.
37. Lemmers, R.J., de Kievit, P., Sandkuijl, L., Padberg, G.W., van Ommen, G.J., Frants, R.R. and van der Maarel, S.M. (2002) Facioscapulohumeral muscular dystrophy is uniquely associated with one of the two variants of the 4q subtelomere. Nat. Genet., 32, 235-236.
38. 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 FSHD identifies a putative gene within each 3.3 kb element. Gene, 236, 25-32.
39. Gabellini, D., Green, M.R. and Tupler, R. (2002) Inappropriate gene activation in FSHD: a repressor complex binds a chromosomal repeat deleted in dystrophic muscle. Cell, 110, 339-348.
40. van Deutekom, J.C., Lemmers, R.J., Grewal, P.K., van Geel, M., Romberg, S., Dauwerse, H.G., Wright, T.J., Padberg, G.W., Hofker, M.H., Hewitt, J.E. and Frants, R.R. (1996) Identification of the first gene (FRG1) from the FSHD region on human chromosome 4q35. Hum. Mol. Genet., 5, 581-590.
41. Roger, B., Moisand, A., Amalric, F. and Bouvet, P. (2002) Repression of RNA polymerase I transcription by nucleolin is independent of the RNA sequence that is transcribed. J. Biol. Chem., 277, 10209-10219.
42. Daniely, Y., Dimitrova, D.D. and Borowiec, J.A. (2002) Stress-dependent nucleolin mobilization mediated by p53-nucleolin complex formation. Mol. Cell. Biol., 22, 6014-6022.
43. Rezai-Zadeh, N., Zhang, X., Namour, F., Fejer, G., Wen, Y.D., Yao, Y.L., Gyory, I., Wright, K. and Seto, E. (2003) Targeted recruitment of a histone H4-specific methyltransferase by the transcription factor YY1. Genes Dev., 17, 1019-1029.
44. Lachner, M., O'Sullivan, R.J. and Jenuwein, T. (2003) An epigenetic road map for histone lysine methlylation. J. Cell Sci., 116, 2117-2124.
45. Orlando, V. (2003) Polycomb, epigenomes, and control of cell identity. Cell, 112, 599-606.
46. Tsien, F., Sun, B., Hopkins, N.E., Vedanarayanan, V., Figlewicz, D., Winokur, S. and Ehrlich, M. (2001) Methylation of the FSHD syndrome-linked subtelomeric repeat in normal and FSHD cell cultures and tissues. Mol. Genet. Metab., 74, 322-331.
47. Inouye, C.J. and Seto, E. (1994) Relief of YY1-induced transcriptional repression by protein-protein interaction with the nucleolar phosphoprotein B23. J. Biol. Chem., 269, 6506-6510.
48. Manuelidis, L. and Borden, J. 1988. Reproducible compartmentalization of individual chromosome domains in human CNS cells revealed by in situ hybridization and three-dimensional reconstruction. Chromosoma, 96, 397-410.
49. Lyle, R., Wright, T.J., Clark, L.N. and Hewitt, J.E. (1995) The FSHD-associated repeat, D4Z4, is a member of a dispersed family of homeobox-containing repeats, subsets of which are clustered on the short arms of the acrocentric chromosomes. Genomics, 28, 389-397.
50. Winokur, S.T., Bengtsson, U., Vargas, J.C., Wasmuth, J.J., Altherr, M.R., Weiffenbach, B. and Jacobsen, S.J. (1996) The evolutionary distribution and structural organization of the homeobox-containing repeat D4Z4 indicates a functional role for the ancestral copy in the FSHD region. Hum. Mol. Genet., 5, 1567-1575.
51. Stout, K., van der Maarel, S., Frants, R.R., Padberg, G.W., Ropers, H.H. and Haaf, T. (1999) Somatic pairing between subtelomeric chromosome regions: implications for human genetic disease? Chromosome Res., 7, 323-329.
52. Yip, D.J. and Picketts, D.J. (2003) Increasing D4Z4 repeat copy number compromises C2C12 myoblast differentiation. FEBS Lett., 537, 133-138.
53. Tufarelli, C., Stanley, J.A., Garrick, D., Sharpe, J.A., Ayyub, H., Wood, W.G. and Higgs, D.R. (2003) Transcription of antisense RNA leading to gene silencing and methylation as a novel cause of human genetic disease. Nat. Genet., 34, 157-165.
54. Rougeulle, C. and Heard, E. (2002) Antisense RNA in imprinting: spreading silence through air. Trends Genet., 18, 434-437.
55. Hampsey, M. and Reinberg, D. (2003) Tails of intrigue. Phosphorylation of RNA polymerase II mediates histone methylation. Cell, 113, 429-432.
56. Kleinjan, D.A. and Van Heyningen, V. (2003) Turned off by RNA. Nat. Genet., 34, 125-126.
57. Allshire, R. (2002). Molecular biology. RNAi and heterochromatin - a hushed-up affair. Science, 297, 1818-1819.
58. Daniels, R., Lowell, S., Bolton, V. and Monk, M. (1997) Transcription of tissue-specific genes in human preimplantation embryos. Hum. Reprod., 12, 2251-2256.
59. Tamaru, H., Zhang, X., McMillen, D., Singh, P.B., Nakayama, J., Grewal, S.I., Allis, C.D., Cheng, X. and Selker, E.U. (2003) Trimethylated lysine 9 of histone H3 is a mark for DNA methylation in Neurospora crassa. Nat. Genet., 34, 75-79.