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The Role of DNMT3B Mutations in the Pathogenesis of ICF Syndrome

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Patho-Epigenetics of Disease

Abstract

DNA methylation plays an important role in epigenetic signaling, having an impact on gene regulation, chromatin structure, development, and disease. The human genetic disease, called immunodeficiency, centromere instability, facial abnormalities (ICF) syndrome, is one example of the consequence of the impaired setting and maintenance of proper DNA methylation patterns. Here, we review the key properties of the mammalian de novo DNA methyltransferase DNMT3B, whose dysfunction is responsible for the ICF molecular phenotype, and take a closer look at the effects of the reported mutations on its methyltransferase activity. Moreover, we focus on the central role of DNMT3B in the epigenetic signaling network and the key questions still unsolved in the field, such as how this enzyme is targeted to specific genomic regions, leaving some others unmethylated, and how the DNA methylation pattern is modified during development and in response to environmental cues. The emerging models are multifaceted, involving both the intrinsic properties of DNMT3B and the influence of its interaction partners. In this regard, the ICF mutations provide us with a valuable model to understand the molecular properties of this DNA methyltransferase. The current knowledge and the proposed hypothesis about these topics will be summarized.

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References

  • Achour, M., Jacq, X., Ronde, P., Alhosin, M., Charlot, C., Chataigneau, T., Jeanblanc, M., Macaluso, M., Giordano, A., Hughes, A. D., Schini-Kerth, V. B. & Bronner, C. (2008). The interaction of the SRA domain of ICBP90 with a novel domain of DNMT1 is involved in the regulation of VEGF gene expression. Oncogene 27, 2187–2197.

    Article  PubMed  CAS  Google Scholar 

  • Aran, D., Toperoff, G., Rosenberg, M. & Hellman, A. (2011). Replication timing-related and gene body-specific methylation of active human genes. Hum Mol Genet 20, 670–680.

    Article  PubMed  CAS  Google Scholar 

  • Bachman, K. E., Rountree, M. R. & Baylin, S. B. (2001). Dnmt3a and Dnmt3b are transcriptional repressors that exhibit unique localization properties to heterochromatin. J Biol Chem 276, 32282–32287.

    Article  PubMed  CAS  Google Scholar 

  • Ball, M. P., Li, J. B., Gao, Y., Lee, J. H., LeProust, E. M., Park, I. H., Xie, B., Daley, G. Q. & Church, G. M. (2009). Targeted and genome-scale strategies reveal gene-body methylation signatures in human cells. Nat Biotechnol 27, 361–368.

    Article  PubMed  CAS  Google Scholar 

  • Barski, A., Cuddapah, S., Cui, K., Roh, T. Y., Schones, D. E., Wang, Z., Wei, G., Chepelev, I. & Zhao, K. (2007). High-resolution profiling of histone methylations in the human genome. Cell 129, 823–837.

    Article  PubMed  CAS  Google Scholar 

  • Bestor, T. H. (2000). The DNA methyltransferases of mammals. Hum Mol Genet 9, 2395–2402.

    Article  PubMed  CAS  Google Scholar 

  • Bird, A. (2002). DNA methylation patterns and epigenetic memory. Genes Dev 16, 6–21.

    Article  PubMed  CAS  Google Scholar 

  • Blanco-Betancourt, C. E., Moncla, A., Milili, M., Jiang, Y. L., Viegas-Pequignot, E. M., Roquelaure, B., Thuret, I. & Schiff, C. (2004). Defective B-cell-negative selection and terminal differentiation in the ICF syndrome. Blood 103, 2683–2690.

    Article  PubMed  CAS  Google Scholar 

  • Borgel, J., Guibert, S., Li, Y., Chiba, H., Schubeler, D., Sasaki, H., Forne, T. & Weber, M. (2010). Targets and dynamics of promoter DNA methylation during early mouse development. Nat Genet 42, 1093–1100.

    Article  PubMed  CAS  Google Scholar 

  • Bostick, M., Kim, J. K., Esteve, P. O., Clark, A., Pradhan, S. & Jacobsen, S. E. (2007). UHRF1 plays a role in maintaining DNA methylation in mammalian cells. Science 317, 1760–1764.

    Article  PubMed  CAS  Google Scholar 

  • Bourc’his, D. & Bestor, T. H. (2004). Meiotic catastrophe and retrotransposon reactivation in male germ cells lacking Dnmt3L. Nature 431, 96–99.

    Article  PubMed  CAS  Google Scholar 

  • Bourc’his, D., Xu, G. L., Lin, C. S., Bollman, B. & Bestor, T. H. (2001). Dnmt3L and the establishment of maternal genomic imprints. Science 294, 2536–2539.

    Article  PubMed  Google Scholar 

  • Brenner, C., Deplus, R., Didelot, C., Loriot, A., Vire, E., De Smet, C., Gutierrez, A., Danovi, D., Bernard, D., Boon, T., Pelicci, P. G., Amati, B., Kouzarides, T., de Launoit, Y., Di Croce, L. & Fuks, F. (2005). Myc represses transcription through recruitment of DNA methyltransferase corepressor. EMBO J 24, 336–346.

    Article  PubMed  CAS  Google Scholar 

  • Brown, K. D. & Robertson, K. D. (2007). DNMT1 knockout delivers a strong blow to genome stability and cell viability. Nat Genet 39, 289–290.

    Article  PubMed  CAS  Google Scholar 

  • Brown, S. E., Fraga, M. F., Weaver, I. C., Berdasco, M. & Szyf, M. (2007). Variations in DNA methylation patterns during the cell cycle of HeLa cells. Epigenetics 2, 54–65.

    Article  PubMed  Google Scholar 

  • Carpenter, N. J., Filipovich, A., Blaese, R. M., Carey, T. L. & Berkel, A. I. (1988). Variable immunodeficiency with abnormal condensation of the heterochromatin of chromosomes 1, 9, and 16. J Pediatr 112, 757–760.

    Article  PubMed  CAS  Google Scholar 

  • Chen, T., Tsujimoto, N. & Li, E. (2004). The PWWP domain of Dnmt3a and Dnmt3b is required for directing DNA methylation to the major satellite repeats at pericentric heterochromatin. Mol Cell Biol 24, 9048–9058.

    Article  PubMed  CAS  Google Scholar 

  • Chen, T., Ueda, Y., Dodge, J. E., Wang, Z. & Li, E. (2003). Establishment and maintenance of genomic methylation patterns in mouse embryonic stem cells by Dnmt3a and Dnmt3b. Mol Cell Biol 23, 5594–5605.

    Article  PubMed  CAS  Google Scholar 

  • Chen, Z. X., Mann, J. R., Hsieh, C. L., Riggs, A. D. & Chedin, F. (2005). Physical and functional interactions between the human DNMT3L protein and members of the de novo methyltransferase family. J Cell Biochem 95, 902–917.

    Article  PubMed  CAS  Google Scholar 

  • Cheng, X. & Blumenthal, R. M. (2008). Mammalian DNA methyltransferases: a structural perspective. Structure 16, 341–350.

    Article  PubMed  CAS  Google Scholar 

  • Chouery, E., Abou-Ghoch, J., Corbani, S., El Ali, N., Korban, R., Salem, N., Castro, C., Klayme, S., Azoury-Abou, R. M., Khoury-Matar, R., Debo, G., Germanos-Haddad, M., Delague, V., Lefranc, G. & Megarbane, A. (2011). A novel deletion in ZBTB24 in a Lebanese family with immunodeficiency, centromeric instability, and facial anomalies syndrome type 2. Clin Genet. doi: 10.1111/j.1399-0004.2011.01783.x.

    Google Scholar 

  • Chuang, L. S., Ian, H. I., Koh, T. W., Ng, H. H., Xu, G. & Li, B. F. (1997). Human DNA-(cytosine-5) methyltransferase-PCNA complex as a target for p21WAF1. Science 277, 1996–2000.

    Article  PubMed  CAS  Google Scholar 

  • Datta, J., Majumder, S., Bai, S., Ghoshal, K., Kutay, H., Smith, D. S., Crabb, J. W. & Jacob, S. T. (2005). Physical and functional interaction of DNA methyltransferase 3A with Mbd3 and Brg1 in mouse lymphosarcoma cells. Cancer Res 65, 10891–10900.

    Article  PubMed  CAS  Google Scholar 

  • De Bonis, M. L., Cerase, A., Matarazzo, M. R., Ferraro, M., Strazzullo, M., Hansen, R. S., Chiurazzi, P., Neri, G. & D’Esposito, M. (2006). Maintenance of X- and Y-inactivation of the pseudoautosomal (PAR2) gene SPRY3 is independent from DNA methylation and associated to multiple layers of epigenetic modifications. Hum Mol Genet 15, 1123–1132.

    Article  PubMed  CAS  Google Scholar 

  • de Greef, J. C., Wang, J., Balog, J., den Dunnen, J. T., Frants, R. R., Straasheijm, K. R., Aytekin, C., van der, B. M., Duprez, L., Ferster, A., Gennery, A. R., Gimelli, G., Reisli, I., Schuetz, C., Schulz, A., Smeets, D. F., Sznajer, Y., Wijmenga, C., van Eggermond, M. C., van Ostaijen-Ten Dam MM, Lankester, A. C., van Tol, M. J., van den Elsen, P. J., Weemaes, C. M. & van der Maarel, S. M. (2011). Mutations in ZBTB24 are associated with immunodeficiency, centromeric instability, and facial anomalies syndrome type 2. Am J Hum Genet 88, 796–804.

    Google Scholar 

  • Deng, Z., Campbell, A. E. & Lieberman, P. M. (2010). TERRA, CpG methylation and telomere heterochromatin: lessons from ICF syndrome cells. Cell Cycle 9, 69–74.

    Article  PubMed  CAS  Google Scholar 

  • Dennis, K., Fan, T., Geiman, T., Yan, Q. & Muegge, K. (2001). Lsh, a member of the SNF2 family, is required for genome-wide methylation. Genes Dev 15, 2940–2944.

    Article  PubMed  CAS  Google Scholar 

  • Doi, A., Park, I. H., Wen, B., Murakami, P., Aryee, M. J., Irizarry, R., Herb, B., Ladd-Acosta, C., Rho, J., Loewer, S., Miller, J., Schlaeger, T., Daley, G. Q. & Feinberg, A. P. (2009). Differential methylation of tissue- and cancer-specific CpG island shores distinguishes human induced pluripotent stem cells, embryonic stem cells and fibroblasts. Nat Genet 41, 1350–1353.

    Article  PubMed  CAS  Google Scholar 

  • Dunn, J. J., McCorkle, S. R., Everett, L. & Anderson, C. W. (2007). Paired-end genomic signature tags: a method for the functional analysis of genomes and epigenomes. Genet Eng (N Y) 28, 159–173.

    Article  CAS  Google Scholar 

  • Dupont, C., Guimiot, F., Perrin, L., Marey, I., Smiljkovski, D., Le Tessier, D., Lebugle, C., Baumann, C., Bourdoncle, P., Tabet, A. C., Aboura, A., Benzacken, B. & Dupont, J. M. (2011). 3D position of pericentromeric heterochromatin within the nucleus of a patient with ICF syndrome. Clin Genet. doi: 10.1111/j.1399-0004.2011.01697.

    Google Scholar 

  • Edgar, A. J., Dover, S. L., Lodrick, M. N., McKay, I. J., Hughes, F. J. & Turner, W. (2005). Bone morphogenetic protein-2 induces expression of murine zinc finger transcription factor ZNF450. J Cell Biochem 94, 202–215.

    Article  PubMed  CAS  Google Scholar 

  • Ehrlich, M. (2002). DNA hypomethylation, cancer, the immunodeficiency, centromeric region instability, facial anomalies syndrome and chromosomal rearrangements. J Nutr 132, 2424S–2429S.

    PubMed  CAS  Google Scholar 

  • Ehrlich, M., Buchanan, K. L., Tsien, F., Jiang, G., Sun, B., Uicker, W., Weemaes, C. M., Smeets, D., Sperling, K., Belohradsky, B. H., Tommerup, N., Misek, D. E., Rouillard, J. M., Kuick, R. & Hanash, S. M. (2001). DNA methyltransferase 3B mutations linked to the ICF syndrome cause dysregulation of lymphogenesis genes. Hum Mol Genet 10, 2917–2931.

    Article  PubMed  CAS  Google Scholar 

  • Esteller, M. (2007). Epigenetic gene silencing in cancer: the DNA hypermethylome. Hum Mol Genet 16, R50–R59.

    Article  PubMed  CAS  Google Scholar 

  • Esteve, P. O., Chin, H. G., Benner, J., Feehery, G. R., Samaranayake, M., Horwitz, G. A., Jacobsen, S. E. & Pradhan, S. (2009). Regulation of DNMT1 stability through SET7-mediated lysine methylation in mammalian cells. Proc Natl Acad Sci U S A 106, 5076–5081.

    Article  PubMed  Google Scholar 

  • Fan, G., Martinowich, K., Chin, M. H., He, F., Fouse, S. D., Hutnick, L., Hattori, D., Ge, W., Shen, Y., Wu, H., ten Hoeve, J., Shuai, K. & Sun, Y. E. (2005). DNA methylation controls the timing of astrogliogenesis through regulation of JAK-STAT signaling. Development 132, 3345–3356.

    Article  PubMed  CAS  Google Scholar 

  • Fatemi, M., Hermann, A., Gowher, H. & Jeltsch, A. (2002). Dnmt3a and Dnmt1 functionally cooperate during de novo methylation of DNA. Eur J Biochem 269, 4981–4984.

    Article  PubMed  CAS  Google Scholar 

  • Feldman, N., Gerson, A., Fang, J., Li, E., Zhang, Y., Shinkai, Y., Cedar, H. & Bergman, Y. (2006). G9a-mediated irreversible epigenetic inactivation of Oct-3/4 during early embryogenesis. Nat Cell Biol 8, 188–194.

    Article  PubMed  CAS  Google Scholar 

  • Feng, J., Zhou, Y., Campbell, S. L., Le, T., Li, E., Sweatt, J. D., Silva, A. J. & Fan, G. (2010). Dnmt1 and Dnmt3a maintain DNA methylation and regulate synaptic function in adult forebrain neurons. Nat Neurosci 13, 423–430.

    Article  PubMed  CAS  Google Scholar 

  • Fuks, F., Burgers, W. A., Godin, N., Kasai, M. & Kouzarides, T. (2001). Dnmt3a binds deacetylases and is recruited by a sequence-specific repressor to silence transcription. EMBO J 20, 2536–2544.

    Article  PubMed  CAS  Google Scholar 

  • Fuks, F., Hurd, P. J., Deplus, R. & Kouzarides, T. (2003). The DNA methyltransferases associate with HP1 and the SUV39H1 histone methyltransferase. Nucleic Acids Res 31, 2305–2312.

    Article  PubMed  CAS  Google Scholar 

  • Gardiner-Garden, M. & Frommer, M. (1987). CpG islands in vertebrate genomes. J Mol Biol 196, 261–282.

    Article  PubMed  CAS  Google Scholar 

  • Gartler, S. M., Varadarajan, K. R., Luo, P., Canfield, T. K., Traynor, J., Francke, U. & Hansen, R. S. (2004). Normal histone modifications on the inactive X chromosome in ICF and Rett syndrome cells: implications for methyl-CpG binding proteins. BMC Biol 2:21.

    Article  PubMed  CAS  Google Scholar 

  • Gatto, S., Della, R. F., Cimmino, A., Strazzullo, M., Fabbri, M., Mutarelli, M., Ferraro, L., Weisz, A., D’Esposito, M. & Matarazzo, M. R. (2010). Epigenetic alteration of microRNAs in DNMT3B-mutated patients of ICF syndrome. Epigenetics 5, 427–443.

    Article  PubMed  CAS  Google Scholar 

  • Geiman, T. M., Sankpal, U. T., Robertson, A. K., Chen, Y., Mazumdar, M., Heale, J. T., Schmiesing, J. A., Kim, W., Yokomori, K., Zhao, Y. & Robertson, K. D. (2004a). Isolation and characterization of a novel DNA methyltransferase complex linking DNMT3B with components of the mitotic chromosome condensation machinery. Nucleic Acids Res 32, 2716–2729.

    Article  PubMed  CAS  Google Scholar 

  • Geiman, T. M., Sankpal, U. T., Robertson, A. K., Zhao, Y., Zhao, Y. & Robertson, K. D. (2004b). DNMT3B interacts with hSNF2H chromatin remodeling enzyme, HDACs 1 and 2, and components of the histone methylation system. Biochem Biophys Res Commun 318, 544–555.

    Article  PubMed  CAS  Google Scholar 

  • Gennery, A. R., Slatter, M. A., Bredius, R. G., Hagleitner, M. M., Weemaes, C., Cant, A. J. & Lankester, A. C. (2007). Hematopoietic stem cell transplantation corrects the immunologic abnormalities associated with immunodeficiency-centromeric instability-facial dysmorphism syndrome. Pediatrics 120, e1341–e1344.

    Article  PubMed  Google Scholar 

  • Gopalakrishnan, S., Sullivan, B. A., Trazzi, S., Della, V. G. & Robertson, K. D. (2009). DNMT3B interacts with constitutive centromere protein CENP-C to modulate DNA methylation and the histone code at centromeric regions. Hum Mol Genet 18, 3178–3193.

    Article  PubMed  CAS  Google Scholar 

  • Gowher, H. & Jeltsch, A. (2002). Molecular enzymology of the catalytic domains of the Dnmt3a and Dnmt3b DNA methyltransferases. J Biol Chem 277, 20409–20414.

    Article  PubMed  CAS  Google Scholar 

  • Gowher, H., Liebert, K., Hermann, A., Xu, G. & Jeltsch, A. (2005). Mechanism of stimulation of catalytic activity of Dnmt3A and Dnmt3B DNA-(cytosine-C5)-methyltransferases by Dnmt3L. J Biol Chem 280, 13341–13348.

    Article  PubMed  CAS  Google Scholar 

  • Hagleitner, M. M., Lankester, A., Maraschio, P., Hulten, M., Fryns, J. P., Schuetz, C., Gimelli, G., Davies, E. G., Gennery, A., Belohradsky, B. H., de Groot, R., Gerritsen, E. J., Mattina, T., Howard, P. J., Fasth, A., Reisli, I., Furthner, D., Slatter, M. A., Cant, A. J., Cazzola, G., van Dijken, P. J., van Deuren, M., de Greef, J. C., van der Maarel, S. M. & Weemaes, C. M. (2008). Clinical spectrum of immunodeficiency, centromeric instability and facial dysmorphism (ICF syndrome). J Med Genet 45, 93–99.

    Article  PubMed  CAS  Google Scholar 

  • Handa, V. & Jeltsch, A. (2005). Profound flanking sequence preference of Dnmt3a and Dnmt3b mammalian DNA methyltransferases shape the human epigenome. J Mol Biol 348, 1103–1112.

    Article  PubMed  CAS  Google Scholar 

  • Hansen, R. S. (2003). X inactivation-specific methylation of LINE-1 elements by DNMT3B: implications for the Lyon repeat hypothesis. Hum Mol Genet 12, 2559–2567.

    Article  PubMed  CAS  Google Scholar 

  • 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., Weemaes, C. M., Laird, C. D. & Gartler, S. M. (2000). Escape from gene silencing in ICF syndrome: evidence for advanced replication time as a major determinant. Hum Mol Genet 9, 2575–2587.

    Article  PubMed  CAS  Google Scholar 

  • Hansen, R. S., Wijmenga, C., Luo, P., Stanek, A. M., Canfield, T. K., Weemaes, C. M. & Gartler, S. M. (1999). The DNMT3B DNA methyltransferase gene is mutated in the ICF immunodeficiency syndrome. Proc Natl Acad Sci U S A 96, 14412–14417.

    Article  PubMed  CAS  Google Scholar 

  • Hellman, A. & Chess, A. (2007). Gene body-specific methylation on the active X chromosome. Science 315, 1141–1143.

    Article  PubMed  CAS  Google Scholar 

  • Hirasawa, R. & Feil, R. (2010). Genomic imprinting and human disease. Essays Biochem 48, 187–200.

    Article  PubMed  CAS  Google Scholar 

  • Holz-Schietinger, C. & Reich, N. O. (2010). The inherent processivity of the human de novo methyltransferase 3A (DNMT3A) is enhanced by DNMT3L. J Biol Chem 285, 29091–29100.

    Article  PubMed  CAS  Google Scholar 

  • Jeanpierre, M., Turleau, C., Aurias, A., Prieur, M., Ledeist, F., Fischer, A. & Viegas-Pequignot, E. (1993). An embryonic-like methylation pattern of classical satellite DNA is observed in ICF syndrome. Hum Mol Genet 2, 731–735.

    Article  PubMed  CAS  Google Scholar 

  • Jefferson, A., Colella, S., Moralli, D., Wilson, N., Yusuf, M., Gimelli, G., Ragoussis, J. & Volpi, E. V. (2010). Altered intra-nuclear organisation of heterochromatin and genes in ICF syndrome. PLoS ONE 5, e11364.

    Article  PubMed  CAS  Google Scholar 

  • Jeltsch, A. (2006). On the enzymatic properties of Dnmt1: specificity, processivity, mechanism of linear diffusion and allosteric regulation of the enzyme. Epigenetics 1, 63–66.

    Article  PubMed  Google Scholar 

  • Jeong, S., Liang, G., Sharma, S., Lin, J. C., Choi, S. H., Han, H., Yoo, C. B., Egger, G., Yang, A. S. & Jones, P. A. (2009). Selective anchoring of DNA methyltransferases 3A and 3B to nucleosomes containing methylated DNA. Mol Cell Biol 29, 5366–5376.

    Article  PubMed  CAS  Google Scholar 

  • Ji, H., Ehrlich, L. I., Seita, J., Murakami, P., Doi, A., Lindau, P., Lee, H., Aryee, M. J., Irizarry, R. A., Kim, K., Rossi, D. J., Inlay, M. A., Serwold, T., Karsunky, H., Ho, L., Daley, G. Q., Weissman, I. L. & Feinberg, A. P. (2010). Comprehensive methylome map of lineage commitment from haematopoietic progenitors. Nature 467, 338–342.

    Article  PubMed  CAS  Google Scholar 

  • Jia, D., Jurkowska, R. Z., Zhang, X., Jeltsch, A. & Cheng, X. (2007). Structure of Dnmt3a bound to Dnmt3L suggests a model for de novo DNA methylation. Nature 449, 248–251.

    Article  PubMed  CAS  Google Scholar 

  • Jiang, Y. L., Rigolet, M., Bourc’his, D., Nigon, F., Bokesoy, I., Fryns, J. P., Hulten, M., Jonveaux, P., Maraschio, P., Megarbane, A., Moncla, A. & Viegas-Pequignot, E. (2005). DNMT3B mutations and DNA methylation defect define two types of ICF syndrome. Hum Mutat 25, 56–63.

    Article  PubMed  CAS  Google Scholar 

  • Jin, B., Tao, Q., Peng, J., Soo, H. M., Wu, W., Ying, J., Fields, C. R., Delmas, A. L., Liu, X., Qiu, J. & Robertson, K. D. (2008). DNA methyltransferase 3B (DNMT3B) mutations in ICF syndrome lead to altered epigenetic modifications and aberrant expression of genes regulating development, neurogenesis and immune function. Hum Mol Genet 17, 690–709.

    Article  PubMed  CAS  Google Scholar 

  • Jones, P. A. (2002). DNA methylation and cancer. Oncogene 21, 5358–5360.

    Article  PubMed  CAS  Google Scholar 

  • Jones, P. A. & Liang, G. (2009). Rethinking how DNA methylation patterns are maintained. Nat Rev Genet 10, 805–811.

    Article  PubMed  CAS  Google Scholar 

  • Jurkowska, R. Z., Anspach, N., Urbanke, C., Jia, D., Reinhardt, R., Nellen, W., Cheng, X. & Jeltsch, A. (2008). Formation of nucleoprotein filaments by mammalian DNA methyltransferase Dnmt3a in complex with regulator Dnmt3L. Nucleic Acids Res 36, 6656–6663.

    Article  PubMed  CAS  Google Scholar 

  • Jurkowska, R. Z., Jurkowski, T. P. & Jeltsch, A. (2011). Structure and function of mammalian DNA methyltransferases. Chembiochem 12, 206–222.

    Article  PubMed  CAS  Google Scholar 

  • Kaneda, M., Okano, M., Hata, K., Sado, T., Tsujimoto, N., Li, E. & Sasaki, H. (2004). Essential role for de novo DNA methyltransferase Dnmt3a in paternal and maternal imprinting. Nature 429, 900–903.

    Article  PubMed  CAS  Google Scholar 

  • Kim, G. D., Ni, J., Kelesoglu, N., Roberts, R. J. & Pradhan, S. (2002). Co-operation and communication between the human maintenance and de novo DNA (cytosine-5) methyltransferases. EMBO J 21, 4183–4195.

    Article  PubMed  CAS  Google Scholar 

  • Kolasinska-Zwierz, P., Down, T., Latorre, I., Liu, T., Liu, X. S. & Ahringer, J. (2009). Differential chromatin marking of introns and expressed exons by H3K36me3. Nat Genet 41, 376–381.

    Article  PubMed  CAS  Google Scholar 

  • Kondo, T., Bobek, M. P., Kuick, R., Lamb, B., Zhu, X., Narayan, A., Bourc’his, D., Viegas-Pequignot, E., Ehrlich, M. & Hanash, S. M. (2000). Whole-genome methylation scan in ICF syndrome: hypomethylation of non-satellite DNA repeats D4Z4 and NBL2. Hum Mol Genet 9, 597–604.

    Article  PubMed  CAS  Google Scholar 

  • Kriaucionis, S. & Heintz, N. (2009). The nuclear DNA base 5-hydroxymethylcytosine is present in Purkinje neurons and the brain. Science 324, 929–930.

    Article  PubMed  CAS  Google Scholar 

  • Laurent, L., Wong, E., Li, G., Huynh, T., Tsirigos, A., Ong, C. T., Low, H. M., Kin Sung, K. W., Rigoutsos, I., Loring, J. & Wei, C. L. (2010). Dynamic changes in the human methylome during differentiation. Genome Res 20, 320–331.

    Article  PubMed  CAS  Google Scholar 

  • Li, E. (2002). Chromatin modification and epigenetic reprogramming in mammalian development. Nat Rev Genet 3, 662–673.

    Article  PubMed  CAS  Google Scholar 

  • Li, E., Bestor, T. H. & Jaenisch, R. (1992). Targeted mutation of the DNA methyltransferase gene results in embryonic lethality. Cell 69, 915–926.

    Article  PubMed  CAS  Google Scholar 

  • Lin, I. G., Han, L., Taghva, A., O’Brien, L. E. & Hsieh, C. L. (2002). Murine de novo methyltransferase Dnmt3a demonstrates strand asymmetry and site preference in the methylation of DNA in vitro. Mol Cell Biol 22, 704–723.

    Article  PubMed  CAS  Google Scholar 

  • Lister, R., Pelizzola, M., Dowen, R. H., Hawkins, R. D., Hon, G., Tonti-Filippini, J., Nery, J. R., Lee, L., Ye, Z., Ngo, Q. M., Edsall, L., Antosiewicz-Bourget, J., Stewart, R., Ruotti, V., Millar, A. H., Thomson, J. A., Ren, B. & Ecker, J. R. (2009). Human DNA methylomes at base resolution show widespread epigenomic differences. Nature 19, 315–322.

    Article  CAS  Google Scholar 

  • Luciani, J. J., Depetris, D., Missirian, C., Mignon-Ravix, C., Metzler-Guillemain, C., Megarbane, A., Moncla, A. & Mattei, M. G. (2005). Subcellular distribution of HP1 proteins is altered in ICF syndrome. Eur J Hum Genet 13, 41–51.

    Article  PubMed  CAS  Google Scholar 

  • Maraschio, P., Zuffardi, O., Dalla, F. T. & Tiepolo, L. (1988). Immunodeficiency, centromeric heterochromatin instability of chromosomes 1, 9, and 16, and facial anomalies: the ICF syndrome. J Med Genet 25, 173–180.

    Article  PubMed  CAS  Google Scholar 

  • Matarazzo, M. R., Boyle, S., D’Esposito, M. & Bickmore, W. A. (2007a). Chromosome territory reorganization in a human disease with altered DNA methylation. Proc Natl Acad Sci U S A 104, 16546–16551.

    Article  PubMed  CAS  Google Scholar 

  • Matarazzo, M. R., De Bonis, M. L., Gregory, R. I., Vacca, M., Hansen, R. S., Mercadante, G., D’Urso, M., Feil, R. & D’Esposito, M. (2002). Allelic inactivation of the pseudoautosomal gene SYBL1 is controlled by epigenetic mechanisms common to the X and Y chromosomes. Hum Mol Genet 11, 3191–3198.

    Article  PubMed  CAS  Google Scholar 

  • Matarazzo, M. R., De Bonis, M. L., Strazzullo, M., Cerase, A., Ferraro, M., Vastarelli, P., Ballestar, E., Esteller, M., Kudo, S. & D’Esposito, M. (2007b). Multiple binding of methyl-CpG and polycomb proteins in long-term gene silencing events. J Cell Physiol 210, 711–719.

    Article  PubMed  CAS  Google Scholar 

  • Matarazzo, M. R., De Bonis, M. L., Vacca, M., Della, R. F. & D’Esposito, M. (2009). Lessons from two human chromatin diseases, ICF syndrome and Rett syndrome. Int J Biochem Cell Biol 41, 117–126.

    Article  PubMed  CAS  Google Scholar 

  • Matzke, M. A. & Birchler, J. A. (2005). RNAi-mediated pathways in the nucleus. Nat Rev Genet 6, 24–35.

    Article  PubMed  CAS  Google Scholar 

  • Miniou, P., Jeanpierre, M., Blanquet, V., Sibella, V., Bonneau, D., Herbelin, C., Fischer, A., Niveleau, A. & Viegas-Pequignot, E. (1994). Abnormal methylation pattern in constitutive and facultative (X inactive chromosome) heterochromatin of ICF patients. Hum Mol Genet 3, 2093–2102.

    Article  PubMed  CAS  Google Scholar 

  • Miniou, P., Jeanpierre, M., Bourc’his, D., Coutinho Barbosa, A. C., Blanquet, V. & Viegas-Pequignot, E. (1997). alpha-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.

    Article  PubMed  CAS  Google Scholar 

  • Moarefi, A. H. & Chedin, F. (2011). ICF syndrome mutations cause a broad spectrum of biochemical defects in DNMT3B-mediated de novo DNA methylation. J Mol Biol 409, 758–772.

    Article  PubMed  CAS  Google Scholar 

  • Mohn, F. & Schubeler, D. (2009). Genetics and epigenetics: stability and plasticity during cellular differentiation. Trends Genet 25, 129–136.

    Article  PubMed  CAS  Google Scholar 

  • Mohn, F., Weber, M., Rebhan, M., Roloff, T. C., Richter, J., Stadler, M. B., Bibel, M. & Schubeler, D. (2008). Lineage-specific polycomb targets and de novo DNA methylation define restriction and potential of neuronal progenitors. Mol Cell 30, 755–766.

    Article  PubMed  CAS  Google Scholar 

  • Mosher, R. A. & Melnyk, C. W. (2010). siRNAs and DNA methylation: seedy epigenetics. Trends Plant Sci 15, 204–210.

    Article  PubMed  CAS  Google Scholar 

  • Oda, M., Yamagiwa, A., Yamamoto, S., Nakayama, T., Tsumura, A., Sasaki, H., Nakao, K., Li, E. & Okano, M. (2006). DNA methylation regulates long-range gene silencing of an X-linked homeobox gene cluster in a lineage-specific manner. Genes Dev 20, 3382–3394.

    Article  PubMed  CAS  Google Scholar 

  • Okano, M., Bell, D. W., Haber, D. A. & Li, E. (1999). DNA methyltransferases Dnmt3a and Dnmt3b are essential for de novo methylation and mammalian development. Cell 99, 247–257.

    Article  PubMed  CAS  Google Scholar 

  • Ooi, S. K., Qiu, C., Bernstein, E., Li, K., Jia, D., Yang, Z., Erdjument-Bromage, H., Tempst, P., Lin, S. P., Allis, C. D., Cheng, X. & Bestor, T. H. (2007). DNMT3L connects unmethylated lysine 4 of histone H3 to de novo methylation of DNA. Nature 448, 714–717.

    Article  PubMed  CAS  Google Scholar 

  • Otani, J., Nankumo, T., Arita, K., Inamoto, S., Ariyoshi, M. & Shirakawa, M. (2009). Structural basis for recognition of H3K4 methylation status by the DNA methyltransferase 3A ATRX-DNMT3-DNMT3L domain. EMBO Rep 10, 1235–1241.

    Article  PubMed  CAS  Google Scholar 

  • Portela, A. & Esteller, M. (2010). Epigenetic modifications and human disease. Nat Biotechnol 28, 1057–1068.

    Article  PubMed  CAS  Google Scholar 

  • Sakaue, M., Ohta, H., Kumaki, Y., Oda, M., Sakaide, Y., Matsuoka, C., Yamagiwa, A., Niwa, H., Wakayama, T. & Okano, M. (2010). DNA methylation is dispensable for the growth and survival of the extraembryonic lineages. Curr Biol 20, 1452–1457.

    Article  PubMed  CAS  Google Scholar 

  • Scarano, M. I., Strazzullo, M., Matarazzo, M. R. & D’Esposito, M. (2005). DNA methylation 40 years later: Its role in human health and disease. J Cell Physiol 204, 21–35.

    Article  PubMed  CAS  Google Scholar 

  • Schuetz, C., Barbi, G., Barth, T. F., Hoenig, M., Schulz, A., Moeller, P., Smeets, D., de Greef, J. C., van der Maarel, S. M., Vogel, W., Debatin, K. M. & Friedrich, W. (2007). ICF syndrome: high variability of the chromosomal phenotype and association with classical Hodgkin lymphoma. Am J Med Genet A 143A, 2052–2057.

    Article  PubMed  CAS  Google Scholar 

  • Stacey, M., Bennett, M. S. & Hulten, M. (1995). FISH analysis on spontaneously arising micronuclei in the ICF syndrome. J Med Genet 32, 502–508.

    Article  PubMed  CAS  Google Scholar 

  • Storre, J., Elsasser, H. P., Fuchs, M., Ullmann, D., Livingston, D. M. & Gaubatz, S. (2002). Homeotic transformations of the axial skeleton that accompany a targeted deletion of E2f6. EMBO Rep 3, 695–700.

    Article  PubMed  CAS  Google Scholar 

  • Straussman, R., Nejman, D., Roberts, D., Steinfeld, I., Blum, B., Benvenisty, N., Simon, I., Yakhini, Z. & Cedar, H. (2009). Developmental programming of CpG island methylation profiles in the human genome. Nat Struct Mol Biol 16, 564–571.

    Article  PubMed  CAS  Google Scholar 

  • Suzuki, M., Yamada, T., Kihara-Negishi, F., Sakurai, T., Hara, E., Tenen, D. G., Hozumi, N. & Oikawa, T. (2006). Site-specific DNA methylation by a complex of PU.1 and Dnmt3a/b. Oncogene 25, 2477–2488.

    Article  PubMed  CAS  Google Scholar 

  • Tachibana, M., Matsumura, Y., Fukuda, M., Kimura, H. & Shinkai, Y. (2008). G9a/GLP complexes independently mediate H3K9 and DNA methylation to silence transcription. EMBO J 27, 2681–2690.

    Article  PubMed  CAS  Google Scholar 

  • Tahiliani, M., Koh, K. P., Shen, Y., Pastor, W. A., Bandukwala, H., Brudno, Y., Agarwal, S., Iyer, L. M., Liu, D. R., Aravind, L. & Rao, A. (2009). Conversion of 5-methylcytosine to 5-hydroxymethylcytosine in mammalian DNA by MLL partner TET1. Science 324, 930–935.

    Article  PubMed  CAS  Google Scholar 

  • Tiepolo, L., Maraschio, P., Gimelli, G., Cuoco, C., Gargani, G. F. & Romano, C. (1979). Multibranched chromosomes 1, 9, and 16 in a patient with combined IgA and IgE deficiency. Hum Genet 51, 127–137.

    Article  PubMed  CAS  Google Scholar 

  • Tuck-Muller, C. M., Narayan, A., Tsien, F., Smeets, D. F., Sawyer, J., Fiala, E. S., Sohn, O. S. & Ehrlich, M. (2000). DNA hypomethylation and unusual chromosome instability in cell lines from ICF syndrome patients. Cytogenet Cell Genet 89, 121–128.

    Article  PubMed  CAS  Google Scholar 

  • Ueda, Y., Okano, M., Williams, C., Chen, T., Georgopoulos, K. & Li, E. (2006). Roles for Dnmt3b in mammalian development: a mouse model for the ICF syndrome. Development 133, 1183–1192.

    Article  PubMed  CAS  Google Scholar 

  • Vakoc, C. R., Sachdeva, M. M., Wang, H. & Blobel, G. A. (2006). Profile of histone lysine methylation across transcribed mammalian chromatin. Mol Cell Biol 26, 9185–9195.

    Article  PubMed  CAS  Google Scholar 

  • van den Brand, M., Flucke, U. E., Bult, P., Weemaes, C. M. & van Deuren, M. (2011). Angiosarcoma in a patient with immunodeficiency, centromeric region instability, facial anomalies (ICF) syndrome. Am J Med Genet A 155A, 622–625.

    PubMed  Google Scholar 

  • Vanyushin, B. F. & Ashapkin, V. V. (2011). DNA methylation in higher plants: past, present and future. Biochim Biophys Acta 1809, 360–368.

    Article  PubMed  CAS  Google Scholar 

  • Velasco, G., Hube, F., Rollin, J., Neuillet, D., Philippe, C., Bouzinba-Segard, H., Galvani, A., Viegas-Pequignot, E. & Francastel, C. (2010). Dnmt3b recruitment through E2F6 transcriptional repressor mediates germ-line gene silencing in murine somatic tissues. Proc Natl Acad Sci U S A 107, 9281–9286.

    Article  PubMed  Google Scholar 

  • Vire, E., Brenner, C., Deplus, R., Blanchon, L., Fraga, M., Didelot, C., Morey, L., Van Eynde, A., Bernard, D., Vanderwinden, J. M., Bollen, M., Esteller, M., Di Croce, L., de Launoit, Y. & Fuks, F. (2006). The Polycomb group protein EZH2 directly controls DNA methylation. Nature 439, 871–874.

    Article  PubMed  CAS  Google Scholar 

  • Wang, Y. A., Kamarova, Y., Shen, K. C., Jiang, Z., Hahn, M. J., Wang, Y. & Brooks, S. C. (2005). DNA methyltransferase-3a interacts with p53 and represses p53-mediated gene expression. Cancer Biol Ther 4, 1138–1143.

    Article  PubMed  CAS  Google Scholar 

  • Weber, M., Hellmann, I., Stadler, M. B., Ramos, L., Paabo, S., Rebhan, M. & Schubeler, D. (2007). Distribution, silencing potential and evolutionary impact of promoter DNA methylation in the human genome. Nat Genet 39, 457–466.

    Article  PubMed  CAS  Google Scholar 

  • Wienholz, B. L., Kareta, M. S., Moarefi, A. H., Gordon, C. A., Ginno, P. A. & Chedin, F. (2010). DNMT3L modulates significant and distinct flanking sequence preference for DNA methylation by DNMT3A and DNMT3B in vivo. PLoS Genet 6, e1001106.

    Article  PubMed  CAS  Google Scholar 

  • 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., Luyten, J. A., Strengman, E., Weemaes, C. & Pearson, P. L. (2000). Genetic variation in ICF syndrome: evidence for genetic heterogeneity. Hum Mutat 16, 509–517.

    Article  PubMed  CAS  Google Scholar 

  • Xie, Z. H., Huang, Y. N., Chen, Z. X., Riggs, A. D., Ding, J. P., Gowher, H., Jeltsch, A., Sasaki, H., Hata, K. & Xu, G. L. (2006). Mutations in DNA methyltransferase DNMT3B in ICF syndrome affect its regulation by DNMT3L. Hum Mol Genet 15, 1375–1385.

    Article  PubMed  CAS  Google Scholar 

  • Yehezkel, S., Segev, Y., Viegas-Pequignot, E., Skorecki, K. & Selig, S. (2008). Hypomethylation of subtelomeric regions in ICF syndrome is associated with abnormally short telomeres and enhanced transcription from telomeric regions. Hum Mol Genet 17, 2776–2789.

    Article  PubMed  CAS  Google Scholar 

  • Zhang, Y., Jurkowska, R., Soeroes, S., Rajavelu, A., Dhayalan, A., Bock, I., Rathert, P., Brandt, O., Reinhardt, R., Fischle, W. & Jeltsch, A. (2010). Chromatin methylation activity of Dnmt3a and Dnmt3a/3L is guided by interaction of the ADD domain with the histone H3 tail. Nucleic Acids Res 38, 4246–4253.

    Article  PubMed  CAS  Google Scholar 

  • Zhu, H., Geiman, T. M., Xi, S., Jiang, Q., Schmidtmann, A., Chen, T., Li, E. & Muegge, K. (2006). Lsh is involved in de novo methylation of DNA. EMBO J 25, 335–345.

    Article  PubMed  CAS  Google Scholar 

  • Zilberman, D., Gehring, M., Tran, R. K., Ballinger, T. & Henikoff, S. (2007). Genome-wide analysis of Arabidopsis thaliana DNA methylation uncovers an interdependence between methylation and transcription. Nat Genet 39, 61–69.

    Article  PubMed  CAS  Google Scholar 

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Gatto, S., D’Esposito, M., Matarazzo, M.R. (2012). The Role of DNMT3B Mutations in the Pathogenesis of ICF Syndrome. In: Minarovits, J., Niller, H. (eds) Patho-Epigenetics of Disease. Springer, New York, NY. https://doi.org/10.1007/978-1-4614-3345-3_2

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