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The impact of MECP2 mutations in the expression patterns of Rett syndrome patients

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Abstract

Rett syndrome (RTT), the second most common cause of mental retardation in females, has been associated with mutations in MeCP2, the archetypical member of the methyl-CpG binding domain (MBD) family of proteins. MeCP2 additionally possesses a transcriptional repression domain (TRD). We have compared the gene expression profiles of RTT- and normal female-derived lymphoblastoid cells by using cDNA microarrays. Clustering analysis allowed the classification of RTT patients according to the localization of the MeCP2 mutation (MBD or TRD) and those with clinically diagnosed RTT but without detectable MeCP2 mutations. Numerous genes were observed to be overexpressed in RTT patients compared with control samples, including excellent candidate genes for neurodevelopmental disease. Chromatin immunoprecipitation analysis confirmed that binding of MeCP2 to corresponding promoter CpG islands was lost in RTT-derived cells harboring a mutation in the region of the MECP2 gene encoding the MBD. Bisulfite genomic sequencing demonstrated that the majority of MeCP2 binding occurred in DNA sequences with methylation-associated silencing. Most importantly, the finding that these genes are also methylated and bound by MeCP2 in neuron-related cells suggests a role in this neurodevelopmental disease. Our results provide new data of the underlying mechanisms of RTT and unveil novel targets of MeCP2-mediated gene repression.

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References

  • Alaminos M, Mora J, Cheung NK, Smith A, Qin J, Chen L, Gerald WL (2003) Genome-wide analysis of gene expression associated with MYCN in human neuroblastoma. Cancer Res 63:4538–4546

    CAS  PubMed  Google Scholar 

  • Allan DW, Thor S (2003) Together at last: bHLH and LIM-HD regulators cooperate to specify motor neurons. Neuron 38:675–677

    Article  CAS  PubMed  Google Scholar 

  • Allen RC, Zoghbi HY, Moseley AB, Rosenblatt HM, Belmont JW (1992) Methylation of HpaII and HhaI sites near the polymorphic CAG repeat in the human androgen-receptor gene correlates with X chromosome inactivation. Am J Hum Genet 51:1229–1239

    CAS  PubMed  Google Scholar 

  • Amir RE, Van den Veyver IB, Wan M, Tran CQ, Francke U, Zoghbi HY (1999) Rett syndrome is caused by mutations in X-linked MeCP2, encoding methyl-CpG-binding protein 2. Nat Genet 23:185–188

    Article  CAS  PubMed  Google Scholar 

  • Armstrong DD (1997) Review of Rett syndrome. J Neuropathol Exp Neurol 56:843–849

    CAS  PubMed  Google Scholar 

  • Ballestar E, Yusufzai TM, Wolffe AP (2000) Effects of Rett syndrome mutations of the methyl-CpG binding domain of the transcriptional repressor MeCP2 on selectivity for association with methylated DNA. Biochemistry 20:7100–7106

    Article  Google Scholar 

  • Ballestar E, Paz MF, Valle L, Wei S, Fraga MF, Espada J, Cigudosa JC, Huang THM, Esteller M (2003) Methyl-CpG binding proteins identify novel sites of epigenetic activation in human cancer. EMBO J 22:6335–6345

    Article  CAS  PubMed  Google Scholar 

  • Bazan NG, Palacios-Pelaez R, Lukiw WJ (2002) Hypoxia signaling to genes: significance in Alzheimer’s disease. Mol Neurobiol 26:269–281

    Article  PubMed  Google Scholar 

  • Bird A, Tweedie S (1995) Transcriptional noise and the evolution of gene number. Philos Trans R Soc Lond B Biol Sci 349:249–253

    CAS  PubMed  Google Scholar 

  • Buschdorf JP, Stratling WH (2004) A WW domain binding region in methyl-CpG-binding protein MeCP2: impact on Rett syndrome. J Mol Med 82:135–143

    Article  CAS  PubMed  Google Scholar 

  • Caruana G (2002) Genetic studies define MAGUK proteins as regulators of epithelial cell polarity. Int J Dev Biol 46:511–518

    CAS  PubMed  Google Scholar 

  • Chan AM, Takai S, Yamada K, Miki T (1996) Isolation of a novel oncogene, NET1, from neuroepithelioma cells by expression cDNA cloning. Oncogene 12:1259–1266

    CAS  PubMed  Google Scholar 

  • Chen WG, Chang Q, Lin Y, Meissner A, West AE, Griffith EC, Jaenisch R, Greenberg ME (2003) Derepression of BDNF transcription involves calcium-dependent phosphorylation of MeCP2. Science 302:885–889

    Article  CAS  PubMed  Google Scholar 

  • Clark SJ, Warnecke PM (2002) DNA methylation analysis in mammalian cells. Methods 27:99–100

    Article  CAS  PubMed  Google Scholar 

  • Cobb J, Miyaike M, Kikuchi A, Handel MA (1999) Meiotic events at the centromeric heterochromatin: histone H3 phosphorylation, topoisomerase II alpha localization and chromosome condensation. Chromosoma 108:412–425

    Article  CAS  PubMed  Google Scholar 

  • Colantuoni C, Jeon OH, Hyder K, Chenchik A, Khimani AH, Narayanan V, Hoffman EP, Kaufmann WE, Naidu S, Pevsner J (2001) Gene expression profiling in postmortem Rett sndrome brain: differential gene expression and patient classification. Neurobiol Dis 8:847–865

    Article  CAS  PubMed  Google Scholar 

  • Dopazo J, Dopazo JM (1997) Phylogenetic reconstruction using an unsupervised growing neural network that adopts the topology of a phylogenetic tree. J Mol Evol 44:226–233

    CAS  PubMed  Google Scholar 

  • Esteller M (2000) Epigenetic lesions causing genetic lesions in human cancer: promoter hypermethylation of DNA repair genes. Eur J Cancer 36:2294–2300

    Article  CAS  PubMed  Google Scholar 

  • Esteller M (2002) CpG island hypermethylation and tumor suppressor genes: a booming present, a brighter future. Oncogene 21:5427–5440

    Article  CAS  PubMed  Google Scholar 

  • Fournier C, Goto Y, Ballestar E, Delaval K, Hever A, Esteller M, Feil R (2002) Allele-specific histone lysine methylation marks regulatory regions at imprinted mouse genes. EMBO J 21:6560–6570

    Article  CAS  PubMed  Google Scholar 

  • Fraga MF, Esteller M (2002) DNA methylation: a profile of methods and applications. Biotechniques 33:632–649

    CAS  PubMed  Google Scholar 

  • Fraga MF, Ballestar E, Montoya G, Taysavang P, Wade PA, Esteller M (2003) The affinity of different MBD proteins for a specific methylated locus depends on their intrinsic binding properties. Nucleic Acids Res 31:1765–1774

    Article  CAS  PubMed  Google Scholar 

  • Georgel PT, Horowitz-Scherer RA, Adkins N, Woodcock CL, Wade PA, Hansen JC (2003) Chromatin compaction by human MeCP2. Assembly of novel secondary chromatin structures in the absence of DNA methylation. J Biol Chem 278:32181–32188

    Article  CAS  PubMed  Google Scholar 

  • Herrero J, Diaz-Uriarte R, Dopazo J (2003) Gene expression data preprocessing. Bioinformatics 19:655–656

    Article  CAS  PubMed  Google Scholar 

  • Hescheler J, Schultz G (1994) Heterotrimeric G proteins involved in the modulation of voltage-dependent calcium channels of neuroendocrine cells. Ann N Y Acad Sci 733:306–312

    CAS  PubMed  Google Scholar 

  • Jones PL, Veenstra GJ, Wade PA, Vermaak D, Kass SU, Landsberger N, Strouboulis J, Wolffe AP (1998) Methylated DNA and MeCP2 recruit histone deacetylase to repress transcription. Nat Genet 19:187–191

    Article  CAS  PubMed  Google Scholar 

  • Kempkes B, Pich D, Zeidler R, Hammerschmidt W (1995) Immortalization of human primary B lymphocytes in vitro with DNA. Proc Natl Acad Sci USA 92:5875–5879

    CAS  PubMed  Google Scholar 

  • Koizume S, Tachibana K, Sekiya T, Hirohashi S, Shiraishi M (2002) Heterogeneity in the modification and involvement of chromatin components of the CpG island of the silenced human CDH1 gene in cancer cells. Nucleic Acids Res 30:4770–4780

    Article  CAS  PubMed  Google Scholar 

  • Kriaucionis S, Bird A (2003) DNA methylation and Rett syndrome. Hum Mol Genet 12 (Spec 2):R221–R227

    Article  CAS  PubMed  Google Scholar 

  • Laccone F, Junemann I, Whatley S, Morgan R, Butler R, Huppke P, Ravine D (2004) Large deletions of the MeCP2 gene detected by gene dosage analysis in patients with Rett syndrome. Hum Mutat 23:234–244

    Article  CAS  PubMed  Google Scholar 

  • Lang AJ, Mirski SE, Cummings HJ, Yu Q, Gerlach JH, Cole SP (1998) Structural organization of the human TOP2A and TOP2B genes. Gene 221:255–266

    Article  CAS  PubMed  Google Scholar 

  • Martinowich K, Hattori D, Wu H, Fouse S, He F, Hu Y, Fan G, Sun YE (2003) DNA methylation-related chromatin remodeling in activity-dependent BDNF gene regulation. Science 302:890–893

    Article  CAS  PubMed  Google Scholar 

  • Mnatzakanian GN, Lohi H, Munteanu I, Alfred SE, Yamada T, MacLeod PJ, Jones JR, Scherer SW, Schanen NC, Friez MJ, Vincent JB, Minassian BA (2004) A previously unidentified MeCP2 open reading frame defines a new protein isoform relevant to Rett syndrome. Nat Genet 36:339–341

    Article  CAS  PubMed  Google Scholar 

  • Monros E, Armstrong J, Aibar E, Poo P, Canos I, Pineda M (2001) Rett syndrome in Spain: mutation analysis and clinical correlations. Brain Dev 23 (Suppl 1):S251–S253

    Article  PubMed  Google Scholar 

  • Moreno-Bueno G, Sanchez-Estevez C, Cassia R, Rodriguez-Perales S, Diaz-Uriarte R, Dominguez O, Hardisson D, Andujar M, Prat J, Matias-Guiu X, Cigudosa JC, Palacios J (2003) Differential gene expression profile in endometrioid and nonendometrioid endometrial carcinoma: STK15 is frequently overexpressed and amplified in nonendometrioid carcinomas. Cancer Res 63:5697–5702

    CAS  PubMed  Google Scholar 

  • Nan X, Bird A (2001) The biological functions of the methyl-CpG-binding protein MeCP2 and its implication in Rett syndrome. Brain Dev 23 (Suppl 1):S32–S37

    Article  PubMed  Google Scholar 

  • Nan X, Ng HH, Johnson CA, Laherty CD, Turner BM, Eisenman RN, Bird A (1998) Transcriptional repression by the methyl-CpG-binding protein MeCP2 involves a histone deacetylase complex. Nature 393:386–389

    Article  CAS  PubMed  Google Scholar 

  • Nguyen CT, Gonzales FA, Jones PA (2001) Altered chromatin structure associated with methylation-induced gene silencing in cancer cells: correlation of accessibility, methylation, MeCP2 binding and acetylation. Nucleic Acids Res 29:4598–4606

    Article  CAS  PubMed  Google Scholar 

  • Orlando V (2000) Mapping chromosomal proteins in vivo by formaldehyde-crosslinked-chromatin immunoprecipitation. Trends Biochem Sci 25:99–104

    Article  CAS  PubMed  Google Scholar 

  • Reik W, Constancia M, Dean W, Davies K, Bowden L, Murrell A, Feil R, Walter J, Kelsey G (2000) Igf2 imprinting in development and disease. Int J Dev Biol 44:145–150

    CAS  PubMed  Google Scholar 

  • Schmidt JT, Morgan P, Dowell N, Leu B (2002) Myosin light chain phosphorylation and growth cone motility. J Neurobiol 52:175–188

    Article  CAS  PubMed  Google Scholar 

  • Schraven B, Schoenhaut D, Bruyns E, Koretzky G, Eckerskorn C, Wallich R, Kirchgessner H, Sakorafas P, Labkovsky B, Ratnofsky S et al (1994) LPAP, a novel 32-kDa phosphoprotein that interacts with CD45 in human lymphocytes. J Biol Chem 269:29102–29111

    CAS  PubMed  Google Scholar 

  • Stancheva I, Collins AL, Van den Veyver IB, Zoghbi H, Meehan RR (2003) A mutant form of MeCP2 protein associated with human Rett syndrome cannot be displaced from methylated DNA by Notch in Xenopus embryos. Mol Cell 12:425–432

    Article  CAS  PubMed  Google Scholar 

  • Strausberg RL, Feingold EA, Grouse LH, Derge JG, Klausner RD, Collins FS, Wagner L, Shenmen CM, Schuler GD, Altschul SF et al (2002) Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences. Proc Natl Acad Sci USA 99:16899–16903

    Article  PubMed  Google Scholar 

  • Sugie H, Sugie Y, Tsurui S, Ito M (1994) Phosphoglycerate kinase deficiency. Neurology 44:1364–1365

    CAS  Google Scholar 

  • Tracey L, Villuendas R, Ortiz P, Dopazo A, Spiteri I, Lombardia L, Rodriguez-Peralto JL, Fernandez-Herrera J et al (2002) Identification of genes involved in resistance to interferon-alpha in cutaneous T-cell lymphoma. Am J Pathol 161:1825–1837

    CAS  PubMed  Google Scholar 

  • Traynor J, Agarwal P, Lazzeroni L, Francke U (2002) Gene expression patterns vary in clonal cell cultures from Rett syndrome females with eight different MeCP2 mutations. BMC Med Genet 3:12

    Article  PubMed  Google Scholar 

  • Troyanskaya O, Cantor M, Sherlock G, Brown P, Hastie T, Tibshirani R, Botstein D, Altman RB (2001) Missing value estimation methods for DNA microarrays. Bioinformatics 17:520–525

    Article  CAS  PubMed  Google Scholar 

  • Tudor M, Akbarian S, Chen RZ, Jaenisch R (2002) Transcriptional profiling of a mouse model for Rett syndrome reveals subtle transcriptional changes in the brain. Proc Natl Acad Sci USA 99:5536–5541

    Article  Google Scholar 

  • Tusher V, Tibshirani R, Chu C (2001) Significance analysis of microarrays applied to ionising radiation response. Proc Natl Acad Sci USA 98:5116–5121

    Article  PubMed  Google Scholar 

  • Vacca M, Filippini F, Budillon A, Rossi V, Della Ragione F, De Bonis ML, Mercadante G, Manzati E, Gualandi F, Bigoni S, Trabanelli C, Pini G, Calzolari E, Ferlini A, Meloni I, Hayek G, Zappella M, Renieri A, D’Urso M, D’Esposito M, Macdonald F, Kerr A, Dhanjal S, Hulten M (2001) MECP2 gene mutation analysis in the British and Italian Rett Syndrome patients: hot spot map of the most recurrent mutations and bioinformatic analysis of a new MeCP2 conserved region. Brain Dev 23 (Suppl 1): S246–S250

    Article  PubMed  Google Scholar 

  • Van den Veyver IB, Zoghbi HY (2000) Methyl-CpG-binding protein 2 mutations in Rett syndrome. Curr Opin Genet Dev 10:275–279

    Article  PubMed  Google Scholar 

  • Webb T, Latif F (2001) Rett syndrome and the MECP2 gene. J Med Genet 38:217–223

    Article  CAS  PubMed  Google Scholar 

  • Willard H, Hendrich BD (1999) Breaking the silence in Rett syndrome. Nat Genet 23:127–128

    Article  CAS  PubMed  Google Scholar 

  • Yusufzai TM, Wolffe AP (2000) Functional consequences of Rett syndrome mutations on human MeCP2. Nucleic Acids Res 28:4172–4179

    Article  CAS  PubMed  Google Scholar 

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Acknowledgements

We are grateful to the Catalan and Valencian Rett Syndrome Associations. We would like to thank Dr. Kevin Petrie for helpful comments. We also thank Drs. Luis Lombardia and Joaquin Dopazo from the Microarray and Bioinformatics laboratories of the CNIO for their technical advice. This work has been supported by the International Rett Syndrome Association and I+D project SAF 2001-0059 and Fondo de Investigación Sanitaria FIS99/0235. E.B. is funded by the Ramón y Cajal Programme.

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Authors and Affiliations

  1. Cancer Epigenetics Laboratory, Molecular Pathology Programme, Spanish National Cancer Centre (CNIO), Melchor Fernández Almagro 3, 28029, Madrid, Spain

    Esteban Ballestar, Santiago Ropero, Miguel Alaminos, Fernando Setien, Ruben Agrelo, Mario F. Fraga, Michel Herranz, Sonia Avila & Manel Esteller

  2. Genetics Section, University Hospital Sant Joan de Deu, Esplugues, Barcelona, Catalonia, Spain

    Judith Armstrong & Eugenia Monros

  3. Neurology Service, University Hospital Sant Joan de Deu, Esplugues, Barcelona, Catalonia, Spain

    Mercedes Pineda

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  1. Esteban Ballestar
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  2. Santiago Ropero
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  3. Miguel Alaminos
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  4. Judith Armstrong
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  5. Fernando Setien
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Correspondence to Manel Esteller.

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Ballestar, E., Ropero, S., Alaminos, M. et al. The impact of MECP2 mutations in the expression patterns of Rett syndrome patients. Hum Genet 116, 91–104 (2005). https://doi.org/10.1007/s00439-004-1200-0

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