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Journal of Nucleic Acids
Volume 2013 (2013), Article ID 689798, 9 pages
http://dx.doi.org/10.1155/2013/689798
Research Article

Comparative (Computational) Analysis of the DNA Methylation Status of Trinucleotide Repeat Expansion Diseases

1Department of Information Systems and Computing, Brunel University, Uxbridge Middlesex UB8 3PH, UK
2Division of Biosciences, School of Health Sciences & Social Care, Brunel University, Uxbridge Middlesex UB8 3PH, UK

Received 3 July 2013; Revised 11 October 2013; Accepted 15 October 2013

Academic Editor: Hiroshi Sugiyama

Copyright © 2013 Mohammadmersad Ghorbani et al. This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

Linked References

  1. A. P. Bird and A. P. Wolffe, “Methylation-induced repression-belts, braces, and chromatin,” Cell, vol. 99, no. 5, pp. 451–454, 1999. View at Google Scholar · View at Scopus
  2. M. Pook, “DNA methylation and trinucleotide repeat expansion diseases,” in DNA Methylation—From Genomics to Technology, T. Tatarinova and O. Kerton, Eds., p. 193, InTech, Rijeka, Croatia, 2012. View at Google Scholar
  3. V. Campuzano, L. Montermini, M. D. Moltò et al., “Friedreich's ataxia: autosomal recessive disease caused by an intronic GAA triplet repeat expansion,” Science, vol. 271, no. 5254, pp. 1423–1427, 1996. View at Google Scholar · View at Scopus
  4. J. R. Brouwer, R. Willemsen, and B. A. Oostra, “The FMR1 gene and fragile X-associated tremor/ataxia syndrome,” American Journal of Medical Genetics B, vol. 150, no. 6, pp. 782–798, 2009. View at Publisher · View at Google Scholar · View at Scopus
  5. A. J. M. H. Verkerk, M. Pieretti, J. S. Sutcliffe et al., “Identification of a gene (FMR-1) containing a CGG repeat coincident with a breakpoint cluster region exhibiting length variation in fragile X syndrome,” Cell, vol. 65, no. 5, pp. 905–914, 1991. View at Publisher · View at Google Scholar · View at Scopus
  6. Y.-H. Fu, D. P. A. Kuhl, A. Pizzuti et al., “Variation of the CGG repeat at the fragile X site results in genetic instability: resolution of the sherman paradox,” Cell, vol. 67, no. 6, pp. 1047–1058, 1991. View at Google Scholar · View at Scopus
  7. U. Schara and B. G. H. Schoser, “Myotonic dystrophies type 1 and 2: a summary on current aspects,” Seminars in Pediatric Neurology, vol. 13, no. 2, pp. 71–79, 2006. View at Publisher · View at Google Scholar · View at Scopus
  8. J. D. Brook, M. E. McCurrach, H. G. Harley et al., “Molecular basis of myotonic dystrophy: expansion of a trinucleotide (CTG) repeat at the 3′ end of a transcript encoding a protein kinase family member,” Cell, vol. 68, no. 4, pp. 799–808, 1992. View at Google Scholar · View at Scopus
  9. A. L. Castel, J. D. Cleary, and C. E. Pearson, “Repeat instability as the basis for human diseases and as a potential target for therapy,” Nature Reviews Molecular Cell Biology, vol. 11, no. 3, pp. 165–170, 2010. View at Publisher · View at Google Scholar · View at Scopus
  10. S. I. S. Grewal and S. Jia, “Heterochromatin revisited,” Nature Reviews Genetics, vol. 8, no. 1, pp. 35–46, 2007. View at Publisher · View at Google Scholar · View at Scopus
  11. K. V. Morris, S. Santoso, A.-M. Turner, C. Pastori, and P. G. Hawkins, “Bidirectional transcription directs both transcriptional gene activation and suppression in human cells,” PLoS Genetics, vol. 4, no. 11, Article ID e1000258, 2008. View at Publisher · View at Google Scholar · View at Scopus
  12. D. H. Cho, C. P. Thienes, S. E. Mahoney, E. Analau, G. N. Filippova, and S. J. Tapscott, “Antisense transcription and heterochromatin at the DM1 CTG repeats are constrained by CTCF,” Molecular Cell, vol. 20, no. 3, pp. 483–489, 2005. View at Publisher · View at Google Scholar · View at Scopus
  13. M. L. Moseley, T. Zu, Y. Ikeda et al., “Bidirectional expression of CUG and CAG expansion transcripts and intranuclear polyglutamine inclusions in spinocerebellar ataxia type 8,” Nature Genetics, vol. 38, no. 7, pp. 758–769, 2006. View at Publisher · View at Google Scholar · View at Scopus
  14. P. D. Ladd, L. E. Smith, N. A. Rabaia et al., “An antisense transcript spanning the CGG repeat region of FMR1 is upregulated in premutation carriers but silenced in full mutation individuals,” Human Molecular Genetics, vol. 16, no. 24, pp. 3174–3187, 2007. View at Publisher · View at Google Scholar · View at Scopus
  15. I. De Biase, Y. K. Chutake, P. M. Rindler, and S. I. Bidichandani, “Epigenetic silencing in Friedreich ataxia is associated with depletion of CTCF (CCCTC-binding factor) and antisense transcription,” PLoS ONE, vol. 4, no. 11, Article ID e7914, 2009. View at Publisher · View at Google Scholar · View at Scopus
  16. D. W. Chung, D. D. Rudnicki, L. Yu, and R. L. Margolis, “A natural antisense transcript at the Huntington's disease repeat locus regulates HTT expression,” Human Molecular Genetics, vol. 20, no. 17, Article ID ddr263, pp. 3467–3477, 2011. View at Publisher · View at Google Scholar · View at Scopus
  17. G. N. Filippova, C. P. Thienes, B. H. Penn et al., “CTCF-binding sites flank CTG/CAG repeats and form a methylation-sensitive insulator at the DM1 locus,” Nature Genetics, vol. 28, no. 4, pp. 335–343, 2001. View at Publisher · View at Google Scholar · View at Scopus
  18. R. J. Klose and A. P. Bird, “Genomic DNA methylation: the mark and its mediators,” Trends in Biochemical Sciences, vol. 31, no. 2, pp. 89–97, 2006. View at Publisher · View at Google Scholar · View at Scopus
  19. G. Yuan, “Prediction of epigenetic target sites by using genomic DNA sequence,” in Anonymous Handbook of Research on Computational and Systems Biology: Interdisciplinary Applications, pp. 187–201, IGI Global, 2011. View at Google Scholar
  20. C. Bock and T. Lengauer, “Computational epigenetics,” Bioinformatics, vol. 24, no. 1, pp. 1–10, 2008. View at Publisher · View at Google Scholar · View at Scopus
  21. Y. Yamada and K. Satou, “Prediction of genomic methylation status on CpG islands using DNA sequence features,” WSEAS Transactions on Biology and Biomedicine, vol. 5, pp. 153–162, 2008. View at Google Scholar
  22. I. Ali and H. Seker, “A comparative study for characterisation and prediction of tissue-specific DNA methylation of CpG islands in chromosomes 6, 20 and 22,” in Proceedings of the 32nd Annual International Conference of the IEEE Engineering in Medicine and Biology Society (EMBC '10), pp. 1832–1835, September 2010. View at Publisher · View at Google Scholar · View at Scopus
  23. C. Previti, O. Harari, I. Zwir, and C. del Val, “Profile analysis and prediction of tissue-specific CpG island methylation classes,” BMC Bioinformatics, vol. 10, article 116, 2009. View at Publisher · View at Google Scholar · View at Scopus
  24. F. A. Feltus, E. K. Lee, J. F. Costello, C. Plass, and P. M. Vertino, “DNA motifs associated with aberrant CpG island methylation,” Genomics, vol. 87, no. 5, pp. 572–579, 2006. View at Publisher · View at Google Scholar · View at Scopus
  25. M. T. McCabe, E. K. Lee, and P. M. Vertino, “A multifactorial signature of DNA sequence and polycomb binding predicts aberrant CpG island methylation,” Cancer Research, vol. 69, no. 1, pp. 282–291, 2009. View at Publisher · View at Google Scholar · View at Scopus
  26. M. Pook, D. Trabzuni, C. Sandi et al., “The Friedreich ataxia GAA repeat expansion mutation induces comparable epigenetic changes in human and transgenic mouse brain and heart tissues,” Human Molecular Genetics, vol. 17, no. 5, pp. 735–746, 2008. View at Publisher · View at Google Scholar · View at Scopus
  27. A. Naumann, N. Hochstein, S. Weber, E. Fanning, and W. Doerfler, “A distinct DNA-methylation boundary in the 5′- upstream sequence of the FMR1 promoter binds nuclear proteins and is lost in fragile X syndrome,” American Journal of Human Genetics, vol. 85, no. 5, pp. 606–616, 2009. View at Publisher · View at Google Scholar · View at Scopus
  28. A. López Castel, M. Nakamori, S. Tomé et al., “Expanded CTG repeat demarcates a boundary for abnormal CpG methylation in myotonic dystrophy patient tissues,” Human Molecular Genetics, vol. 20, no. 1, pp. 1–15, 2011. View at Google Scholar · View at Scopus
  29. L. Lu, K. Lin, Z. Qian et al., “Predicting DNA methylation status using word composition,” Journal of Biomedical Science and Engineering, vol. 3, pp. 672–676, 2010. View at Google Scholar
  30. V. A. Chernukhin, Y. G. Kashirina, K. S. Sukhanova, M. A. Abdurashitov, D. A. Gonchar, and S. K. Degtyarev, “Isolation and characterization of biochemical properties of DNA methyltransferase FauIA modifying the second cytosine in the nonpalindromic sequence 5′-CCCGC-3′,” Biochemistry, vol. 70, no. 6, pp. 685–691, 2005. View at Publisher · View at Google Scholar · View at Scopus
  31. I.H. Witten, E. Frank, and M. A. Hall, Data Mining: Practical Machine Learning Tools and Techniques: Practical Machine Learning Tools and Techniques, Elsevier Science, 2011.
  32. A. Hogart, J. Lichtenberg, S.S. Ajay et al., “Genome-wide DNA methylation profiles in hematopoietic stem and progenitor cells reveal overrepresentation of ETS transcription factor binding sites,” Genome Research, vol. 22, pp. 1407–1418, 2012. View at Google Scholar
  33. S. J. Cooper, N. D. Trinklein, L. Nguyen, and R. M. Myers, “Serum response factor binding sites differ in three human cell types,” Genome Research, vol. 17, no. 2, pp. 136–144, 2007. View at Publisher · View at Google Scholar · View at Scopus
  34. M. E. Lucas, K. S. Crider, D. R. Powell, P. Kapoor-Vazirani, and P. M. Vertino, “Methylation-sensitive regulation of TMS1/ASC by the Ets factor, GA-binding protein-α,” Journal of Biological Chemistry, vol. 284, no. 22, pp. 14698–14709, 2009. View at Publisher · View at Google Scholar · View at Scopus
  35. T. Wang, M. Chen, L. Liu et al., “Nicotine induced CpG methylation of Pax6 binding motif in StAR promoter reduces the gene expression and cortisol production,” Toxicology and Applied Pharmacology, vol. 257, no. 3, pp. 328–337, 2011. View at Publisher · View at Google Scholar · View at Scopus
  36. I. W. McKinnell, J. Ishibashi, F. Le Grand et al., “Pax7 activates myogenic genes by recruitment of a histone methyltransferase complex,” Nature Cell Biology, vol. 10, no. 1, pp. 77–84, 2008. View at Publisher · View at Google Scholar · View at Scopus
  37. E. Hervouet, F. M. Vallette, and P.-F. Cartron, “Dnmt3/transcription factor interactions as crucial players in targeted DNA methylation,” Epigenetics, vol. 4, no. 7, pp. 487–499, 2009. View at Publisher · View at Google Scholar · View at Scopus
  38. M. V. Iorio, C. Piovan, and C. M. Croce, “Interplay between microRNAs and the epigenetic machinery: an intricate network,” Biochimica et Biophysica Acta, vol. 1799, no. 10–12, pp. 694–701, 2010. View at Publisher · View at Google Scholar · View at Scopus
  39. E. Grabczyk, D. Kumari, and K. Usdin, “Fragile X syndrome and Friedreich's ataxia: two different paradigms for repeat induced transcript insufficiency,” Brain Research Bulletin, vol. 56, no. 3-4, pp. 367–373, 2001. View at Publisher · View at Google Scholar · View at Scopus