Comparative (computational) analysis of the DNA methylation status of trinucleotide repeat expansion diseases

Journal of Nucleic Acids

Volumn 2013, Issue , 2013, Pages

  Ghorbani, Mohammadmersad ^a   Taylor, Simon J E ^a   Pook, Mark A ^a   Payne, Annette ^a  

^a BRUNEL UNIVERSITY   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

EID: 84893443083     PISSN: 20900201     EISSN: 2090021X     Source Type: Journal    
DOI: 10.1155/2013/689798     Document Type: Article

References (39)

1. A. P. Bird and A. P. Wolffe, "Methylation-induced repression-belts, braces, and chromatin," Cell, vol. 99, no. 5, pp. 451-454, 1999.
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.
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. (Pubitemid 26089479)
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.
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. (Pubitemid 121001321)
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. (Pubitemid 121001519)
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. (Pubitemid 44486821)
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.
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.
10. S. I. S. Grewal and S. Jia, "Heterochromatin revisited," Nature Reviews Genetics, vol. 8, no. 1, pp. 35-46, 2007.
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.
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. (Pubitemid 41572304)
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. (Pubitemid 43980596)
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.
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.
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.
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.
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.
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.
20. C. Bock and T. Lengauer, "Computational epigenetics," Bioinformatics, vol. 24, no. 1, pp. 1-10, 2008.
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.
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.
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.
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.
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.
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. (Pubitemid 351292262)
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.
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.
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.
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.
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.
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. (Pubitemid 46220758)
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.
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.
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.
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.
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.
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. (Pubitemid 33062363)