Bio-CAP: A versatile and highly sensitive technique to purify and characterise regions of non-methylated DNA

Nucleic Acids Research

Volumn 40, Issue 4, 2012, Pages

  Blackledge, Neil P ^a   Long, Hannah K ^a   Zhou, Jin C ^a   Kriaucionis, Skirmantas ^b   Patient, Roger ^a   Klose, Robert J ^a  

^a JOHN RADCLIFFE HOSPITAL   (United Kingdom)

^b UNIVERSITY OF OXFORD   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

DNA; GENOMIC DNA; NONMETHYLATED DNA; UNCLASSIFIED DRUG;

ANIMAL CELL; ARTICLE; BIOTINYLATION; CPG ISLAND; DNA DETERMINATION; DNA METHYLATION; DNA PURIFICATION; DNA STRUCTURE; EMBRYO; INFORMATION PROCESSING; INTERMETHOD COMPARISON; MAGNETISM; MOUSE; NONHUMAN; PRIORITY JOURNAL; ZINC FINGER MOTIF;

BIOTINYLATION; CHROMATOGRAPHY, AFFINITY; CPG ISLANDS; DNA; DNA METHYLATION; HIGH-THROUGHPUT NUCLEOTIDE SEQUENCING; SEQUENCE ANALYSIS, DNA; ZINC FINGERS;

VERTEBRATA;

EID: 84863256915     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gkr1207     Document Type: Article

References (33)

1. Klose, R. J. and Bird, A. P. (2006) Genomic DNA methylation: the mark and its mediators. Trends Biochem. Sci., 31, 89-97. (Pubitemid 43221841)
2. 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. et al. (2009) Human DNA methylomes at base resolution show widespread epigenomic differences. Nature, 462, 315-322.
3. Cooper, D. N., Taggart, M. H. and Bird, A. P. (1983) Unmethylated domains in vertebrate DNA. Nucleic Acids Res., 11, 647-658.
4. Bird, A., Taggart, M., Frommer, M., Miller, O. J. and Macleod, D. (1985) A fraction of the mouse genome that is derived from islands of nonmethylated, CpG-rich DNA. Cell, 40, 91-99. (Pubitemid 15169310)
5. Gardiner-Garden, M. and Frommer, M. (1987) CpG islands in vertebrate genomes. J. Mol. Biol., 196, 261-282. (Pubitemid 17122132)
6. Larsen, F., Gundersen, G., Lopez, R. and Prydz, H. (1992) CpG islands as gene markers in the human genome. Genomics, 13, 1095-1107.
7. Herman, J. G., Latif, F., Weng, Y., Lerman, M. I., Zbar, B., Liu, S., Samid, D., Duan, D. S., Gnarra, J. R., Linehan, W. M. et al. (1994) Silencing of the VHL tumor-suppressor gene by DNA methylation in renal carcinoma. Proc. Natl Acad. Sci. USA, 91, 9700-9704. (Pubitemid 24311875)
8. Merlo, A., Herman, J. G., Mao, L., Lee, D. J., Gabrielson, E., Burger, P. C., Baylin, S. B. and Sidransky, D. (1995) 50 CpG island methylation is associated with transcriptional silencing of the tumour suppressor p16/CDKN2/MTS1 in human cancers. Nat. Med., 1, 686-692.
9. Herman, J. G. and Baylin, S. B. (2003) Gene silencing in cancer in association with promoter hypermethylation. N. Engl. J. Med., 349, 2042-2054. (Pubitemid 37448928)
10. Edwards, C. A. and Ferguson-Smith, A. C. (2007) Mechanisms regulating imprinted genes in clusters. Curr. Opin. Cell Biol., 19, 281-289. (Pubitemid 46899514)
11. Reik, W. (2007) Stability and flexibility of epigenetic gene regulation in mammalian development. Nature, 447, 425-432. (Pubitemid 46816749)
12. Laird, P. W. (2010) Principles and challenges of genomewide DNA methylation analysis. Nat. Rev. Genet., 11, 191-203.
13. Ji, H., Ehrlich, L. I., Seita, J., Murakami, P., Doi, A., Lindau, P., Lee, H., Aryee, M. J., Irizarry, R. A., Kim, K. et al. (2010) Comprehensive methylome map of lineage commitment from haematopoietic progenitors. Nature, 467, 338-342.
14. Shiraishi, M., Sekiguchi, A., Oates, A. J., Terry, M. J., Miyamoto, Y. and Sekiya, T. (2004) Methyl-CpG binding domain column chromatography as a tool for the analysis of genomic DNA methylation. Anal. Biochem., 329, 1-10. (Pubitemid 38596895)
15. Down, T. A., Rakyan, V. K., Turner, D. J., Flicek, P., Li, H., Kulesha, E., Graf, S., Johnson, N., Herrero, J., Tomazou, E. M. et al. (2008) A Bayesian deconvolution strategy for immunoprecipitation-based DNA methylome analysis. Nat. Biotechnol., 26, 779-785. (Pubitemid 351961453)
16. Bock, C., Tomazou, E. M., Brinkman, A. B., Muller, F., Simmer, F., Gu, H., Jager, N., Gnirke, A., Stunnenberg, H. G. and Meissner, A. (2010) Quantitative comparison of genome-wide DNA methylation mapping technologies. Nat. Biotechnol., 28, 1106-1114.
17. Voo, K. S., Carlone, D. L., Jacobsen, B. M., Flodin, A. and Skalnik, D. G. (2000) Cloning of a mammalian transcriptional activator that binds unmethylated CpG motifs and shares a CXXC domain with DNA methyltransferase, human trithorax, and methyl-CpG binding domain protein 1. Mol. Cell Biol., 20, 2108-2121. (Pubitemid 30123826)
18. Illingworth, R., Kerr, A., Desousa, D., Jorgensen, H., Ellis, P., Stalker, J., Jackson, D., Clee, C., Plumb, R., Rogers, J. et al. (2008) A novel CpG island set identifies tissue-specific methylation at developmental gene loci. PLoS Biol., 6, e22.
19. Illingworth, R. S., Gruenewald-Schneider, U., Webb, S., Kerr, A. R., James, K. D., Turner, D. J., Smith, C., Harrison, D. J., Andrews, R. and Bird, A. P. (2010) Orphan CpG islands identify numerous conserved promoters in the mammalian genome. PLoS Genet., 6, e1001134.
20. Blackledge, N. P., Zhou, J. C., Tolstorukov, M. Y., Farcas, A. M., Park, P. J. and Klose, R. J. (2010) CpG islands recruit a histone H3 lysine 36 demethylase. Mol. Cell, 38, 179-190.
21. Kumaki, Y., Oda, M. and Okano, M. (2008) QUMA: quantification tool for methylation analysis. Nucleic Acids Res., 36, W170-W175.
22. Langmead, B., Trapnell, C., Pop, M. and Salzberg, S. L. (2009) Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol., 10, R25.
23. Ye, T., Krebs, A. R., Choukrallah, M. A., Keime, C., Plewniak, F., Davidson, I. and Tora, L. (2011) seqMINER: an integrated ChIP-seq data interpretation platform. Nucleic Acids Res., 39, e35.
24. Schatz, P. J. (1993) Use of peptide libraries to map the substrate specificity of a peptide-modifying enzyme: a 13 residue consensus peptide specifies biotinylation in Escherichia coli. Biotechnology (N Y), 11, 1138-1143. (Pubitemid 23307458)
25. Beckett, D., Kovaleva, E. and Schatz, P. J. (1999) A minimal peptide substrate in biotin holoenzyme synthetase-catalyzed biotinylation. Protein Sci., 8, 921-929. (Pubitemid 29165423)
26. Green, N. M. (1963) Avidin. 1 The use of (14-C)biotin for kinetic studies and for assay. Biochem. J., 89, 585-591.
27. Hiller, Y., Gershoni, J. M., Bayer, E. A. and Wilchek, M. (1987) Biotin binding to avidin. Oligosaccharide side chain not required for ligand association. Biochem. J., 248, 167-171. (Pubitemid 17161037)
28. Liu, J., Yu, S., Litman, D., Chen, W. and Weinstein, L. S. (2000) Identification of a methylation imprint mark within the mouse Gnas locus. Mol. Cell Biol., 20, 5808-5817. (Pubitemid 30613030)
29. Kriaucionis, S. and Heintz, N. (2009) The nuclear DNA base 5-hydroxymethylcytosine is present in Purkinje neurons and the brain. Science, 324, 929-930.
30. Tahiliani, M., Koh, K. P., Shen, Y., Pastor, W. A., Bandukwala, H., Brudno, Y., Agarwal, S., Iyer, L. M., Liu, D. R., Aravind, L. et al. (2009) Conversion of 5-methylcytosine to 5-hydroxymethylcytosine in mammalian DNA by MLL partner TET1. Science, 324, 930-935.
31. Weber, M., Davies, J. J., Wittig, D., Oakeley, E. J., Haase, M., Lam, W. L. and Schubeler, D. (2005) Chromosome-wide and promoter-specific analyses identify sites of differential DNA methylation in normal and transformed human cells. Nat. Genet., 37, 853-862. (Pubitemid 41077111)
32. Brinkman, A. B., Simmer, F., Ma, K., Kaan, A., Zhu, J. and Stunnenberg, H. G. (2010) Whole-genome DNA methylation profiling using MethylCap-seq. Methods, 52, 232-236.
33. Harris, R. A., Wang, T., Coarfa, C., Nagarajan, R. P., Hong, C., Downey, S. L., Johnson, B. E., Fouse, S. D., Delaney, A., Zhao, Y. et al. (2010) Comparison of sequencing-based methods to profile DNA methylation and identification of monoallelic epigenetic modifications. Nat. Biotechnol., 28, 1097-1105.