Accurate measurement of 5-methylcytosine and 5-hydroxymethylcytosine in human cerebellum DNA by oxidative bisulfite on an array (OxBS-Array)

PLoS ONE

Volumn 10, Issue 2, 2015, Pages

  Field, Sarah F ^a   Beraldi, Dario ^a   Bachman, Martin ^a   Stewart, Sabrina K ^b   Beck, Stephan ^b   Balasubramanian, Shankar ^a  

^a UNIVERSITY OF CAMBRIDGE   (United Kingdom)

^b UNIVERSITY COLLEGE LONDON   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

5 HYDROXYMETHYLCYTOSINE; 5 METHYLCYTOSINE; BISULFITE; CELL PROTEIN; DNA; PROTEIN MSPI; UNCLASSIFIED DRUG; 5-HYDROXYMETHYLCYTOSINE; CYTOSINE; HYDROGEN SULFITE; SULFITE;

ADULT; AEROBIC METABOLISM; ARTICLE; CEREBELLUM; DNA DETERMINATION; DNA METHYLATION; DNA MICROARRAY; DNA PROBE; HUMAN; HUMAN TISSUE; MALE; MEASUREMENT ACCURACY; POLYMERASE CHAIN REACTION; PROTEIN DEGRADATION; PROTEIN GLYCOSYLATION; REPRODUCIBILITY; ANALOGS AND DERIVATIVES; METABOLISM; OXIDATION REDUCTION REACTION; PHYSIOLOGY; PROCEDURES;

5-METHYLCYTOSINE; ADULT; CEREBELLUM; CYTOSINE; DNA; DNA METHYLATION; HUMANS; MALE; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; OXIDATION-REDUCTION; REPRODUCIBILITY OF RESULTS; SULFITES;

EID: 84923278597     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0118202     Document Type: Article

References (26)

1. Deaton AM, Bird A (2011) CpG islands and the regulation of transcription. Genes Dev 25: 1010-1022. doi: 10.1101/gad.2037511 PMID: 21576262
2. Pan H, Chen L, Dogra S, Teh AL, Tan JH, et al. (2012) Measuring the methylome in clinical samples: improved processing of the Infinium Human Methylation450 BeadChip Array. Epigenetics 7: 1173-1187. Available: http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=3469459&tool=pmcentrez&rendertype=abstract. doi: 10.4161/epi.22102 PMID: 22964528
3. Ehrlich M, Gama-Sosa MA, Huang LH, Midgett RM, Kuo KC, et al. (1982) Amount and distribution of 5-methylcytosine in human DNA from different types of tissues of cells. Nucleic Acids Res 10: 2709-2721. PMID: 7079182
4. Kriaucionis S, Heintz N (2009) The nuclear DNA base 5-hydroxymethylcytosine is present in Purkinje neurons and the brain. Science 324: 929-930. doi: 10.1126/science.1169786. PMID: 19372393
5. Tahiliani M, Koh KP, Shen Y, Pastor WA, Bandukwala H, et al. (2009) Conversion of 5-methylcytosine to 5-hydroxymethylcytosine in mammalian DNA by MLL partner TET1. Science 324: 930-935. doi: 10.1126/science.1170116 PMID: 19372391
6. Ito S, Shen L, Dai Q, Wu SC, Collins LB, et al. (2011) Tet proteins can convert 5-methylcytosine to 5-for-mylcytosine and 5-carboxylcytosine. Science 333: 1300-1303. doi: 10.1126/science.1210597. PMID: 21778364
7. Shen L, Wu H, Diep D, Yamaguchi S, D'Alessio AC, et al. (2013) Genome-wide analysis reveals TET- and TDG-dependent 5-methylcytosine oxidation dynamics. Cell 153: 692-706. doi: 10.1016/j.cell.2013.04.002 PMID: 23602152
8. Hashimoto H, Hong S, Bhagwat AS, Zhang X, Cheng X (2012) Excision of 5-hydroxymethyluracil and 5-carboxylcytosine by the thymine DNA glycosylase domain: its structural basis and implications for active DNA demethylation. Nucleic Acids Res 40: 10203-10214. Available: http://www.ncbi.nlm.nih.gov/pubmed/22962365. doi: 10.1093/nar/gks845 PMID: 22962365
9. Maiti A, Drohat AC (2011) Thymine DNA Glycosylase Can Rapidly Excise 5-Formylcytosine and 5-Carboxylcytosine: POTENTIAL IMPLICATIONS FOR ACTIVE DEMETHYLATION OF CpG SITES. J Biol Chem 286: 35334-35338. doi: 10.1074/jbc.C111.284620. PMID: 21862836
10. Ficz G, Branco MR, Seisenberger S, Santos F, Krueger F, et al. (2011) Dynamic regulation of 5-hydroxymethylcytosine in mouse ES cells and during differentiation. Nature 473: 398-402. doi: 10.1038/nature10008. PMID: 21460836
11. Lister R, Mukamel E, Nery JR, Urich M, Puddifoot C, et al. (2013) Global epigenomic reconfiguration during mammalian brain development. Science 341: 1237905. Available: http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=3785061&tool=pmcentrez&rendertype=abstract. doi: 10.1126/ science.1237905 PMID: 23828890
12. Branco MR, Ficz G, Reik W (2012) Uncovering the role of 5-hydroxymethylcytosine in the epigenome. Nat Rev Genet 13: 7-13. Available: http://www.ncbi.nlm.nih.gov/pubmed/22083101. Accessed 2014 Feb 21. doi: 10.1038/nrg3080 PMID: 22083101
13. Liu S, Wang J, Su Y, Guerrero C, Zeng Y, et al. (2013) Quantitative assessment of Tet-induced oxidation products of 5-methylcytosine in cellular and tissue DNA. Nucleic Acids Res 41: 6421-6429. Available: http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=3711458&tool=pmcentrez&rendertype=abstract. doi: 10.1093/nar/gkt360 PMID: 23658232
14. Mastroeni D, Grover A, Delvaux E, Whiteside C, Coleman PD, et al. (2010) Epigenetic changes in Alzheimer's disease: Decrements in DNA methylation. Neurobiol Aging 31: 2025-2037. doi: 10.1016/j.neurobiolaging.2008.12.005 PMID: 19117641
15. Rudenko A, Dawlaty MM, Seo J, Cheng AW, Meng J, et al. (2013) Tet1 is critical for neuronal activityregulated gene expression and memory extinction. Neuron 79: 1109-1122. Available: http://www.sciencedirect.com/science/article/pii/S0896627313007149\nhttp://www.ncbi.nlm.nih.gov/pubmed/24050401. doi: 10.1016/j.neuron.2013.08.003 PMID: 24050401
16. Mellén M, Ayata P, Dewell S, Kriaucionis S, Heintz N (2012) MeCP2 binds to 5hmC enriched within active genes and accessible chromatin in the nervous system. Cell 151: 1417-1430. doi: 10.1016/j.cell.2012.11.022 PMID: 23260135
17. Shapiro R, DiFate V, Welcher M (1974) Deamination of cytosine derivatives by bisulfite. Mechanism of the reaction. J Am Chem Soc 96: 906-912. doi: 10.1021/ja00810a043. PMID: 4814744
18. Hayatsu H, Wataya Y, Kai K, Iida S (1970) Reaction of sodium bisulfite with uracil, cytosine, and their derivatives. Biochemistry 9: 2858-2865. doi: 10.1021/ja00706a062. PMID: 5459538
19. Booth MJ, Branco MR, Ficz G, Oxley D, Krueger F, et al. (2012) Quantitative sequencing of 5-methylcytosine and 5-hydroxymethylcytosine at single-base resolution. Science 336: 934-937. Available: http://www.ncbi.nlm.nih.gov/pubmed/22539555. Accessed 2014 Feb 21. doi: 10.1126/science.1220671 PMID: 22539555
20. Booth MJ, Ost TWB, Beraldi D, Bell NM, Branco MR, et al. (2013) Oxidative bisulfite sequencing of 5-methylcytosine and 5-hydroxymethylcytosine. Nat Protoc 8: 1841-1851. Available: http://www.ncbi.nlm.nih.gov/pubmed/24008380. doi: 10.1038/nprot.2013.115 PMID: 24008380
21. Ruzov A, Tsenkina Y, Serio A, Dudnakova T, Fletcher J, et al. (2011) Lineage-specific distribution of high levels of genomic 5-hydroxymethylcytosine in mammalian development. Cell Res 21: 1332-1342. doi: 10.1038/cr.2011.113. PMID: 21747414
22. Chopra P, Papale L a, White AT, Hatch A, Brown RM, et al. (2014) Array-based assay detects genomewide 5-mC and 5-hmC in the brains of humans, non-human primates, and mice. BMC Genomics 15: 131. Available: http://www.ncbi.nlm.nih.gov/pubmed/24524199. Accessed 2014 Feb 20. doi: 10.1186/1471-2164-15-131 PMID: 24524199
23. Robertson AB, Dahl JA, Vågbø CB, Tripathi P, Krokan HE, et al. (2011) A novel method for the efficient and selective identification of 5-hydroxymethylcytosine in genomic DNA. Nucleic Acids Res 39: e55. doi: 10.1093/nar/gkr051 PMID: 21300643
24. Stewart SK, Morris TJ, Guilhamon P, Bulstrode H, Bachman M, et al. (n.d.) oxBS-450K: A method for analysing hydroxymethylation using 450K BeadChips. Epigenomics. doi: 10.2217/epi.14.89 PMID: 25590359
25. Aryee M, Jaffe A, Corrada-Bravo H, Ladd-Acosta C, Feinberg A, et al. (2014) Minfi: A flexible and comprehensive Bioconductor package for the analysis of Infinium DNA Methylation microarrays. Bioinformatics: 1-8. Available: http://bioinformatics.oxfordjournals.org/content/early/2014/01/28/bioinformatics.btu049.short. doi: 10.1186/1471-2105-15-1 PMID: 25189783
26. Makismovic J, Gordon L, Oshlack A (2012) SWAN: Subset-quantile Within Array Normalization for Illumina Infinium HumanMethylation450 BeadChips. Genome Biol 13: R44. doi: 10.1186/gb-2012-13-6-r44. PMID: 22703947