Abstract
DNA methylation is an indispensible epigenetic modification required for regulating the expression of mammalian genomes. Immunoprecipitation-based methods for DNA methylome analysis are rapidly shifting the bottleneck in this field from data generation to data analysis, necessitating the development of better analytical tools. In particular, an inability to estimate absolute methylation levels remains a major analytical difficulty associated with immunoprecipitation-based DNA methylation profiling. To address this issue, we developed a cross-platform algorithm—Bayesian tool for methylation analysis (Batman)—for analyzing methylated DNA immunoprecipitation (MeDIP) profiles generated using oligonucleotide arrays (MeDIP-chip) or next-generation sequencing (MeDIP-seq). We developed the latter approach to provide a high-resolution whole-genome DNA methylation profile (DNA methylome) of a mammalian genome. Strong correlation of our data, obtained using mature human spermatozoa, with those obtained using bisulfite sequencing suggest that combining MeDIP-seq or MeDIP-chip with Batman provides a robust, quantitative and cost-effective functional genomic strategy for elucidating the function of DNA methylation.
This is a preview of subscription content, access via your institution
Access options
Subscribe to this journal
Receive 12 print issues and online access
$209.00 per year
only $17.42 per issue
Rent or buy this article
Prices vary by article type
from$1.95
to$39.95
Prices may be subject to local taxes which are calculated during checkout
Similar content being viewed by others
Accession codes
References
Bernstein, B.E., Meissner, A. & Lander, E.S. The mammalian epigenome. Cell 128, 669–681 (2007).
Bird, A. DNA methylation patterns and epigenetic memory. Genes Dev. 16, 6–21 (2002).
Beck, S. & Rakyan, V.K. The methylome: approaches for global DNA methylation profiling. Trends Genet. 24, 231–237 (2008).
Tompa, R. et al. Genome-wide profiling of DNA methylation reveals transposon targets of CHROMOMETHYLASE3. Curr. Biol. 12, 65–68 (2002).
Lippman, Z. et al. Role of transposable elements in heterochromatin and epigenetic control. Nature 430, 471–476 (2004).
Khulan, B. et al. Comparative isoschizomer profiling of cytosine methylation: the HELP assay. Genome Res. 16, 1046–1055 (2006).
Schumacher, A. et al. Microarray-based DNA methylation profiling: Technology and applications. Nucleic Acids Res. 34, 528–542 (2006).
Ordway, J.M. et al. Comprehensive DNA methylation profiling in a human cancer genome identifies novel epigenetic targets. Carcinogenesis 27, 2409–2423 (2006).
Ching, T.T. et al. Epigenome analyses using BAC microarrays identify evolutionary conservation of tissue-specific methylation of SHANK3. Nat. Genet. 37, 645–651 (2005).
Shen, L. et al. Genome-wide profiling of DNA methylation reveals a class of normally methylated CpG island promoters. PLoS Genet. 3, 2023–2036 (2007).
Rollins, R.A. et al. Large-scale structure of genomic methylation patterns. Genome Res. 16, 157–163 (2006).
Frommer, M. et al. A genomic sequencing protocol that yields a positive display of 5-methylcytosine residues in individual DNA strands. Proc. Natl. Acad. Sci. USA 89, 1827–1831 (1992).
Gitan, R.S. et al. Methylation-specific oligonucleotide microarray: a new potential for high-throughput methylation analysis. Genome Res. 12, 158–164 (2002).
Adorjan, P. et al. Tumour class prediction and discovery by microarray-based DNA methylation analysis. Nucleic Acids Res. 30, e21 (2002).
Bibikova, M. et al. High-throughput DNA methylation profiling using universal bead arrays. Genome Res. 16, 383–393 (2006).
Reinders, J. et al. Genome-wide, high-resolution DNA methylation profiling using bisulfite-mediated cytosine conversion. Genome Res. 18, 469–476 (2008).
Rakyan, V.K. et al. DNA methylation profiling of the human major histocompatibility complex: a pilot study for the human epigenome project. PLoS Biol. 2, e405 (2004).
Eckhardt, F. et al. DNA methylation profiling of human chromosomes 6, 20 and 22. Nat. Genet. 38, 1378–1385 (2006).
Cokus, S.J. et al. Shotgun bisulphite sequencing of the Arabidopsis genome reveals DNA methylation patterning. Nature 452, 215–219 (2008).
Weber, M. et al. Chromosome-wide and promoter-specific analyses identify sites of differential DNA methylation in normal and transformed human cells. Nat. Genet. 37, 853–862 (2005).
Keshet, I. et al. Evidence for an instructive mechanism of de novo methylation in cancer cells. Nat. Genet. 38, 149–153 (2006).
Zhang, X. et al. Genome-wide high-resolution mapping and functional analysis of DNA methylation in Arabidopsis . Cell 126, 1189–1201 (2006).
Gebhard, C. et al. Genome-wide profiling of CpG methylation identifies novel targets of aberrant hypermethylation in myeloid leukemia. Cancer Res. 66, 6118–6128 (2006).
Rauch, T., Li, H., Wu, X. & Pfeifer, G.P. MIRA-assisted microarray analysis, a new technology for the determination of DNA methylation patterns, identifies frequent methylation of homeodomain-containing genes in lung cancer cells. Cancer Res. 66, 7939–7947 (2006).
Illingworth, R. et al. A novel CpG island set identifies tissue-specific methylation at developmental gene loci. PLoS Biol. 6, e22 (2008).
Zilberman, D., Gehring, M., Tran, R.K., Ballinger, T. & Henikoff, S. Genome-wide analysis of Arabidopsis thaliana DNA methylation uncovers an interdependence between methylation and transcription. Nat. Genet. 39, 61–69 (2006).
Weber, M. et al. Distribution, silencing potential and evolutionary impact of promoter DNA methylation in the human genome. Nat. Genet. 39, 457–466 (2007).
Yasui, D.H. et al. Integrated epigenomic analyses of neuronal MeCP2 reveal a role for long-range interaction with active genes. Proc. Natl. Acad. Sci. USA 104, 19416–19421 (2007).
Jacinto, F.V., Ballestar, E., Ropero, S. & Esteller, M. Discovery of epigenetically silenced genes by methylated DNA immunoprecipitation in colon cancer cells. Cancer Res. 67, 11481–11486 (2007).
Cheng, A.S. et al. Epithelial progeny of estrogen-exposed breast progenitor cells display a cancer-like methylome. Cancer Res. 68, 1786–1796 (2008).
Fouse, S.D. et al. Promoter CpG methylation contributes to ES cell gene regulation in parallel with Oct4/Nanog, PcG complex, and histone H3 K4/K27 trimethylation. Cell Stem Cell 2, 160–169 (2008).
Flicek, P. et al. Ensembl 2008. Nucleic Acids Res. 36, D707–D714 (2008).
Qi, Y. et al. High-resolution computational models of genome binding events. Nat. Biotechnol. 24, 963–970 (2006).
Barski, A. et al. High-resolution profiling of histone methylations in the human genome. Cell 129, 823–837 (2007).
Mikkelsen, T.S. et al. Genome-wide maps of chromatin state in pluripotent and lineage-committed cells. Nature 448, 553–560 (2007).
Sandovici, I. et al. Interindividual variability and parent of origin DNA methylation differences at specific human Alu elements. Hum. Mol. Genet. 14, 2135–2143 (2005).
Flanagan, J.M. et al. Intra- and interindividual epigenetic variation in human germ cells. Am. J. Hum. Genet. 79, 67–84 (2006).
Morgan, H.D., Sutherland, H.G., Martin, D.I. & Whitelaw, E. Epigenetic inheritance at the agouti locus in the mouse. Nat. Genet. 23, 314–318 (1999).
Rakyan, V.K. et al. Transgenerational inheritance of epigenetic states at the murine AxinFu allele occurs after maternal and paternal transmission. Proc. Natl. Acad. Sci. USA 100, 2538–2543 (2003).
Bestor, T.H. The host defence function of genomic methylation patterns. Novartis Found. Symp. 214, 187–195 (1999).
Irizarry, R.A. et al. Comprehensive high-throughput arrays for relative methylation (CHARM). Genome Res. 18, 780–790 (2008).
Mukhopadhyay, R. et al. The binding sites for the chromatin insulator protein CTCF map to DNA methylation-free domains genome-wide. Genome Res. 14, 1594–1602 (2004).
Oberley, M.J. & Farnham, P.J. Probing chromatin immunoprecipitates with CpG-island microarrays to identify genomic sites occupied by DNA-binding proteins. Methods Enzymol. 371, 577–596 (2003).
Slater, G.S. & Birney, E. Automated generation of heuristics for biological sequence comparison. BMC Bioinformatics 6, 31–34 (2005).
Acknowledgements
T.A.D., E.M.T., L.B., K.L.H., D.K.J., M.M.M., H.L., T.J.P.H., S.B., D.J.T., R.D. were supported by the Wellcome Trust. V.K.R. was supported by the Barts and The London Charitable Trust, and a C.J. Martin Fellowship from the National Health and Medical Research Council, Australia. S.G., N.J. and M.H. were supported by an EU grant (High-throughput Epigenetic Regulatory Organization in Chromatin (HEROIC), LSHG-CT-2005-018883) under the 6th Framework Program to S.B. (M.H.) and E.B. (S.G., N.J.). N.P.T., J.C.M. and S.T. were supported by grant C14303/A8646 from Cancer Research UK.
Author information
Authors and Affiliations
Contributions
T.A.D. co-conceived the study, wrote the Batman algorithm, co-analyzed data and co-wrote the paper; V.K.R. co-conceived the study, performed the bulk of the experimental work, co-analyzed data, co-wrote the paper and provided overall project management; D.J.T. performed the Illumina Genome Analyzer sequencing; H.L. performed the maq analysis; P.F., E.K., S.G., N.J. and J.H. performed some data analysis and designed the Ensembl web display for the data reported here; E.M.T., L.B. and M.H. performed experimental work; K.L.H. and D.K.J. assisted with array design; N.P.T. and J.C.M. performed preliminary array analysis; M.M.M. supplied materials; E.B., T.J.P.H., R.D. and S.T. provided intellectual input; S.B. co-conceived the study, co-wrote the paper and provided overall project management. T.A.D. and V.K.R. contributed equally to this work.
Corresponding authors
Supplementary information
Supplementary Text and Figures
Figures 1–6, Tables 1–3 (PDF 943 kb)
Rights and permissions
About this article
Cite this article
Down, T., Rakyan, V., Turner, D. et al. A Bayesian deconvolution strategy for immunoprecipitation-based DNA methylome analysis. Nat Biotechnol 26, 779–785 (2008). https://doi.org/10.1038/nbt1414
Received:
Accepted:
Published:
Issue Date:
DOI: https://doi.org/10.1038/nbt1414
This article is cited by
-
MBD4 loss results in global reactivation of promoters and retroelements with low methylated CpG density
Journal of Experimental & Clinical Cancer Research (2023)
-
Genome-wide DNA methylation analysis in schizophrenia with tardive dyskinesia: a preliminary study
Genes & Genomics (2023)
-
Anchor-based bisulfite sequencing determines genome-wide DNA methylation
Communications Biology (2022)
-
Environmental enrichment influences novelty reactivity, novelty preference, and anxiety via distinct genetic mechanisms in C57BL/6J and DBA/2J mice
Scientific Reports (2021)
-
Ten-eleven translocation 1 mediated-DNA hydroxymethylation is required for myelination and remyelination in the mouse brain
Nature Communications (2021)