An Integrated Workflow for DNA Methylation Analysis

Department of Plant & Soil Sciences, Delaware Biotechnology Institute, University of Delaware, Newark, DE 19711, USA

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Corresponding author: E-mail address: meyers@dbi.udel.edu (Blake C. Meyers)

摘要

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Abstract: The analysis of cytosine methylation provides a new way to assess and describe epigenetic regulation at a whole-genome level in many eukaryotes. DNA methylation has a demonstrated role in the genome stability and protection, regulation of gene expression and many other aspects of genome function and maintenance. BS-seq is a relatively unbiased method for profiling the DNA methylation, with a resolution capable of measuring methylation at individual cytosines. Here we describe, as an example, a workflow to handle DNA methylation analysis, from BS-seq library preparation to the data visualization. We describe some applications for the analysis and interpretation of these data. Our laboratory provides public access to plant DNA methylation data via visualization tools available at our “Next-Gen Sequence” websites (http://mpss.udel.edu), along with small RNA, RNA-seq and other data types.
- DNA methylation /
- BS-seq /
- Epigenetics

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参考文献(69)

[1]	Beck, S. Taking the measure of the methylome Nat. Biotechnol., 28 (2010),pp. 1026-1028
[2]	Benjamini, Y., Hochberg, Y. Controlling the false discovery rate: a practical and powerful approach to multiple testing J. R. Stat. Soc. Ser. B, 57 (1995),pp. 289-300
[3]	Bock, C. Analysing and interpreting DNA methylation data Nat. Rev. Genet., 13 (2012),pp. 705-719
[4]	Booth, M.J., Branco, M.R., Ficz, G. et al. Quantitative sequencing of 5-methylcytosine and 5-hydroxymethylcytosine at single-base resolution Science, 336 (2012),pp. 934-937
[5]	Calarco, J.P., Borges, F., Donoghue, M.T.A. et al. Cell, 151 (2012),pp. 194-205
[6]	Cao, X., Aufsatz, W., Zilberman, D. et al. Role of the DRM and CMT3 methyltransferases in RNA-directed DNA methylation Curr. Biol., 13 (2003),pp. 2212-2217
[7]	Chen, P.-Y., Cokus, S.J., Pellegrini, M. BS Seeker: precise mapping for bisulfite sequencing BMC Bioinformatics, 11 (2010),pp. 203-208
[8]	Chen, Z., Liu, Q., Nadarajah, S. A new statistical approach to detecting differentially methylated loci for case control Illumina array methylation data Bioinformatics, 28 (2012),pp. 1109-1113
[9]	Cokus, S.J., Feng, S., Zhang, X. et al. Nature, 452 (2008),pp. 215-219
[10]	Coleman-Derr, D., Zilberman, D. DNA methylation, H2A.Z, and the regulation of constitutive expression Cold Spring Harb. Symp. Quant. Biol (2012)
[11]	Cox, M.P., Peterson, D.A., Biggs, P.J. SolexaQA: at-a-glance quality assessment of Illumina second-generation sequencing data BMC Bioinformatics, 11 (2010),pp. 485-490
[12]	Dinh, H.Q., Dubin, M., Sedlazeck, F.J. et al. PLoS ONE, 7 (2012),p. e41528
[13]	Dowen, R.H., Pelizzola, M., Schmitz, R.J. et al. Widespread dynamic DNA methylation in response to biotic stress Proc. Natl. Acad. Sci. USA, 109 (2012),pp. E2183-E2191
[14]	Du, J., Zhong, X., Bernatavichute, Y.V. et al. Dual binding of chromomethylase domains to H3K9me2-containing nucleosomes directs DNA methylation in plants Cell, 151 (2012),pp. 167-180
[15]	Dudoit, S., van der Laan, M.J.
[16]	Finnegan, E.J., Dennis, E.S. Nucleic Acids Res., 21 (1993),pp. 2383-2388
[17]	Finnegan, E.J., Peacock, W.J., Dennis, E.S. Proc. Natl. Acad. Sci. USA, 93 (1996),pp. 8449-8454
[18]	Flusberg, B.A., Webster, D.R., Lee, J.H. et al. Direct detection of DNA methylation during single-molecule, real-time sequencing Nat. Methods, 7 (2010),pp. 461-465
[19]	Fojtová, M., Kovařı́k, A., Matyášek, R. Cytosine methylation of plastid genome in higher plants. Fact or artefact? Plant Sci., 160 (2001),pp. 585-593
[20]	Harris, R.A., Wang, T., Coarfa, C. et al. Comparison of sequencing-based methods to profile DNA methylation and identification of monoallelic epigenetic modifications Nat. Biotechnol., 28 (2010),pp. 1097-1105
[21]	He, X.-J., Chen, T., Zhu, J.-K. Regulation and function of DNA methylation in plants and animals Cell Res., 21 (2011),pp. 442-465
[22]	Hsieh, T.F., Ibarra, C.A., Silva, P. et al. Science, 324 (2009),pp. 1451-1454
[23]	Huang, Y., Pastor, W.A., Shen, Y. et al. The behaviour of 5-hydroxymethylcytosine in bisulfite sequencing PLoS ONE, 5 (2010),p. e8888
[24]	Jacinto, F.V., Ballestar, E., Esteller, M. Methyl-DNA immunoprecipitation (MeDIP): hunting down the DNA methylome BioTechniques, 44 (2008),pp. 35-43
[25]	Jackson, J.P., Lindroth, A.M., Cao, X. et al. Control of CpNpG DNA methylation by the KRYPTONITE histone H3 methyltransferase Nature, 416 (2002),pp. 556-560
[26]	Jaffe, A.E., Murakami, P., Lee, H. et al. Bump hunting to identify differentially methylated regions in epigenetic epidemiology studies Inter. J. Epidemiol., 41 (2012),pp. 200-209
[27]	Jeddeloh, J.A., Stokes, T.L., Richards, E.J. Maintenance of genomic methylation requires a SWI2/SNF2-like protein Nat. Genet., 22 (1999),pp. 94-97
[28]	Jones, L., Ratcliff, F., Baulcombe, D.C. RNA-directed transcriptional gene silencing in plants can be inherited independently of the RNA trigger and requires Met1 for maintenance Curr. Biol., 11 (2001),pp. 747-757
[29]	Jones, P.A. Functions of DNA methylation: islands, start sites, gene bodies and beyond Nat. Rev. Genet., 13 (2012),pp. 484-492
[30]	Kent, W.J., Sugnet, C.W., Furey, T.S. et al. The human genome browser at UCSC Genome Res., 12 (2002),pp. 996-1006
[31]	Krueger, F., Andrews, S.R. Bismark: a flexible aligner and methylation caller for Bisulfite-Seq applications Bioinformatics, 27 (2011),pp. 1571-1572
[32]	Krueger, F., Kreck, B., Franke, A. et al. DNA methylome analysis using short bisulfite sequencing data Nat. Methods, 9 (2012),pp. 145-151
[33]	Krzywinski, M., Schein, J., Birol, I. et al. Circos: an information aesthetic for comparative genomics Genome Res., 19 (2009),pp. 1639-1645
[34]	Laird, P.W. Principles and challenges of genome-wide DNA methylation analysis Nat. Rev. Genet., 11 (2010),pp. 191-203
[35]	Langmead, B., Trapnell, C., Pop, M. et al. Ultrafast and memory-efficient alignment of short DNA sequences to the human genome Genome Biol., 10 (2009),p. R25
[36]	Law, J.A., Jacobsen, S.E. Establishing, maintaining and modifying DNA methylation patterns in plants and animals Nat. Rev. Genet., 11 (2010),pp. 204-220
[37]	Lindroth, A.M., Cao, X., Jackson, J.P. et al. Requirement of CHROMOMETHYLASE3 for maintenance of CpXpG methylation Science, 292 (2001),pp. 2077-2080
[38]	Lister, R., Ecker, J.R. Finding the fifth base: genome-wide sequencing of cytosine methylation Genome Res., 19 (2009),pp. 959-966
[39]	Lister, R., O'Malley, R.C., Tonti-Filippini, J. et al. Cell, 133 (2008),pp. 523-536
[40]	Meyers, B.C., Lee, D.K., Vu, T.H. et al. Plant Physiol., 135 (2004),pp. 801-813
[41]	Nakano, M., Nobuta, K., Vemaraju, K. et al. Plant MPSS databases: signature-based transcriptional resources for analyses of mRNA and small RNA Nucleic Acids Res., 34 (2006),pp. D731-D735
[42]	Nicol, J.W., Helt, G.A., Blanchard, S.G. et al. The Integrated Genome Browser: free software for distribution and exploration of genome-scale datasets Bioinformatics, 25 (2009),pp. 2730-2731
[43]	Noble, W.S. How does multiple testing correction work? Nat. Biotechnol., 27 (2009),pp. 1135-1137
[44]	Nouzova, M., Holtan, N., Oshiro, M.M. et al. Epigenomic changes during leukemia cell differentiation: analysis of histone acetylation and cytosine methylation using CpG island microarrays J. Pharmacol. Exp. Ther., 311 (2004),pp. 968-981
[45]	Okano, M., Bell, D.W., Haber, D.A. et al. Cell, 99 (1999),pp. 247-257
[46]	Otto, C., Stadler, P.F., Hoffmann, S. Fast and sensitive mapping of bisulfite-treated sequencing data Bioinformatics, 28 (2012),pp. 1698-1704
[47]	Poage, G.M., Butler, R.A., Houseman, E.A. et al. Identification of an epigenetic profile classifier that is associated with survival in head and neck cancer Cancer Res., 72 (2012),pp. 2728-2737
[48]	Robinson, J.T., Thorvaldsdóttir, H., Winckler, W. et al. Integrative genomics viewer Nat. Biotechnol., 29 (2011),pp. 24-26
[49]	Ronemus, M.J., Galbiati, M., Ticknor, C. et al. Science, 273 (1996),pp. 654-657
[50]	Ruike, Y., Imanaka, Y., Sato, F. et al. Genome-wide analysis of aberrant methylation in human breast cancer cells using methyl-DNA immunoprecipitation combined with high-throughput sequencing BMC Genomics, 11 (2010),p. 137
[51]	Schmieder, R., Edwards, R. Quality control and preprocessing of metagenomic datasets Bioinformatics, 27 (2011),pp. 863-864
[52]	Schumacher, A., Kapranov, P., Kaminsky, Z. et al. Microarray-based DNA methylation profiling: technology and applications Nucleic Acids Res., 34 (2006),pp. 528-542
[53]	Srinivasan, P.R., Borek, E. Enzymatic alteration of nucleic acid structure Science, 145 (1964),pp. 548-553
[54]	Storey, J.D., Tibshirani, R. Statistical significance for genomewide studies Proc. Natl. Acad. Sci. USA, 100 (2003),pp. 9440-9445
[55]	Stroud, H., Greenberg, M.V.C., Feng, S. et al. Cell, 152 (2013),pp. 352-364
[56]	Taiwo, O., Wilson, G.A., Morris, T. et al. Methylome analysis using MeDIP-seq with low DNA concentrations Nat. Protoc., 7 (2012),pp. 617-636
[57]	Thorvaldsdottir, H., Robinson, J.T., Mesirov, J.P. Integrative Genomics Viewer (IGV): high-performance genomics data visualization and exploration Brief. Bioinform., 14 (2013),pp. 178-192
[58]	Tompa, R., McCallum, C.M., Delrow, J. et al. Genome-wide profiling of DNA methylation reveals transposon targets of CHROMOMETHYLASE3 Curr. Biol., 12 (2002),pp. 65-68
[59]	Tran, R.K., Henikoff, J.G., Zilberman, D. et al. Curr. Biol., 15 (2005),pp. 154-159
[60]	Vining, K.J., Pomraning, K.R., Wilhelm, L.J. et al. BMC Genomics, 13 (2012),p. 27
[61]	Vongs, A., Kakutani, T., Martienssen, R.A. et al. Science, 260 (1993),pp. 1926-1928
[62]	Wang, D., Yan, L., Hu, Q. et al. IMA: an R package for high-throughput analysis of Illumina's 450K Infinium methylation data Bioinformatics, 28 (2012),pp. 729-730
[63]	Wang, S. Method to detect differentially methylated loci with case-control designs using Illumina arrays Genet. Epidemiol., 35 (2011),pp. 686-694
[64]	Warnecke, P.M., Stirzaker, C., Song, J. et al. Identification and resolution of artifacts in bisulfite sequencing Methods, 27 (2002),pp. 101-107
[65]	Wierzbicki, A.T., Cocklin, R., Mayampurath, A. et al. Genes Dev., 26 (2012),pp. 1825-1836
[66]	Xi, Y., Li, W. BSMAP: whole genome bisulfite sequence MAPping program BMC Bioinformatics, 10 (2009),p. 232
[67]	Yan, P.S., Potter, D., Deatherage, D.E. et al. Differential methylation hybridization: profiling DNA methylation with a high-density CpG island microarray Methods Mol. Biol., 507 (2009),pp. 89-106
[68]	Zhang, Y., Liu, H., Lv, J. et al. QDMR: a quantitative method for identification of differentially methylated regions by entropy Nucleic Acids Res., 39 (2011)
[69]	Zhuang, J., Widschwendter, M., Teschendorff, A.E. A comparison of feature selection and classification methods in DNA methylation studies using the Illumina Infinium platform BMC Bioinformatics, 13 (2012),p. 59