Abstract
DNA methylation is a major epigenetic modification that regulates gene expression, genome imprinting, and development and has a role in diseases including cancer. There are various methods for whole-genome methylation profiling that differ in cost and resolution. Recent advances in high-throughput sequencing technologies coupled with bisulfite treatment enable absolute DNA methylation quantification and genome-wide single-nucleotide resolution analysis. In this chapter, we provide detailed protocols for whole-genome bisulfite sequencing (WGBS), which captures the complete methylome. Using WGBS, we are able to generate a reference DNA methylome for normal or malignant hematopoietic cells.
This is a preview of subscription content, log in via an institution to check access.
Access this chapter
Tax calculation will be finalised at checkout
Purchases are for personal use only
Similar content being viewed by others
References
Laird PW (2010) Principles and challenges of genomewide DNA methylation analysis. Nat Rev Genet 11:191–203
Jeong M, Sun D, Luo M et al (2014) Large conserved domains of low DNA methylation maintained by Dnmt3a. Nat Genet 46:17–23
Urich MA, Nery JR, Lister R, Schmitz RJ, Ecker JR (2015) MethylC-seq library preparation for base-resolution whole-genome bisulfite sequencing. Nat Protoc 10:475–483
Gu H, Smith ZD, Bock C et al (2011) Preparation of reduced representation bisulfite sequencing libraries for genome-scale DNA methylation profiling. Nat Protoc 6:468–481
Boyle P, Clement K, Gu H et al (2012) Gel-free multiplexed reduced representation bisulfite sequencing for large-scale DNA methylation profiling. Genome Biol 13:R92
Hayatsu H (2008) Discovery of bisulfite-mediated cytosine conversion to uracil, the key reaction for DNA methylation analysis--a personal account. Proc Jpn Acad Ser B Phys Biol Sci 84:321–330
Weber M, Davies JJ, Wittig D et al (2005) Chromosome-wide and promoter-specific analyses identify sites of differential DNA methylation in normal and transformed human cells. Nat Genet 37:853–862
Jacinto FV, Ballestar E, Esteller M (2008) Methyl-DNA immunoprecipitation (MeDIP): hunting down the DNA methylome. BioTechniques 44:35, 37, 39 passim
Tan L, Xiong L, Xu W et al (2013) Genome-wide comparison of DNA hydroxymethylation in mouse embryonic stem cells and neural progenitor cells by a new comparative hMeDIP-seq method. Nucleic Acids Res 41:e84
Pastor WA, Pape UJ, Huang Y et al (2011) Genome-wide mapping of 5-hydroxymethyl-cytosine in embryonic stem cells. Nature 473:394–397
Li D, Zhang B, Xing X, Wang T (2015) Combining MeDIP-seq and MRE-seq to investigate genome-wide CpG methylation. Methods 72:29–40
Booth MJ, Ost TW, Beraldi D et al (2013) Oxidative bisulfite sequencing of 5-methylcytosine and 5-hydroxymethylcytosine. Nat Protoc 8:1841–1851
Yu M, Hon GC, Szulwach KE et al (2012) Tet-assisted bisulfite sequencing of 5-hydroxy-methylcytosine. Nat Protoc 7:2159–2170
Acknowledgments
This work was supported by the NIH (DK092883, CA183252, CA125123, P50CA126752, T32DK060445), the Edward P Evans Foundation, the Adrienne Helis Malvin Medical Research Foundation, and by CPRIT (RR140053).
Author information
Authors and Affiliations
Corresponding author
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2017 Springer Science+Business Media LLC
About this protocol
Cite this protocol
Jeong, M., Guzman, A.G., Goodell, M.A. (2017). Genome-Wide Analysis of DNA Methylation in Hematopoietic Cells: DNA Methylation Analysis by WGBS. In: Fortina, P., Londin, E., Park, J., Kricka, L. (eds) Acute Myeloid Leukemia. Methods in Molecular Biology, vol 1633. Humana Press, New York, NY. https://doi.org/10.1007/978-1-4939-7142-8_9
Download citation
DOI: https://doi.org/10.1007/978-1-4939-7142-8_9
Published:
Publisher Name: Humana Press, New York, NY
Print ISBN: 978-1-4939-7140-4
Online ISBN: 978-1-4939-7142-8
eBook Packages: Springer Protocols