Abstract
Epigenetic modification are heritable changes in gene expression not encoded by the DNA sequence therefore playing a significant role in a broad range of biological processes and diseases.
A key player of the epigenetic modifications is the DNA methylation, a process involving the covalent transfer of a methyl group to the C-5 position of the cytosine ring of DNA forming 5-methylcytosine (5mC), catalyzed by DNA methyltransferases. Altering the structure of the chromatin, DNA methylation has the potential to down-regulate gene expression.
The here presented protocol shows a method to obtain DNA samples ready for NGS sequencing for genome-wide methylation analysis.
Access this chapter
Tax calculation will be finalised at checkout
Purchases are for personal use only
Similar content being viewed by others
References
Allis D, Caparros ML, Jenuwein T, Reinberg D (eds) (2015) Epigenetics, 2nd edn. Cold Spring Harbor, New York
Gardiner-Garden M, Frommer M (1987) CpG islands in vertebrate genomes. J Mol Biol 196:261–282
Barter MJ, Bui C, Young DA (2012) Epigenetic mechanisms in cartilage and osteoarthritis: DNA methylation, histone modifications and microRNAs. Osteoarthr Cartil 20:339–349
Rodriguez J, Frigola J, Vendrell E et al (2006) Chromosomal instability correlates with genome-wide DNA demethylation in human primary colorectal cancers. Cancer Res 66:8462–9468
Di Giacomo M, Comazzetto S, Saini H et al (2013) Multiple epigenetic mechanisms and the piRNA pathway enforce LINE1 silencing during adult spermatogenesis. Mol Cell 50:601–608
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
Frommer M, McDonald LE, Millar DS et al (1992) A genomic sequencing protocol that yields a positive display of 5-methylcytosine residues in individual DNA strands. Proc Natl Acad Sci U S A 89:1827–1831
Clark SJ, Statham A, Stirzaker C et al (2006) DNA methylation: bisulphite modification and analysis. Nat Protoc 1:2353–2364
Meissner A, Gnirke A, Bell GW et al (2005) Reduced representation bisulfite sequencingfor comparative high-resolution DNA methylation analysis. Nucleic Acids Res 33:5868–5877
Gu H, Bock C, Mikkelsen TS, Jäger N et al (2010) Genome-scale DNA methylation mapping of clinical samples at single-nucleotide resolution. Nat Methods 7:133–136
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
van Gurp TP, Wagemaker NC, Wouters B et al (2016) epiGBS: reference-free reduced representation bisulfite sequencing. Nat Methods 13:322–324
Martinez-Arguelles DB, Lee S, Papadopoulos V (2014) In silico analysis identifies novel restriction enzyme combinations that expand reduced representation bisulfite sequencing CpG coverage. BMC Res Notes 7:534
Huang Y, Pastor WA, Shen Y et al (2010) The behaviour of 5-hydroxymethylcytosine in bisulfite sequencing. PLoS One 5:e8888
Wang J, Tang J, Lai M et al (2014) 5-Hydroxymethylcytosine and disease. Mutat Res Rev Mutat Res 762:167–175
Song CX, Yin S, Ma L et al (2010) 5-Hydroxymethylcytosine signatures in cell-free DNA provide information about tumor types and stages. Cell Res 27:1231–1242
Li FJ, Li LM, Zhang RH et al (2017) The role of 5-hydroxymethylcytosine in melanoma. Melanoma Res 27:175–179
Ecsedi S, Rodríguez-Aguilera JR, Hernandez-Vargas H (2018) 5-Hydroxymethylcytosine (5hmC), or how to identify your favorite cell. Epigenomes 2:3
Booth MJ, Ost TW, Beraldi D et al (2013) Oxidative bisulfite sequencing of 5-methylcytosine and 5-hydroxymethylcytosine. Nat Protoc 8:1841–1851
Krueger F, Andrews SR (2011) Bismark: a flexible aligner and methylation caller for bisulfite-Seq applications. Bioinformatics 27:1571–1572
Kent WJ, Sugnet CW, Furey TS et al (2002) The human genome browser at UCSC. Genome Res 12:996–1006
Thorvaldsdóttir H, Robinson JT, Mesirov JP (2013) Integrative genomics viewer (IGV): high-performance genomics data visualization and exploration. Brief Bioinform 14:178–192
Yoon D, Bae K, Lee MK et al (2018) Galanin is an epigenetically silenced tumor suppressor gene in gastric cancer cells. PLoS One 13:e0193275
Tahiliani M, Koh KP, Shen Y et al (2009) Conversion of 5-methylcytosine to 5-hydroxymethylcytosine in mammalian DNA by MLL partner TET1. Science 324:930–935
Author information
Authors and Affiliations
Corresponding author
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2022 The Author(s), under exclusive license to Springer Science+Business Media, LLC, part of Springer Nature
About this protocol
Cite this protocol
Mancia, A. (2022). Genome-Wide DNA Methylation Protocol for Epigenetics Studies. In: Verde, C., Giordano, D. (eds) Marine Genomics. Methods in Molecular Biology, vol 2498. Humana, New York, NY. https://doi.org/10.1007/978-1-0716-2313-8_2
Download citation
DOI: https://doi.org/10.1007/978-1-0716-2313-8_2
Published:
Publisher Name: Humana, New York, NY
Print ISBN: 978-1-0716-2312-1
Online ISBN: 978-1-0716-2313-8
eBook Packages: Springer Protocols