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Nanotoxicity pp 181-227 | Cite as

DNA Methylation Analysis

  • Lingfang Feng
  • Jianlin Lou
Protocol
Part of the Methods in Molecular Biology book series (MIMB, volume 1894)

Abstract

DNA methylation is a process by which methyl groups are added to cytosine or adenine. DNA methylation can change the activity of the DNA molecule without changing the sequence. Methylation of 5-methylcytosine (5mC) is widespread in both eukaryotes and prokaryotes, and it is a very important epigenetic modification event, which can regulate gene activity and influence a number of key processes such as genomic imprinting, cell differentiation, transcriptional regulation, and chromatin remodeling. Profiling DNA methylation across the genome is critical to understanding the influence of methylation in normal biology and diseases including cancer. Recent discoveries of 5-methylcytosine (5mC) oxidation derivatives including 5-hydroxymethylcytosine (5hmC), 5-formylcytsine (5fC), and 5-carboxycytosine (5caC) in mammalian genome further expand our understanding of the methylation regulation. Genome-wide analyses such as microarrays and next-generation sequencing technologies have been used to assess large fractions of the methylome. A number of different quantitative approaches have also been established to map the DNA epigenomes with single-base resolution, as represented by the bisulfite-based methods, such as classical bisulfite sequencing, pyrosequencing etc. These methods have been used to generate base-resolution maps of 5mC and its oxidation derivatives in genomic samples. The focus of this chapter is to provide the methodologies that have been developed to detect the cytosine derivatives in the genomic DNA.

Key words

DNA methylation Whole-genome bisulfite sequencing (WGBS) Reduced representation bisulfite sequencing (RRBS) Methyl-binding domain capture sequencing (MBDCap-Seq) Methylated DNA immunoprecipitation-sequencing (MeDIP-Seq) Methylation-sensitive restriction enzyme followed by sequencing (MRE-Seq) Infinium Methylation450 BeadChips (450K) Bisulfite sequencing (BS) Pyrosequencing Methylation-specific PCR (MSP)/quantitative methylation-specific PCR (QMSP) Single molecule real-time bisulfite sequencing (SMRT-BS) Targeted bisulfite sequencing (TBS) 

Notes

Acknowledgment

This work was supported by grants from the National Natural Science Foundation of China (No. 81472960, 81001242, 81502794), Zhejiang Province Natural Science Foundation of China (Y13H260011), Zhejiang Provincial Program for the Cultivation of High-level Innovative Health talents (2014), and Zhejiang Medical Health Science and Technology Foundation (2015RCA007).

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Copyright information

© Springer Science+Business Media, LLC, part of Springer Nature 2019

Authors and Affiliations

  • Lingfang Feng
    • 1
  • Jianlin Lou
    • 1
  1. 1.Institute of Occupational DiseasesZhejiang Academy of Medical SciencesHangzhouP. R. China

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