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Implications of Genotype and Environment on Variation in DNA Methylation

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Handbook of Nutrition, Diet, and Epigenetics

Abstract

The epigenome is highly plastic and reacts to the changing external conditions such as diet, lifestyle, and toxins throughout the lifespan. Epigenome-wide association studies (EWAS) provide an opportunity to identify epigenetic variants associated with such exposures and the associated suboptimal health outcomes. DNA methylation at 5-methylcytosine is a routinely interrogated epigenetic mark in such EWAS studies. However, depending upon the choice of biological sample, a reliable quantification of the change in methylome at a genomic locus is often confounded by cellular heterogeneity. In addition, the interpretation of cause and effect of this methylation diversity in epigenomes is further complicated by the contributions from genotype and its interaction with the environment, thereby warranting a more sophisticated approach to reliably measure and interpret EWAS findings. This chapter discusses the factors influencing the variability in DNA methylome and its implications on biological interpretations.

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Abbreviations

AHRR:

Aryl-hydrocarbon receptor repressor

ASM:

Allele-specific methylation

CGI:

CpG islands

CNV:

Copy number variation

CYP1A1:

Cytochrome P450 family 1 subfamily A member 1

DNMT1:

DNA methyltransferase 1

eQTL:

Expression quantitative trait locus

EWAS:

Epigenome-wide association study

FKBP5:

FK506 binding protein 5

GNAS:

Guanine nucleotide binding protein, Alpha stimulating

GRB10:

Growth factor receptor bound protein 10

HIF1A:

Hypoxia-inducible factor 1-alpha

LD:

Linkage disequilibrium

MAT:

Methionine adenosyltransferase

meQTL:

Methylation quantitative trait locus

P-ASM:

Parent-of-origin allele-specific methylation

PCR:

Polymerase chain reaction

POP:

Persistent organic pollutant

PTSD:

Post-traumatic stress disorder

SAM:

S-adenosylmethionine

S-ASM:

Sequence-dependent allele-specific methylation

SNP:

Single nucleotide polymorphism

TET:

Ten-eleven translocation

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Authors and Affiliations

  1. Singapore Institute for Clinical Sciences (SICS), A*STAR, Brenner Centre for Molecular Medicine, 30 Medical Drive, Singapore, 117609, Singapore

    Ives Y. Lim, Xinyi Lin & Neerja Karnani

Authors
  1. Ives Y. Lim
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  2. Xinyi Lin
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  3. Neerja Karnani
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Correspondence to Neerja Karnani .

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Editors and Affiliations

  1. c/o Editorial Board 978-0-387-78665 , Heidelberg, Baden-Württemberg, Germany

    Vinood Patel

  2. Kings College , London, United Kingdom

    Victor Preedy

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Lim, I.Y., Lin, X., Karnani, N. (2017). Implications of Genotype and Environment on Variation in DNA Methylation. In: Patel, V., Preedy, V. (eds) Handbook of Nutrition, Diet, and Epigenetics. Springer, Cham. https://doi.org/10.1007/978-3-319-31143-2_56-1

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  • DOI: https://doi.org/10.1007/978-3-319-31143-2_56-1

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  • Print ISBN: 978-3-319-31143-2

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