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. 2016 Jan 15;183(2):96-109.
doi: 10.1093/aje/kwv187. Epub 2015 Dec 30.

Genome-Wide Epigenetic Studies in Human Disease: A Primer on -Omic Technologies

Huihuang Yan, Shulan Tian, Susan L Slager, Zhifu Sun, Tamas Ordog

Genome-Wide Epigenetic Studies in Human Disease: A Primer on -Omic Technologies

Huihuang Yan et al. Am J Epidemiol. .

Abstract

Epigenetic information encoded in covalent modifications of DNA and histone proteins regulates fundamental biological processes through the action of chromatin regulators, transcription factors, and noncoding RNA species. Epigenetic plasticity enables an organism to respond to developmental and environmental signals without genetic changes. However, aberrant epigenetic control plays a key role in pathogenesis of disease. Normal epigenetic states could be disrupted by detrimental mutations and expression alteration of chromatin regulators or by environmental factors. In this primer, we briefly review the epigenetic basis of human disease and discuss how recent discoveries in this field could be translated into clinical diagnosis, prevention, and treatment. We introduce platforms for mapping genome-wide chromatin accessibility, nucleosome occupancy, DNA-binding proteins, and DNA methylation, primarily focusing on the integration of DNA methylation and chromatin immunoprecipitation-sequencing technologies into disease association studies. We highlight practical considerations in applying high-throughput epigenetic assays and formulating analytical strategies. Finally, we summarize current challenges in sample acquisition, experimental procedures, data analysis, and interpretation and make recommendations on further refinement in these areas. Incorporating epigenomic testing into the clinical research arsenal will greatly facilitate our understanding of the epigenetic basis of disease and help identify novel therapeutic targets.

Keywords: DNA methylation; cancer; complex diseases; epigenome; histone modification.

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Figures

Figure 1.
Figure 1.
Epigenetic features that mark active and repressed genes. Active enhancers, promoters, and gene bodies are marked by H3K4me1+H3K27ac, H3K4me3+H3K9ac, and H3K79me2+ H3K36me3, respectively; 5-methylcytosine (5meC) is often detected in the gene bodies. Inactive enhancers, promoters, and gene bodies are marked by H3K9me2/3 and H3K27me3; 5meC also occurs in the promoters. H3K4me1, histone H3 lysine 4 monomethylation; H3K4me3, histone H3 lysine 4 trimethylation; H3K9ac, histone H3 lysine 9 acetylation; H3K9me2, histone H3 lysine 9 dimethylation; H3K9me3, histone H3 lysine 9 trimethylation; H3K27ac, histone H3 lysine 27 acetylation; H3K27me3, histone H3 lysine 27 trimethylation; H3K36me3, histone H3 lysine 36 trimethylation; H3K79me2, histone H3 lysine 79 dimethylation.
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