Academic journal article Genetics

Prediction of Plant Height in Arabidopsis Thaliana Using DNA Methylation Data

Academic journal article Genetics

Prediction of Plant Height in Arabidopsis Thaliana Using DNA Methylation Data

Article excerpt

(ProQuest: ... denotes formulae omitted.)

EPIGENETICS focuses on heritable changes of genetic materials that do not reside in the sequence of DNA, called epigenetic modifications (Riggs et al. 1996; Riggs and Porter 1996). Major forms of these changes are DNA methylation, histone modification, and noncoding RNAs (ncRNAs) (Rivera and Bennett 2010). DNA methylation is the most common epigenetic modification, which can have various forms depending on the targeting nucleotide of the modification (Ratel et al. 2006). In vertebrates and flowering plants, it is usually referred to as the covalent addition of a methyl group (-CH3) to the 5-position carbon atom (5C) of the cytosine pyrimidine ring, resulting in 5-methylcytosine (m5C) (Jeltsch 2002; Meissner et al. 2005; Vanyushin 2006). Thus, "DNA methylation" stands for m5C throughout this article. Histone modification is the multivalent modification of histone tails of the core histones, which can be acetylation, methylation, phosphorylation, ubiquitination, and symoylation (Kouzarides 2007; Ruthenburg et al. 2007). Both DNA methylation and histone modification interact with the entering and binding of transcription factors (TFs) to the DNA molecule such that gene expression is altered. Usually, DNA methylation is associated with reduced gene expression (Bird 1984; Razin and Cedar 1991; Lim and Maher 2010) and histone modification can either enhance or repress expression, according to different modification targets (e.g., which amino acids are at the histone tail) and modification types (e.g., methylation or acetylation) (Berger 2002; Cheung and Lau 2005). Recently, ncRNAs were found to be composed of a hidden layer of internal signals that control various levels of gene expression associated with physiological and developmental processes. Their role in epigenetic regulation has been acknowledged as well (Zhou et al. 2010; Kaikkonen et al. 2011).

Epigenetic modifications have an important role in gene expression regulation, and malfunctioning of the regulation process can have severe consequences. In epidemiology and humangenetics,many diseasesand disorders, includingcancer, have been confirmed to have an epigenetic basis (Jones and Baylin 2002, 2007; Jiang et al. 2004; Esteller 2008; Pembrey 2012; Tollefsbol 2012). For example, Prader-Willi syndrome (PWS) and Angelman syndrome (AS) are sister imprintingrelated disorders involving deletion of DNA segments derived from different parents at the same genomic region (Meijers-Heijboer et al. 1992; Nicholls et al. 1998; Cassidy et al. 2000). Another example of epigenetics-related diseases is that of oncogenes; these exist in almost everyone's genome while only a small proportion of the population develops a cancer. Here, the promoter region of a tumor suppressor gene is usually unmethylated such that the gene is expressed normally and, therefore, it prevents the formation of a tumor. In cases where there is hypermethylation in the promoter region, the tumor suppressor is deactivated and a cancer develops (Jones and Baylin 2002; Robertson 2002; Egger et al. 2004).

Due to the potentially important role of epigenetics in diseases, epigenome-wide association studies (EWAS), a counterpart of genome-wide association studies (GWAS) at the epigenome level, have been conducted in recent years (MacArthur 2008; Rakyan et al. 2011; Bell 2013), aiming at finding associations between epigenetic polymorphisms and traits of interest, instead of using DNA polymorphisms (e.g., SNPs). Although epigenetic regulation is not restricted to DNA methylation, the latter is the most commonly used biomarker in EWAS at present, because it is more stable and easier to be quantified than other epigenetic regulatory mechanisms (Flanagan 2015). In EWAS, DNA methylation across the whole genome is converted into a certain measurement reflecting the "methylation level," using methylationsensitive enzyme digestion (Waalwijk and Flavell 1978; Kaput and Sneider 1979), methylated DNA immunoprecipitation (MeDIP) (Weber et al. …

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