TABLE 1

Commonly used terms in epigenetic studies

TermDefinition
CpG siteDNA sequence where a cytosine nucleotide is followed by a guanine nucleotide
CpG is shorthand for 5′—C—phosphate—G—3′, that is, cytosine and guanine separated by only one phosphate group in the 5′ to 3′ direction
The cytosine in CpG sites can be dynamically methylated and demethylated
CpG island (CGI)A CpG-dense region of DNA that often overlaps regulatory sequences
Methylation of CpG islands can dynamically regulate gene expression, with decreased methylation often associated with increased expression
ChromatinDNA wrapped around histone core proteins for the purpose of tight packaging of DNA into a small volume to fit into the nucleus of a cell and protect the DNA structure and sequence
Differentially methylated positionA single CpG site that is statistically significantly differentially methylated among study groups
Differentially methylated regionA group of CpG sites across a region of DNA that is statistically significantly differentially methylated among study groups
DNA methylationDNA methylation is a process by which methyl groups are added to the DNA molecule
Methylation can change transcriptional activity of a DNA segment without changing the sequence
EnhancerA region of DNA that binds to transcription factors, which then interact with promoter regions to upregulate gene expression
EpigenomeCollection of epigenetic marks throughout the genome; genome-wide distribution of transcriptional regulators believed to mediate the memory of past cellular events
Epigenome-wide association study (EWAS)A study of the epigenome that looks for association between epigenetic variation and a high-level trait, such as disease status across individuals, or for association of a difference in organisation of a genomic regulator
Genome-wide association study (GWAS)A study that looks for association between genetic variation and a high-level trait such as disease across individuals, typically scanning millions of genetic variants genome-wide for association signals
Histone modificationA histone modification is a covalent post-translational modification (PTM) to histone proteins
The PTMs made to histones can impact gene expression by altering chromatin structure or recruiting histone modifiers
PromoterA region of DNA upstream of gene transcription start sites bound by RNA polymerase and transcription factors to facilitate gene expression