Table 2.

Summary of epigenetic modifications and their effects on gene expression.

Epigenetic modification	Found in	Relation to gene transcription	Study methods
Chromatin accessibility	Promoters and GREs	Activating	ATAC-seq DNAse-seq MNase-seq
H3K27ac	Active enhancers and TSS	Activating
H3K4me3	TSS	Activating
H3K4me1	Gene body Primed enhancers	Activating	ChIP-seq Cut&Run
H3K27me3	Bivalent/inactive enhancers, promoters and intergenic regions	Repressing	Cut&Tag
H3K9me3	Constitutive heterochromatin	Repressing
DNA methylation	Enhancers, promoters, gene body (CpG rich regions)	Repressing	Bisulfite sequencing