epigenomics

Epigenomics is the branch of genomics that studies the epigenome—heritable changes in gene activity that do not alter the DNA sequence. It examines how chemical modifications to DNA and histone proteins, chromatin structure, and non-coding RNAs regulate when and where genes are expressed in cells and tissues.

Key components include DNA methylation, especially at CpG dinucleotides, histone modifications such as methylation and acetylation (for example H3K4me3, H3K27ac), and the organization of chromatin into accessible or repressed states. Together with chromatin remodeling and RNA-mediated mechanisms, these marks influence transcriptional programs.

Methods generate genome-wide maps: bisulfite sequencing for methylation, ChIP-seq for histone marks, ATAC-seq for open chromatin, and Hi-C for three-dimensional genome architecture. Large consortia such as ENCODE, Roadmap Epigenomics, and the International Human Epigenome Consortium have produced reference epigenomes across tissues and developmental stages.

The epigenome is dynamic and responsive to development, aging, and environmental factors such as diet, toxins, and stress. Abnormal epigenetic regulation is associated with cancers, imprinting disorders, neurological diseases, and other conditions. Epigenetic information can be inherited during cell division and, in some contexts, across generations, though the extent and mechanisms remain debated.

Applications include epigenome editing to modify gene expression, biomarker development, and potential therapies; however, challenges include tissue heterogeneity, context-dependent effects, and distinguishing cause from consequence.