Epigenomegenome

Epigenomegenome is a term used to describe an integrated view that combines an organism's genome sequence with its epigenome—the collection of chemical modifications and chromatin features that regulate gene expression without altering the DNA sequence. The genome provides the primary genetic blueprint; the epigenome modulates when, where, and how this blueprint is read in a tissue- and time-specific manner.

Epigenetic marks include DNA methylation, histone modifications, chromatin accessibility, and higher-order genome organization. These features are dynamic and influenced by development, environmental exposures, aging, and disease. Epigenome-genome analyses aim to map both layers, identify regulatory elements such as promoters and enhancers, and link epigenetic states to transcriptional outcomes and phenotypes. Technologies used in this field include genome sequencing, whole-genome bisulfite sequencing for DNA methylation, ChIP-seq for histone marks, ATAC-seq for chromatin accessibility, and Hi-C for 3D genome architecture. Integrated analyses can reveal methylation quantitative trait loci (mQTLs), expression quantitative trait loci (eQTLs), and regulatory interactions between enhancers and promoters.

Applications span cancer epigenetics, developmental biology, aging research, and precision medicine. Epigenome-genome data underpin epigenome-wide association studies (EWAS) that link epigenetic variation to traits and diseases. Epigenome editing and drugs targeting epigenetic enzymes offer therapeutic potential, though establishing causality and tissue specificity remains challenging. Common limitations include tissue heterogeneity, temporal dynamics, and the complexity of data integration and interpretation. The epigenome-genome framework continues to evolve as researchers seek to understand how inherited sequence variation and acquired epigenetic states together shape biology and disease.