Cellular identity, environment, stimuli, and physiological rhythms all require a static genome to respond dynamically, and sometimes reversibly while preserving the underlying genetic code. Epigenetic layers such as DNA methylation, and chromatin remodeling provide mechanisms for enabling these responses by altering accessibility and facilitating interactions between loci and with associated RNA and proteins. Although the stable maintenance of some epigenetic layers is essential, epigenetic regulation exhibits considerable plasticity, permitting the adaptability of a single genome into a functional organism.

Epigenetic dysregulation is implicated in a wide array of conditions and may occur in combination with genetic mutations or environmental insults. Understanding how these modifications to the DNA and chromatin alter their function and developing tools and therapies to restore function are of critical importance and are highly studied in many contexts of human health.

The growing toolkit of methods available in the field has allowed researchers to study the epigenome at several levels including detection (e.g., whole-genome bisulfite sequencing, chromatin immunoprecipitation, chromosome conformation capture, ATAC-seq), visualization (e.g., in situ microscopy), and editing (e.g., CRISPR). This methods collection aims to highlight such techniques and more, which enable the examination of both targeted and genome-wide epigenetic modifications at the DNA and chromatin levels.