Population Epigenomics: Advancing Understanding of Phenotypic Plasticity, Acclimation, Adaptation and Diseases

Abstract

Advances in chromatin state mapping, high-throughput DNA sequencing, and bioinformatics have revolutionized the study and interpretability of epigenomic variation. The increasing feasibility of obtaining and analyzing detailed information on epigenetic mechanisms across many individuals and populations has enabled the study of epigenomic variation at the population level and its contributions to phenotypic variation, acclimation, ecological adaptation, and disease traits. Over the past decade, researchers from disparate life sciences ranging from epidemiology to marine conservation have begun approaching their subjects through the lens of population epigenomics. Epigenetic mechanisms involve molecular alterations in chromatin through DNA methylation and histone modifications, as well as complex non-coding RNAs and enzyme machinery, all leading to altered transcription and post-transcriptional RNA processing resulting in changes in gene expression. Genetic and environmental variation and stochastic epimutations give rise to epigenomic variation. Notably, some forms of epigenomic variation are quite stable and in some instances may be transmitted through one or more rounds of meiosis. Epigenomic variation can contribute significantly to phenotypic plasticity, stress responses, disease conditions, and acclimation and adaptation to habitat conditions across a wide variety of organisms during their lifetime but also across multiple generations. The purpose of this chapter is to provide an overview of population epigenomics concepts, approaches, challenges, and applications. We discuss the molecular basis of epigenetic mechanisms and their variation and heritability across diverse tissues and taxa. We then discuss the sources of epigenomic variation, within – and among – population epigenomic variation in plants and animals, and the evolutionary context of epigenomic variation before reviewing current molecular and bioinformatics methods for screening epigenomic variation. We then explore the contribution and association of epigenomic variation with phenotypic and ecological adaptation traits in plants and common disease conditions in humans and pharmacoepigenomics, as well as the main challenges and future research directions in population epigenomics. We emphasize challenges and potential solutions unique to the study of epigenomes and how those challenges are amplified by the diversity of pathways by which genes and environments can affect gene expression. With proper application and interpretation, the field of population epigenomics will continue to yield profound insights toward a better understanding of phenotypic plasticity, acclimation, ecological adaptation, heritability, human diseases, and pharmacogenomics.