The functional ghost in the genome machine: Holistic mapping of environmentally induced changes in the epigenome of a soil sentinel

Abstract

The realization that toxicants and other stressors can remodel or corrupt the epigenome opens an exciting new dimension for to our understanding of (eco)toxicology. Apart from elucidating mechanisms whereby populations evolve adaptations to local environmental challenges, the functional interplay between the epigenome and the genome underpins answers to important questions relating to ecotoxicology (mechanism and persistence of effects) and field-based risk assessment (potential for plasticity and adaptation). Earthworms possess an unusually high DNA methylation level (∼13%) suggesting an important regulatory role for the epigenome. Interestingly, some experts have questioned the validity of ‘traditional’ laboratory model invertebrates (e.g. nematodes and fruit flies) for epigenetic studies because these have no or very low levels of DNA methylation. Earthworms, as indicated by their high genome methylation status, however, offer to be ecologically relevant targets for epigenomic study. We have explored the epigenetic modifications focusing on alterations in miRNAs and DNA methylation induced in response to environmental cues, including chemical (heavy metals) and physical (temperature and hypoxia/hypercapnia) stress in a number of sentinel earthworm species. These observations have provided key insights into the contribution of epigenetic modification in long term (micro-evolution/adaptation) and short term (acclimatisation) response to chemical and physical challenges. Informatic linkage of contaminated modified epigenetic alterations to modulation in the global transcriptome provides insights into the mechanisms basis that underpins an organism's toxicological response.