Abstract
Highly dynamic epigenetic signaling is influenced mainly by (micro)environmental stimuli and genetic factors. The exact mechanisms affecting particular epigenomic patterns differ dependently on the context. In the current review, we focus on the causes and effects of the dynamic signatures of the human epigenome as evaluated with the high-throughput profiling data and single-gene approaches. We will discuss three different aspects of phenotypic outcomes occurring as a consequence of epigenetics interplaying with genotype and environment. The first issue is related to the cases of environmental impacts on epigenetic profile, and its adverse and advantageous effects related to human health and evolutionary adaptation. The next topic will present a model of the interwoven co-evolution of genetic and epigenetic patterns exemplified with transposable elements (TEs) and their epigenetic repressors Krüppel-associated box zinc finger proteins (KRAB–ZNFs). The third aspect concentrates on the mitosis-based microevolution that takes place during carcinogenesis, leading to clonal diversity and expansion of tumor cells. The whole picture of epigenome plasticity and its role in distinct biological processes is still incomplete. However, accumulating data define epigenomic dynamics as an essential co-factor driving adaptation at the cellular and inter-species levels with a benefit or disadvantage to the host.
Highlights
Genetic mutation and epigenetic alterations determine species diversity and adaptability to changing environmental conditions
The alterations in DNA methylation were associated with the genes involved in hypoxia response and HIV infection (i.e., APOBEC3G, MT1G) [64], suggesting that epigenetic mechanisms may contribute to evolutionary adaptation towards external stimuli
This study demonstrated that the majority of human-specific differentially methylated regions (DMRs) overlap with repressed promoters, whereas hypomethylated DMRs occur within active promoters and bivalent domains, as well as enhancers distal from the promoter regions
Summary
Genetic mutation and epigenetic alterations determine species diversity and adaptability to changing environmental conditions. We report the concepts on the genetic and epigenetic co-evolution processes associated with clonal heterogeneity and expansion occurring during cancer development These three examples represent different but partially overlapping, context-dependent mechanisms responsible for the evolution of epigenomic signatures. Post-translational modifications on histones and other epigenomic signatures create a communication platform to mark various genomic regions (e.g., active promoters or enhancers) and mediate specific. The parental histones with repressive modifications are re-deposited locally to the same DNA domains, while the histones with active marks lose their local distribution [31] These observations underpin the complexity of the mechanisms implicated in the epigenetic inheritance of histone modifications
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