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Review
. 2022 Mar 8;225(Suppl_1):jeb243411.
doi: 10.1242/jeb.243411. Epub 2022 Mar 8.

Epigenomics as a paradigm to understand the nuances of phenotypes

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Review

Epigenomics as a paradigm to understand the nuances of phenotypes

Cornelia Fanter et al. J Exp Biol. .

Abstract

Quantifying the relative importance of genomic and epigenomic modulators of phenotype is a focal challenge in comparative physiology, but progress is constrained by availability of data and analytic methods. Previous studies have linked physiological features to coding DNA sequence, regulatory DNA sequence, and epigenetic state, but few have disentangled their relative contributions or unambiguously distinguished causative effects ('drivers') from correlations. Progress has been limited by several factors, including the classical approach of treating continuous and fluid phenotypes as discrete and static across time and environment, and difficulty in considering the full diversity of mechanisms that can modulate phenotype, such as gene accessibility, transcription, mRNA processing and translation. We argue that attention to phenotype nuance, progressing to association with epigenetic marks and then causal analyses of the epigenetic mechanism, will enable clearer evaluation of the evolutionary path. This would underlie an essential paradigm shift, and power the search for links between genomic and epigenomic features and physiology. Here, we review the growing knowledge base of gene-regulatory mechanisms and describe their links to phenotype, proposing strategies to address widely recognized challenges.

Keywords: Epigenetics; Gene regulation; Phenotype; Physiology.

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Conflict of interest statement

Competing interests The authors declare no competing or financial interests.

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