Epigenetics across the evolutionary tree: New paradigms from non‐model animals

Abstract

All animals have evolved solutions to manage their genomes, enabling the efficient organization of meters of DNA strands in the nucleus and allowing for nuanced regulation of gene expression while keeping transposable elements suppressed. Epigenetic modifications are central to accomplishing all these. Recent advances in sequencing technologies and the development of techniques that profile epigenetic marks and chromatin accessibility using reagents that can be used in any species has catapulted epigenomic studies in diverse animal species, shedding light on the multitude of epigenomic mechanisms utilized across the evolutionary tree. Now, comparative epigenomics is a rapidly growing field that is uncovering mechanistic aspects of epigenetic modifications and chromatin organization in non-model invertebrates, ranging from octopus to sponges. This review puts recent discoveries in the epigenetics of non-model invertebrates in historical context, and describes new insight into the patterning and functions of DNA methylation and other highly conserved epigenetic modifications.

Shaping eukaryotic epigenetic systems by horizontal gene transfer

“…Here, we are adding the third methyl mark, 4mC, to the eukaryotic repertoire, and begin to explore 4mC/N4-MTase occurrence throughout eukaryotes and its potential to shape epigenetic landscapes and to participate in TE silencing. While TE suppression has always been an underlying theme in most epigenetic studies, [121][122][123] a newly acquired MTase would not specifically target TEs without undergoing evolutionary adaptation.…”

Identification of 5mC within heterogenous tissue usingde-novosomatic mutations

“…As such, epigenetic models for the identification of cell-lineage and tissue origin are only possible in well-studied, primarily model, taxa (Tanay & Sebé-Pedrós, 2021). Characterization of epigenetic modifications and their roles in development of non-model organisms remain important to understanding acclimation, adaptation, and comparative evolution (Lamka et al, 2022; Sadler, 2023).…”

“…Efforts in applied and comparative epigenetics have largely revolved around CpG sites and 5mC modification. Though not universal, methylation of cytosine to form 5-methyl-cytosine (5mC) is among the best-studied forms of epigenetic modification (de Mendoza et al, 2020), and has formed a focal point for the study of gene regulation in model and non-model organisms alike (Sadler, 2023; Schmitz et al, 2019). They occur in at least four of the five supergroups of Eukaryotes—SAR (Hoguin et al, 2023), Archaeplastida (Zhang et al, 2018), Amoebozoa (Fisher et al, 2004), and Opisthokonta (Bewick et al, 2019)—but are poorly conserved within these (Aliaga et al, 2019).…”