DNA methylation in adults and during development of the self‐fertilizing mangrove rivulus, Kryptolebias marmoratus

Abstract

In addition to genetic variation, epigenetic mechanisms such as DNA methylation might make important contributions to heritable phenotypic diversity in populations. However, it is often difficult to disentangle the contributions of genetic and epigenetic variation to phenotypic diversity. Here, we investigated global DNA methylation and mRNA expression of the methylation‐associated enzymes during embryonic development and in adult tissues of one natural isogenic lineage of mangrove rivulus fish, Kryptolebias marmoratus. Being the best‐known self‐fertilizing hermaphroditic vertebrate affords the opportunity to work with genetically identical individuals to examine, explicitly, the phenotypic effects of epigenetic variance. Using the LUminometric Methylation Assay (LUMA), we described variable global DNA methylation at CpG sites in adult tissues, which differed significantly between hermaphrodite ovotestes and male testes (79.6% and 87.2%, respectively). After fertilization, an immediate decrease in DNA methylation occurred to 15.8% in gastrula followed by re‐establishment to 70.0% by stage 26 (liver formation). Compared to zebrafish, at the same embryonic stages, this reprogramming event seems later, deeper, and longer. Furthermore, genes putatively encoding DNA methyltransferases (DNMTs), Ten‐Eleven Translocation (TET), and MeCP2 proteins showed specific regulation in adult gonad and brain, and also during early embryogenesis. Their conserved domains and expression profiles suggest that these proteins play important roles during reproduction and development. This study raises questions about mangrove rivulus’ peculiar reprogramming period in terms of epigenetic transmission and physiological adaptation of individuals to highly variable environments. In accordance with the general‐purpose genotype model, epigenetic mechanisms might allow for the expression of diverse phenotypes among genetically identical individuals. Such phenotypes might help to overcome environmental challenges, making the mangrove rivulus a valuable vertebrate model for ecological epigenetic studies. The mangrove rivulus, Kryptolebias marmoratus, is the best‐known self‐fertilizing hermaphroditic vertebrate that allows to work with genetically identical individuals to examine, explicitly, the phenotypic effects of epigenetic variance. The reprogramming event is later, more dramatic and longer than in other described vertebrates. High evolutionary conservation and expression patterns of DNMT, TET, and MeCP2 proteins in K. marmoratus suggest biological roles for each member in gametogenesis and development.

Genome Survey of Chromatin-Modifying Enzymes in Threespine Stickleback: A Crucial Epigenetic Toolkit for Adaptation?

“…Our phylogenetic analyses and the presence of a catalytic domain and additional motifs suggest species-specific differences in genes underlying DNA methylation/hydroxymethylation. As also shown in zebrafish (Campos et al, 2012), bluehead wrasses (Todd et al, 2019), and mangrove rivulus (Fellous et al, 2018), DNMT3A and DNMT3B show duplication events, and DNMT3l is also absent in stickleback. This calls into question the generality of evolutionary conservation of de novo methylation and genomic imprinting genes in fishes.…”

“…Although fish are widely used as model organisms in aquaculture, medicine, ecology, evolution, and ecotoxicology (Cossins and Crawford, 2005), most of our knowledge of their epigenetic mechanisms is mainly focused on laboratory-cultured zebrafish (Horsfield, 2019). However, studies of enzyme evolution (Best et al, 2018) and epigenetic regulation of fish development (Potok et al, 2013;Fellous et al, 2018;Wang and Bhandari, 2019) support the idea of species-specific mechanisms. For instance, an increasing number of studies show an influence of epigenetic modifications in developmental plasticity of trout and salmon, which have implications for species-specific conservation through hatchery rearing programs (Le Luyer et al, 2017;Gavery et al, 2019).…”

“…For instance, an increasing number of studies show an influence of epigenetic modifications in developmental plasticity of trout and salmon, which have implications for species-specific conservation through hatchery rearing programs (Le Luyer et al, 2017;Gavery et al, 2019). Despite the increasing availability of teleost genomic resources, the comparative biology of teleost epigenetic mechanisms remains limited, particularly for nonmodel species and wild populations (Metzger and Schulte, 2016;Firmino et al, 2017;Labbé et al, 2017;Best et al, 2018;Fellous et al, 2018Fellous et al, , 2019aTodd et al, 2019). Hence, our ability to assess the role of epigenetic modifications in adaptive potential and population persistence of ecologically relevant species is still in its infancy.…”

“…These studies were crucial to advances in cancer diagnostics and prognostics (Costa-pinheiro and Montezuma, 2015), to understanding of plant production and plant responses to the environment (Baulcombe and Dean, 2014;Wang and Köhler, 2017), and to understanding of the mechanistic basis of transgenerational epigenetic inheritance in mammals (Van Otterdijk and Michels, 2016). Importantly, recent studies of the DNA methyltransferase family have also revealed that changes in gene copy numbers and molecular interactions can modulate enzyme activity and their role in transcriptional regulation (Lyko, 2018), and that a vast diversity of epigenetic and transcriptional patterns during development are observed among species (Riviere et al, 2013;Eckersley-maslin et al, 2018;Fellous et al, 2018Fellous et al, , 2019cHorsfield, 2019;Vastenhouw et al, 2019). This diversity, coupled with a variable number of genes FIGURE 1 | Schmatic view of marine stickleback life cycle illustrating the potential for this species as a model to elucidate the synergistic role of epigenetic mechanisms in aquaculture and eco-evolutionary studies.…”

The round goby genome provides insights into mechanisms that may facilitate biological invasions

“…For example, non-methylated genome regions in fish are unexpectedly CG-poor [142], fish differ from mammals with respect to the distribution of methylated CpGs in the genome [143], algorithms developed on mammals fail to identify CpG islands in fish [144], genome-wide CpG island predictions in cold-blooded animals consist primarily of false positives [145], and fish CG methylation occurs mainly in coding regions, where it correlates positively with gene expression levels [146]. DNA methylation dynamics in the germline follows distinct and non-mammalian patterns in zebrafish [147,148], mangrove fish [149], and medaka [150], and copy number variations in the de novo DNA methyltransferase DNMT3 in teleosts do not reflect teleost genome duplication events [116]. Together with distinct spatiotemporal expression patterns particularly during development [151][152][153][154], the peculiarities of the fish DNA methylation machinery clearly warrant an in-depth and species-aware exploration of the role of DNA methylation in fish.…”