DNA methyltransferase 3a mediates developmental thermal plasticity

Loughland et al. BMC Biology (2021) 19:11 https://doi.org/10.1186/s12915-020-00942-w RESEARCH ARTICLE Open Access DNA methyltransferase 3a mediates developmental thermal plasticity Isabella Loughland1, Alexander Little2 and Frank Seebacher1* Abstract Background: Thermal plasticity is pivotal for evolution in changing climates and in mediating resilience to its potentially negative effects. The efficacy to respond to environmental change depends on underlying mechanisms. DNA methylation induced by DNA methyltransferase 3 enzymes in the germline or during early embryonic development may be correlated with responses to environmental change. This developmental plasticity can interact with reversible acclimation within adult organisms, which would increase the speed of response and could alleviate potential mismatches between parental or early embryonic environments and those experienced at later life stages. Our aim was to determine whether there is a causative relationship between DNMT3 enzyme and developmental thermal plasticity and whether either or both interact with short-term acclimation to alter fitness and thermal responses in zebrafish (Danio rerio). Results: We developed a novel DNMT3a knock-out model to show that sequential knock-out of DNA methyltransferase 3a isoforms (DNMT3aa−/− and DNMT3aa−/−ab−/−) additively decreased survival and increased deformities when cold developmental temperatures in zebrafish offspring mismatched warm temperatures experienced by parents. Interestingly, short-term cold acclimation of parents before breeding rescued DNMT3a knock-out offspring by restoring survival at cold temperatures. DNMT3a knock-out genotype interacted with developmental temperatures to modify thermal performance curves in offspring, where at least one DNMT3a isoform was necessary to buffer locomotion from increasing temperatures. The thermal sensitivity of citrate synthase activity, an indicator of mitochondrial density, was less severely affected by DNMT3a knock-out, but there was nonetheless a significant interaction between genotype and developmental temperatures. Conclusions: Our results show that DNMT3a regulates developmental thermal plasticity and that the phenotypic effects of different DNMT3a isoforms are additive. However, DNMT3a interacts with other mechanisms, such as histone (de)acetylation, induced during short-term acclimation to buffer phenotypes from environmental change. Interactions between these mechanisms make phenotypic compensation for climate change more efficient and make it less likely that thermal plasticity incurs a cost resulting from environmental mismatches. Keywords: DNA methylation, Acclimation, Transgenerational plasticity, Epigenetics, Cost of plasticity, Metabolism, Locomotor performance, Zebrafish * Correspondence: 1 School of Life and Environmental Sciences A08, University of Sydney, Sydney, NSW 2006, Australia Full list of author information is available at the end of the article © The Author(s). 2021 Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article's Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article's Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated in a credit line to the data. Loughland et al. BMC Biology (2021) 19:11 Background The capacity to remodel the thermal sensitivity of physiological rates in response to temperature cues during development can be highly advantageous because it can match phenotypes to future thermal conditions [1]. Such developmental plasticity typically results in phenotypic changes that can be relatively stable during the lifetime [2]. A potential cost is incurred when developmental conditions do not match those prevalent later in life [1]. In contrast, thermal acclimation reversibly alters the thermal sensitivity of reaction rates in response to environmental changes lasting days to weeks [3]. It is therefore possible that thermal acclimation can negate the costs of developmental plasticity [4]. The potential interaction between developmental plasticity and acclimation is important for theories explaining the evolution of plasticity, and it could increase the efficacy of plastic responses to reduce vulnerability to climate change. Developmental plasticity can be mediated epigenetically via DNA methylation in response to internal or external environmental cues [5]. DNA methylation by DNA methyltransferases (DNMTs) can prevent binding of transcription factors to DNA and thereby alter gene expression and phenotypes [6]. There are two functionally distinct DNMTs in vertebrates: DNMT1, which is primarily associated with maintaining existing methylation marks in replicating cells, and DNMT3, which is responsible for de novo methylation in response to environmental signals [7, 8]. In stickleback (Gasterosteus aculeatus), for example, shifts in embryonic temperatures are correlated with different DNA methylation profiles [9]. Here, our aim was to determine whether there is a causative relationship between DNMT3 and developmental thermal plasticity and whether either or both interact with short-term acclimation to alter thermal sensitivity of physiological rates in zebrafish. Zebrafish are an ideal model organism to address these aims because they show both thermal developmental plasticity and acclimation [10], and DNMT3 gene sequences and expression profiles have been investigated [11] . Zebrafish have six DNMT3 genes, two paralogues of mammalian DNMT3a (DNMT3aa and DNMT3ab) and four paralogues of DNMT3b [12]. The two isoforms of DNMT3a (aa and ab) are expressed in a temperaturesensitive manner later in development (mostly > 72 h post-fertilisation) compared to DNMT3b isoforms (blastula) and are more highly expressed in developing muscle and adult fish [11, 12]. We therefore used CRIS PR-Cas9 to knock-out DNMT3aa (also known as DNMT3a2 or DNMT8) and DNMT3ab (also known as DNMT3a1 or DNMT6) to test their effects on developmental plasticity. We created a single isoform DNMT3aa−/− knock-out line and then generated a Page 2 of 11 double isoform DNMT3aa−/−ab−/− knockout line to determine both the individual and additive effects of (...truncated)