Describing histone acetylation machinery in rivulus

Describing histone acetylation machinery in rivulus will provide a basis for understanding the role of epigenetic mechanisms in mediating phenotypic variation, by guiding both phenotypic flexibility in adults and developmental plasticity in young. Together with its biological characteristics, rivulus is a very good model to work on sex determination, development, ecophysiology, behaviour, evolution, ecotoxicology (Kelley et al., 2012; Voisin et al., 2016), and it allows biologists to explicitly disentangle the epigenetic, genetic or combined contributions to phenotypic variation within and among isogenic lineages. In this study, we used in silico analyses to describe the molecular characterization and determine the phylogenetic position of putative KAT and HDAC proteins. Their mRNA expression profiles also were investigated by RT-qPCR throughout embryogenesis, and in adult brain, gonads and liver.
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Results
Discussion Our work identified forty-four genes coding putative lysine acetyltransferase (KAT) and histone deacetylase (HDAC) proteins, and described patterns of transcript expression of these genes in rivulus embryos and adults. These results establish an important foundation for understanding histone acetylation in rivulus, a model (Kelley et al., 2012) that allows for explicit examination of the epigenetic contributions to phenotypic variability within a great diversity of naturally isogenic lineages. Our study also adds to our knowledge of histone acetylation-modifying enzymes during fish development and gametogenesis, as their characterization has, to date, only been examined with respect to zebrafish embryogenesis (He et al., 2014; Ignatius et al., 2013; Karmodiya et al., 2014; Yamaguchi et al., 2005). Concerning deacetylase enzymes, our analysis reveals that the four HDAC Difopein australia (Class I, IIA, IIB, IV) and the four Sirtuin sub-classes (Ia, Ib, II, III, IVa, IVb) that already exist in other characterized species (de Ruijter et al., 2003; North & Verdin, 2004) are present in the mangrove rivulus. The presence of catalytic domains, on both HDACs and Sirtuins, suggests that rivulus deacetylases might be active proteins (North & Verdin, 2004; Seto & Yoshida, 2014). Furthermore, despite an absence of duplication in the well-characterized zebrafish (Best et al., 2018), some HDAC (Hdac1, Hdac4, Hdac7) are possibly duplicated in Kryptolebias marmoratus. They illustrate the complexity of the teleost gene evolution history and a complete molecular characterization must be done to confirm it. Gene expression patterns demonstrated that HDAC transcripts are regulated throughout the rivulus life cycle. During embryogenesis, Hdac4, Hdac8 and Hdac10 transcripts levels suggest an accumulation during the gametogenesis, while the others might be activated with the zygotic transition. Furthermore, a peak in expression at the gastrula stage and irregular peaks throughout development indicates that HDACs may have conserved important, complementary roles in gastrulation and organogenesis, leading to an autonomous embryo able to feed and swim just after hatching (Koenig & Chasar, 1984; Mourabit et al., 2011). Thus, in fish, HDAC expressions have only been studied in zebrafish and a crucial role is demonstrated in retinal neurogenesis (Yamaguchi et al., 2005), heart formation (Kim et al., 2012), liver formation (Farooq et al., 2008) and embryonic posterior line development (He et al., 2014). In adult, rivulus HDAC expressions in the hermaphrodite ovotestes (Hdac1, Hdac3, Hdac4, Hdac5, Hdac7) and in the male testes (Hdac9) suggest that histone deacetylase enzymes contribute to the correct gametogenesis. Indeed, while hdac1 accumulates in Xenopus oocytes (Ryan et al., 1999), histone deacetylases mediate genome inactivation, chromatin remodeling in mature sperm (Burlibaşa & Zarnescu, 2013), and transcriptional silencing during oocyte maturation (Lee et al., 2015) in mice. Finally, together with later embryonic stage mRNA levels, brain HDAC expressions indicate that rivulus deacetylase might have specific functions in regulating developmental/adult neurogenesis, and maybe behavior in accordance with their putative role in lamprey neuronal regeneration (Chen et al., 2016) or with the behavioral regulation of zebrafish (Román et al., 2018).