Faculty of Biosciences and Aquaculture, Nord University, Bodø, Norway.
Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology, Trondheim, Norway.
Epigenetics. 2023 Dec;18(1):2282323. doi: 10.1080/15592294.2023.2282323. Epub 2023 Nov 27.
Phenotypic plasticity of metabolism and growth are essential for adaptation to new environmental conditions, such as those experienced during domestication. Epigenetic regulation plays a key role in this process but the underlying mechanisms are poorly understood, especially in the case of hydroxymethylation. Using reduced representation 5-hydroxymethylcytosine profiling, we compared the liver hydroxymethylomes in full-sib Nile tilapia with distinct growth rates (3.8-fold difference) and demonstrated that DNA hydroxymethylation is strongly associated with phenotypic divergence of somatic growth during the early stages of domestication. The 2677 differentially hydroxymethylated cytosines between fast- and slow-growing fish were enriched within gene bodies (79%), indicating a pertinent role in transcriptional regulation. Moreover, they were found in genes involved in biological processes related to skeletal system and muscle structure development, and there was a positive association between somatic growth and 5hmC levels in genes coding for growth factors, kinases and receptors linked to myogenesis. Single nucleotide polymorphism analysis revealed no genetic differentiation between fast- and slow-growing fish. In addition to unveiling a new link between DNA hydroxymethylation and epigenetic regulation of growth in fish during the initial stages of domestication, this study suggests that epimarkers may be applied in selective breeding programmes for superior phenotypes.
代谢和生长的表型可塑性对于适应新的环境条件至关重要，例如在驯化过程中所经历的那些条件。表观遗传调控在这个过程中起着关键作用，但潜在的机制知之甚少，特别是在羟甲基化的情况下。使用简化代表性 5-羟甲基胞嘧啶分析，我们比较了具有不同生长速度（相差 3.8 倍）的全同胞尼罗罗非鱼的肝脏羟甲基组，并证明 DNA 羟甲基化与驯化早期体生长的表型差异强烈相关。在快速生长和缓慢生长的鱼之间，2677 个差异羟甲基化的胞嘧啶被富集在基因体内（79%），表明其在转录调控中具有重要作用。此外，这些差异羟甲基化的胞嘧啶位于与骨骼系统和肌肉结构发育相关的生物过程的基因中，并且编码与肌发生相关的生长因子、激酶和受体的基因中的 5hmC 水平与体生长之间存在正相关。单核苷酸多态性分析显示，快速生长和缓慢生长的鱼之间没有遗传分化。除了揭示 DNA 羟甲基化与驯化初期鱼类生长的表观遗传调控之间的新联系外，本研究还表明，epimarkers 可能应用于选择性繁殖计划，以获得更优的表型。
