Histone post-translational modifications (PTMs) are epigenetic marks that play a critical role in the expression and maintenance of DNA, but they remain largely uninvestigated in non-model organisms due to technical challenges. To begin alleviating this issue, we developed a workflow for histone PTM analysis in the Mozambique tilapia (Oreochromis mossambicus), being a widespread and environmentally hardy fish, using mass spectrometry methods. By incorporating multiple protein digestion methods into the preparation of each sample, we reliably quantified 503 biologically relevant histone PTMs. All of these histone PTMs, collectively referred to as the global histone PTM landscape, were characterized in the gills, kidney, and testes of this fish. By comparing the global histone PTM landscape between the three tissues, we found that 90.46% of histone PTMs were tissue-dependent. The workflow and tools for histone PTM analysis described in this study are now publicly available and enable comprehensive investigation into the influence of environmental stress on histone PTMs in non-model organisms. Given the functionality and flexibility of histone PTMs, we anticipate that the study of histone PTMs in ecologically relevant contexts will provide ground-breaking insights into comparative physiology and evolution.

Twenty-four Mozambique tilapia with an average weight of 60.64 ± 3.35 g were sacrificed and dissected for their gills, kidney, and if male, testes. These dissections yielded n = 24 samples of gills, n = 24 samples of kidney, and n = 18 samples of testes. Each tissue sample was divided into three aliquots so that they could be processed for histone PTM analysis using three different methods. Four kidney samples were excluded from statistical analyses due to inadequate recovery of tissue during dissection, which led to an insufficient protein concentration once samples were divided three ways. Therefore, n = 20 kidney samples were used in subsequent statistical analyses. The use of these animals was approved by the UC Davis IACUC under Protocol #21846.

The gills, kidney, and testes of Mozambique tilapia were sampled for histone PTM analysis. Samples are labeled in corresponding files such that the last letter in the sample name corresponds to the tissue type (e.g., G = gills, T = testes, and K = kidney).