A Strategy to Characterize the Global Landscape of Histone Post-Translational Modifications Within Tissues of Nonmodel Organisms

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 nonmodel organisms
due to technical challenges. To begin alleviating this issue, we developed
a workflow for histone PTM analysis in 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 214 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 91.59% 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 nonmodel
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.