Dynamic DNA methylation remodeling in the brain during flatfish metamorphosis

The metamorphosis of flatfishes involves a significant transformation from a pelagic larval stage to a benthic juvenile stage. This process is driven by thyroid hormone signaling and involves extensive morphological and functional remodeling. While the regulation of gene expression is central to this process, the epigenetic mechanisms coordinating these transitions remain poorly understood. Although DNA methylation has been implicated in vertebrate metamorphosis, its role in coordinating the epigenetic regulation of flatfish brain metamorphosis remains largely unexplored. In this study, we examine the epigenetic and transcriptional dynamics of the brain, a critical regulator of metamorphosis, by analyzing chromatin accessibility, DNA methylation and transcriptomic profiles across three developmental stages (pre-metamorphosis, metamorphic climax and post-metamorphosis) in turbot (Scophthalmus maximus). We identify widespread DNA methylation remodeling during metamorphosis, characterized by dynamic changes in DNA methylation. Differentially methylated regions (DMRs) exhibit a bimodal distribution at the pre-metamorphic stage, shift toward intermediate methylation levels at the metamorphic climax, and return to a bimodal pattern following metamorphosis. Notably, DMRs are predominantly associated with open chromatin regions and are significantly enriched at CpG islands. Furthermore, DNA methylation levels near transcription start sites are inversely related to gene expression, suggesting a regulatory role in transcriptional control. Collectively, our findings reveal dynamic epigenetic remodeling in the brain during flatfish metamorphosis, provide insights into how DNA methylation contributes to the coordination of developmental transitions, and extend current knowledge of vertebrate developmental epigenetics by providing the first integrative analysis of DNA methylation, chromatin accessibility, and transcriptional regulation during flatfish brain metamorphosis.