Epigenetic signatures in in vitro-expanded equine chondrocytes induced by a histone deacetylase inhibitor

We have explored the impact of DNA methylation changes on gene transcription in expanded equine chondrocytes treated with the histone deacetylase inhibitor (HDACi), Trichostatin A (TSA). The subjects were DNA and RNA samples prepared from articular cartilage cells derived from four animals in our previous study. Using Reduced Representation Bisulfite Sequencing (RRBS), we determined differentially methylated sites (DMS) and regions (DMRs) in the genomes of TSA-treated cells. We linked them to gene differential expression, as obtained from 3’ mRNA sequencing data and the single-locus quantification results of mRNA abundance (Real-time PCR) for the four chondrocyte cell lines. We have identified a set of genes exhibiting a negative correlation between methylation and gene expression, which are involved in cartilage development, cell proliferation, and chromatin organization. While TSA was found to hypermethylate and downregulate genes crucial for chondrocyte function, it also hypomethylated and upregulated genes involved in cartilage and bone formation. The findings highlight the TSA's selective activity in modifying epigenetic marks, suggesting its potential as well as limitations in promoting chondrocyte differentiation and regeneration, which is notably relevant for regenerative medicine applications in treating cartilage damage.