HDAC Inhibition Reshapes Splicing of Synaptic Plasticity-Related Genes and Neural Network Dynamics.

Alternative splicing (AS) serves as a fundamental mechanism governing proteomic diversity in brain cells throughout development and adulthood, profoundly influencing cell differentiation and synaptic plasticity. In this study we used a model system of rat primary neuron cultures to examine how global chromatin remodeling induced by the broad-spectrum HDAC inhibitor trichostatin A (TSA) influences local AS patterns in plasticity-related genes and explored their possible functional implications for synaptic functioning. Analysis of transcriptomic data uncovered a widespread dynamic AS-induced changes in plasticity-related genes through both transcription-coupled and post-transcriptional mechanisms. We found that prolonged TSA treatment preferentially alters the exon composition in genes involved in synapse organization and signal transduction. Using quantitative PCR, we validated these results for selected genes encoding involved in synaptic functioning cell adhesion molecules (Nrxn1, Nrxn2), scaffold proteins (Shank2, Dlgap1), glutamate receptors (Gria4), and signaling molecules (Syngap1, Prkcz). To determine whether these molecular changes correlate with neural network activity, we performed calcium imaging in neuron cultures expressing the genetically encoded calcium sensor GCaMP6s. We found that molecular rearrangements accompanied the temporally delayed substantial network reorganization, which appeared at 19 h as an increased synchronization of neuronal activity, followed by elevated neuronal excitability at 48 h. These results establish a novel mechanistic link between epigenetic regulation, AS dynamics, and synaptic functioning, explaining how the HDAC inhibitors can enhance synaptic plasticity. Furthermore, our findings provide novel insights into molecular basis of neurological disorders associated with splicing dysregulation, offering new directions for therapeutic interventions.