Motor learning drives region-specific transcriptomic remodeling in the motor cortex and dorsal striatum

Summary Motor learning depends on coordinated activity across the motor cortex (M1) and dorsal striatum (dSTR), yet the molecular mechanisms driving learning-related synaptic and circuit remodeling remain unclear. Here, we combine activity-dependent genetic labeling (TRAP) with single-cell RNA sequencing to generate an unbiased, cell type-resolved transcriptional atlas of behaviorally engaged populations during a forelimb reaching task. We identify diverse activated neurons across M1 and dSTR, including a striking enrichment of Htr3a-expressing interneurons (Htr3a INs) in M1 that are selectively recruited during skilled reaching, as confirmed by two-photon calcium imaging. Corticostriatal projection neurons and striatal spiny projection neurons show subtype-and region-specific transcriptional remodeling involving genes linked to synaptic function, translation, and metabolism. Glial cells—including astrocytes, oligodendrocytes, and microglia— exhibit similarly robust, stage-and region-dependent gene regulation. These findings provide a comprehensive molecular framework for motor learning and highlight coordinated, cell type-specific transcriptional programs in neurons and glia that shape the encoding and retrieval of motor memory. Highlights - Motor learning activates interneuron cell types in motor cortex and striatum - Htr3a-expressing interneurons in motor cortex are specifically activated while performing a learned reaching behavior - Transcriptome remodeling exhibited distinct patterns between motor cortex and striatum - Glial cells showed stage- and region-specific transcriptomic alteration patterns that align with those in neurons