Endogenous patterned activity-regulated genes specifically regulate different phases of synaptogenesis in the auditory system

In the auditory system, spatiotemporal patterning of correlated activity that originates in immature hair cells (HC) instructs refinement of synaptic connections and tonotopy. Patterned activity-dependent synaptic pruning requires the interplay between Hebbian plasticity and activity-regulated genes (ARGs). However, the genetic basis of this process is incompletely understood. Here we demonstrate that developing spiral ganglion neurons (SGNs) transiently generate discrete bursts of spikes and that blocking burst activity in this critical window causes profound deafness in mice. Using RNA sequencing, we profile ARG programs by genetically disrupting endogenous activity patterns of SGNs without changing spontaneous firing of inner HCs. Gene knockdown reveals that Nptx2 mediates initial synaptic formations at early stage, whereas Them5, which is important for cardiolipin remodeling that enhances mitochondrial function, specifically regulates synaptic pruning at later stage of development. These results suggest that ARGs dictate different phases of synaptogenesis and that Them5-depedent mitochondrial function might underlie synaptic pruning. Gene expression profiling analysis of RNA-seq data from postnatal days 7 mouse auditory spiral ganglion neurons. Approximately 50 spiral ganglion neurons as one biological replicate. Neurons are captured and collected by micro-pipette. Samples were collected from three conditions: control group ( aav-carried EGFP), dominant negtive SK3 channel group (aav-carried truncated SK3 channel), and dominant-negative HCN2 goup (aav-carried site-mutated HCN2 channel). Each condition also include two different regions (apex and base) in mouse cochlea.