Neuronal activation triggers rapid biphasic FMRP-mediated translational control linking synaptic and nuclear regulation [RiboTag]

A central question in protein synthesis–dependent synaptic plasticity is how translation of neuronal mRNAs is dynamically regulated in time and space. Here, we develop Opto-CLIP, integrating optogenetic stimulation with cell-type-specific crosslinking immunoprecipitation (CLIP) of FMRP in CA1 neurons to define activity-dependent RNA regulation. Following patterned neuronal activation, we identify dynamic changes in FMRP-mediated translational control at minute-scale resolution. Within five minutes, FMRP is released from synaptic transcripts, accompanied by increased ribosome association. By 30 minutes, FMRP dissociates from transcripts encoding nuclear and RNA regulatory factors, also accompanied by increased ribosome association. At this stage, despite a marked reduction in protein levels, FMRP selectively reassociates with synaptic transcripts, coincident with reduced ribosome association. These coordinated shifts define temporally structured waves of translational control linking synaptic and nuclear programs. Our findings reveal a biphasic program of FMRP-mediated translational control that couples local synaptic responses to delayed nuclear regulation, providing a mechanistic framework linking activity-dependent RNA regulation, its disruption in Fragile X syndrome, and homeostatic plasticity.