Localized mRNAs and protein synthesis in cortical layer 1

Cortical layer 1 plays an essential role for brain function, integrating many streams of information and undergoing synaptic plasticity during learning. Yet, we understand little of the underlying molecular processes, and whether they are specialized to achieve layer-specific functions. Here, we show that layer 1 and its synapses are metabolically active. Using laser capture RNA-sequencing and fluorescence in situ hybridization, we report an abundance of synaptic transcripts localized to layer 1. We purified layer 1 excitatory and inhibitory synapses and characterized their enriched transcriptomes, identifying candidate proteins that can be locally synthesized to maintain and regulate synaptic transmission in layer 1. Furthermore, we find significant differences between the transcriptome of synapses in layer 1 and in deeper, somatic layers, suggesting that local translation might confer specialized function. Finally, by comparing our tissue data with the transcriptome from the hippocampal CA1 strata, we discover a strong similarity between cortical layer 1 and stratum lacunosum moleculare, suggesting that these distal layers share a common molecular environment. Together, our results establish that local protein synthesis is an important mechanism for layer 1, and provide the first comprehensive characterization of the transcripts localized to layer 1 and its synapses.