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Establishment and validation of the NEX-RiboTag system for profiling the excitatory neuronal translatome in the postnatal mouse forebrain

ABSTRACT: Excitatory neurons are the principal neurons of the mammalian cortex and hippocampus and are essential for postnatal circuit maturation. Although single-cell RNA sequencing has refined their molecular taxonomy, dissociation-induced stress artifacts and the disconnect between transcript abundance and translational output can limit functional interpretation. Bulk proteomics lacks cell-type specificity, while single-cell proteomics remains constrained by limited sensitivity and throughput. These limitations leave a gap between transcriptional identity and cell-type-resolved translational output. Because translation directly governs the selective recruitment of mRNAs for protein synthesis, defining excitatory neuron-specific translatome in vivo is valuable to bridge this gap. Here, we established and validated a NEX-RiboTag mouse line for targeted profiling of ribosome-associated mRNAs in cortical and hippocampal excitatory neurons. By crossing Neurod6 (NEX)-Cre mice with RiboTag reporter mice, we achieved Cre-dependent ribosomal tagging in excitatory neurons of the cortex and the hippocampus. RNA sequencing analysis at the 1-week postnatal stage demonstrated enrichment of excitatory neuronal markers and depletion of inhibitory neuronal and glial transcripts. Comparative analysis revealed a clear separation between the whole-tissue transcriptome and the ribosome-associated fractions, with enrichment of synaptic and metabolic pathways characteristic of excitatory neurons. Together, these datasets provide a valuable resource for investigating translational regulation in postnatal excitatory neurons and for studying molecular programs underlying neuronal maturation and synapse formation.

ORGANISM(S): Mus musculus

PROVIDER: GSE331310 | GEO | 2026/06/23

REPOSITORIES: GEO

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Establishment and validation of the NEX-RiboTag system for profiling the excitatory neuronal translatome in the postnatal mouse forebrain

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