Single cell and isoform-specific translational profiling of the mouse brain [Bulk RNA-seq]

The brain displays the richest repertoire of post-transcriptional mechanisms regulating mRNA translation1–12. Among these, alternative isoform expression has been shown to drive cell type specificity and, when disrupted, is strongly linked to neurological disorders13–18. However, genome-wide measurements of mRNA translation with isoform-sensitivity at single-cell resolution have not been achieved. To address this, we deployed Ribo-STAMP (Surveying Ribosomal Targets by APOBEC-Mediated Profiling) coupled with short- and long-read single-cell RNA-sequencing in the brain19. We generated the first isoform-sensitive single cell translatomes of the mouse hippocampus, discovering 797 alternative isoforms across 325 genes, with CA1 exhibiting the most differentially expressed and CA3 the most differentially translated isoforms. We defined high and low translational states in CA1 and CA3 neurons, with ribosomal, metabolic, and synaptic genes enriched in high states. Surprisingly, we found that CA3 neurons exhibited higher basal translation compared to CA1, as confirmed by metabolic labeling of newly synthesized proteins and immunohistochemistry of mRNA translation factors. This easily adoptable platform will expand our understanding of how isoform-specific translation drives brain physiology and disease.