Fig. 2

Unique patterns in the translation efficiency of cell type-specific genes in the brain. a The broad range of translation efficiencies (TEs) across genes expressed in the mouse brain based on ligation-free ribosome profiling. b TEs measured in two different mouse brains with ligation-free ribosome profiling were combined with cell type-specific RNA-Seq data to systematically associate cell type-specific gene expression and TE. We used gene set enrichment analysis (GSEA) to associate gene sets assembled from genes with similar TEs with a ranked list of all genes ordered by cell type-specificity for each cell type in the brain. The resulting heatmaps show the enrichment of genes with different TEs in cell type-specific genes for each cell type. Cell type-specific genes were identified using either RNA-Seq data from sorted populations or RiboTag RNA-Seq data (for Camk2a-expressing neurons). OPC oligodendrocyte precursor cell. c The RiboTag mouse model shows how the Camk2a-RiboTag mouse was generated. This provides an orthogonal means of identifying neuron-specific genes that are actively translated. HA hemagglutinin, IP immunoprecipitation. d Fluorescence imaging shows that Rpl22-HA (from the RiboTag allele) expression is specific to Rbfox3+ (NeuN+) cells (a pan-neuronal marker). e Heatmap of the RiboTag enrichment scores following immunoprecipitation of polysomes from Camk2a-RiboTag mouse brains demonstrates strong enrichment of genes specific to excitatory neurons and depletion of genes specific to other cell types in the brain in two different mouse brains