Extended Data Fig. 3: Ribosome profiling of SMN-primed ribosomes reveals enriched mRNAs organized in functionally well-defined communities.
From: SMN-primed ribosomes modulate the translation of transcripts related to spinal muscular atrophy
a, Examples of immunoprecipitation of SMN-ribosomes from ribo-pellet in control mouse brain lysates after RNaseI treatment. RPL26 was used as control. The experiment was repeated independently three times. b, Transcript types enriched in fragments protected by SMN-primed ribosomes that protect predominantly RNAs associated with protein coding genes. c, Venn diagram showing the intersection of SMN-specific protein coding transcripts covered by short (24–26 nucleotides) and long (32–34 nucleotides) reads. d, Percentage of P-sites according to the three reading frames for the first five codons of the CDSs and for the remaining region of the sequences. A clear trinucleotide periodicity in the correct frame is detectable only at the beginning of the coding sequence. Results are shown as the average ± SEM among n=3 biologically independent samples. The statistical significance from two-sided t-test comparing frames 1 and 2 with respect to frame 0 are reported. e, Representative RPF coverage tracks for SMN-specific transcripts in SMN-specific RiboSeq. The average normalized coverage and the standard error among replicates are represented in each profile. The structure of the transcript, showing the boundaries of CDS and UTR regions, is outlined below each profile. f, Over-representation of tissue-specific markers among genes enriched in SMN-primed ribosomes. Tissues where SMN levels were previously measured are displayed. The enrichment score was calculated with enrichR. g, Gene ontology and pathway enrichment analysis of genes enriched in SMN-primed ribosomes. The number of genes is displayed on the right of the bars. (GO_BP:biological process, GO_CC:cellular component, GO_MF: molecular function). h, Comparative annotation enrichment analysis of transcripts belonging to the seven SMN-specific communities. The heatmaps are colored according to the significance of the enrichments. The analysis was performed on Gene Ontology terms: Biological Process (left) and cellular component (right). Statistical source data and unprocessed blots are provided in Source data Extended data Fig. 3.
