Fig. 5: In the retina MSI1 binds to UAG motifs located predominantly in introns and 3'-UTRs.

a Distribution of MSI1 binding sites as identified by eCLIP-Seq on mouse retinal samples across mRNA features. b eCLIP crosslink frequency relative to the top scoring motif (BUAG) identified by DREME. c UCSC Genome browser tracks showing the eCLIP-seq signal enrichment over the 3'-UTR of the Gnat1 gene (orange box). Replicates are stacked and indicated by different shading colors. Scales are 0 to −1155 for the eCLIP IP and 0 to −24 for the eCLIP input. d RNA binding protein map showing MSI1 binding relative to an alternative metaexon. Exons upregulated by the Musashi proteins (downregulated in the Msi1/Msi2 double knockout) are shown in red, exons downregulated by the Musashi proteins are shown in blue and alternative exons remaining unchanged in the knockout are shown in black. Gray shading indicates the 99.5% confidence interval derived from 1000 random permutations. MSI1 binding sites are enriched downstream of alternative exons upregulated by the Musashi proteins. e UCSC Genome browser tracks showing MSI1 binding (orange box) downstream of an alternative exon in the Prom1 gene regulated by the Musashi proteins (green box). RNA-Seq tracks show the read density for retinal samples derived from photoreceptor-specific Msi1/Msi2 double knockouts and matched controls. Replicates are stacked and indicated by different shading colors. Scales are 0 to −5.5 for the eCLIP IP and 0 to −1.3 for the eCLIP input.