biostudies-literatureWeber RSwiss National Science FoundationEuropean Research Council638-650https://www.ebi.ac.uk/biostudies/studies/S-EPMC9957725biostudies-literatureUnknown42(9)Transcriptional and translational control are key determinants of gene expression, however, to what extent these two processes can be collectively coordinated is still poorly understood. Here, we use Nanopore long-read sequencing and cap analysis of gene expression (CAGE-seq) to document the landscape of 5' and 3' untranslated region (UTR) isoforms and transcription start sites of epidermal stem cells, wild-type keratinocytes and squamous cell carcinomas. Focusing on squamous cell carcinomas, we show that a small cohort of genes with alternative 5'UTR isoforms exhibit overall increased translational efficiencies and are enriched in ribosomal proteins and splicing factors. By combining polysome fractionations and CAGE-seq, we further characterize two of these UTR isoform genes with identicaOncogeneMonitoring the 5'UTR landscape reveals isoform switches to drive translational efficiencies in cancer.PMC9957725176825759006Bernasconi MSpies DDure COrmiston MRenz PFYamahachi HSendoel ATaborsky DGhoshdastider UValdivia-Francia FForny MYigit MWeber RfalseMonitoring the 5'UTR landscape reveals isoform switches to drive translational efficiencies in cancer.Transcriptional and translational control are key determinants of gene expression, however, to what extent these two processes can be collectively coordinated is still poorly understood. Here, we use Nanopore long-read sequencing and cap analysis of gene expression (CAGE-seq) to document the landscape of 5' and 3' untranslated region (UTR) isoforms and transcription start sites of epidermal stem cells, wild-type keratinocytes and squamous cell carcinomas. Focusing on squamous cell carcinomas, we show that a small cohort of genes with alternative 5'UTR isoforms exhibit overall increased translational efficiencies and are enriched in ribosomal proteins and splicing factors. By combining polysome fractionations and CAGE-seq, we further characterize two of these UTR isoform genes with identica2023-01-01T00:00:00Z2023 Feb2026-05-28T17:47:39.451Z2024-11-08T20:27:12.441ZS-EPMC99577253655036010.1038/s41388-022-02578-2