Pervasive changes of mRNA splicing in <i>upf1</i> -deficient zebrafish identify <i>rpl10a</i> as a regulator of T cell development

Abstract

The transcriptome of eukaryotic cells is constantly monitored for errors to avoid the production of undesired protein variants. The evolutionarily conserved nonsense-mediated mRNA decay (NMD) pathway degrades aberrant mRNAs, but also functions in the regulation of transcript abundance in response to changed physiological states. Here, we describe a zebrafish mutant of <i>upf1</i>, encoding the central component of the NMD machinery. Fish homozygous for the <i>upf1</i>^{<i>t</i>20450} allele (Y163X) survive until day 10 after fertilization, presenting with impaired T cell development as one of the most conspicuous features of the mutant phenotype. Analysis of differentially expressed genes identified dysregulation of the pre-mRNA splicing pathway, accompanied by perturbed autoregulation of canonical splicing activators (SRSF) and repressors (HNRNP). In <i>upf1</i>-deficient mutants, NMD-susceptible transcripts of ribosomal proteins that are known for their role as noncanonical splicing regulators were greatly increased, most notably, <i>rpl10a</i> When the levels of NMD-susceptible <i>rpl10a</i> transcripts were artificially increased in zebrafish larvae, T cell development was significantly impaired, suggesting that perturbed autoregulation of <i>rpl10a</i> splicing contributes to failing T cell development in <i>upf1</i> deficiency. Our results identify an extraribosomal tissue-specific function to <i>rpl10a</i> in the immune system, and thus exemplify the advantages of the zebrafish model to study the effects of <i>upf1</i>-deficiency in the context of a vertebrate organism.