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RNA-seq profiling of the Tg(myo6b:GFP-2A-rpl10a-3xHA) zebrafish hair cell IP vs. whole fish IN

ABSTRACT: We have developed and tested the efficiency of the Tg(myo6b:GFP-2A-rpl10a-3xHA) zebrafish to specifically enrich for and evaluate the translatome of inner ear and lateral line sensory hair cells (IP) compared to the whole fish transcriptome (IN). We show through RNA-seq that HA-tagged ribosome immunoprecipitation significantly enriches for RNA transcripts of known zebrafish hair cell expressed transcripts.

ORGANISM(S): Danio rerio

PROVIDER: GSE102861 | GEO | 2018/04/24

REPOSITORIES: GEO

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Pervasive changes of mRNA splicing in upf1 deficient zebrafish identify rpl10a as a regulator of T cell development

Project description: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. As a result of its essential functions, only few animal models of impaired NMD activity have been developed. Here, we describe a zebrafish mutant of upf1, encoding the central component of the NMD machinery. Fish homozygous for the upf1t20450 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 auto-regulation of canonical splicing activators (SRSF) and repressors (HNRNP). In upf1-deficient mutants, NMD-susceptible transcripts of ribosomal proteins that are known for their role as non-canonical splicing regulators were greatly increased, most notably, rpl10a. When the levels of NMD-susceptible rpl10a transcripts were artifically increased in zebrafish morphants, T cell development was significantly impaired, suggesting that perturbed autoregulation of rpl10a splicing contributes to failing T cell development in upf1 deficiency. Our results identify an extra-ribosomal tissue-specific function to rpl10a in the immune system, and thus exemplify the advantages of the zebrafish model to study the effects of upf1-deficiency in the context of a vertebrate organism.

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Whole-genome hypothalamic transcriptome data collected from wild-type and ob/ob Pdyn-eGFP-RPL10a mice using BAC TRAP procedure

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Pervasive changes of mRNA splicing in upf1 deficient zebrafish identify rpl10a as a regulator of T cell development

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Project description:Ethanol induced transcriptional and translational changes in Aldh1l1-EGFP/Rpl10a cortical astrocyte cultures

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