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

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

PROVIDER: PRJNA563011 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR10038904_1.fastq.gz	Fastqsanger.gz
	SRR10038904_2.fastq.gz	Fastqsanger.gz
	SRR10038905_1.fastq.gz	Fastqsanger.gz
	SRR10038905_2.fastq.gz	Fastqsanger.gz
	SRR10038906_1.fastq.gz	Fastqsanger.gz

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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.

2020-07-13 | GSE136669 | GEO

Pervasive changes of mRNA splicing in <i>upf1</i>-deficient zebrafish identify <i>rpl10a</i> 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. Here, we describe a zebrafish mutant of upf1, encoding the central component of the NMD machinery. Fish homozygous for the upf1 t20450 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 upf1-deficient mutants, NMD-susceptible transcripts of ribosomal proteins that are known for their role as noncanonical splicing regulators were greatly increased, most notably, rpl10a When the levels of NMD-susceptible rpl10a transcripts were artificially increased in zebrafish larvae, 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 extraribosomal 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.

| S-EPMC7354994 | biostudies-literature

Upf1

Project description:Drosophila melanogaster Upf1, Upf1 RNA helicase, is differentially expressed in 11 experiment(s);

| FBgn0030354 | ExpressionAtlas

Upf1

Project description:Drosophila melanogaster Upf1, Upf1 RNA helicase, is expressed in 4 baseline experiment(s);

| FBgn0030354 | ExpressionAtlas

Upf1

Project description:Rattus norvegicus Upf1, UPF1, RNA helicase and ATPase [Source:RGD Symbol;Acc:1589127], is differentially expressed in 1 experiment(s);

| ENSRNOG00000020134 | ExpressionAtlas

Upf1

Project description:Rattus norvegicus Upf1, UPF1, RNA helicase and ATPase [Source:RGD Symbol;Acc:1589127], is expressed in 8 baseline experiment(s);

| ENSRNOG00000020134 | ExpressionAtlas

UPF1

Project description:Sus scrofa UPF1, UPF1 RNA helicase and ATPase [Source:VGNC Symbol;Acc:VGNC:94718], is expressed in 7 baseline experiment(s);

| ENSSSCG00000039301 | ExpressionAtlas

UPF1

Project description:Macaca mulatta UPF1, UPF1 RNA helicase and ATPase [Source:VGNC Symbol;Acc:VGNC:79971], is differentially expressed in 1 experiment(s);

| ENSMMUG00000023286 | ExpressionAtlas

UPF1

Project description:Monodelphis domestica UPF1, UPF1 RNA helicase and ATPase [Source:HGNC Symbol;Acc:HGNC:9962], is expressed in 2 baseline experiment(s);

| ENSMODG00000003689 | ExpressionAtlas

UPF1

Project description:Equus caballus UPF1, UPF1 RNA helicase and ATPase [Source:VGNC Symbol;Acc:VGNC:24804], is expressed in 1 baseline experiment(s);

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