PUBLICATION

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

Authors

Lawir, D.F., Sikora, K., O'Meara, C.P., Schorpp, M., Boehm, T.

ID

ZDB-PUB-200624-5

Date

2020

Source

Proceedings of the National Academy of Sciences of the United States of America 117(27): 15799-15808 (Journal)

Registered Authors

Boehm, Tom, Schorpp, Michael

Keywords

NMD, evolution, ribosomal protein, thymus

Datasets

GEO:GSE136669

MeSH Terms

Codon, Nonsense/genetics
Animals
Fertilization/genetics
Humans
Zebrafish Proteins/genetics*
RNA Splicing/genetics*
T-Lymphocytes/immunology*
Gene Expression Regulation, Developmental/genetics
Glutathione/analogs & derivatives*
Glutathione/genetics
Zebrafish/genetics
Transcription Factors/genetics
Nonsense Mediated mRNA Decay/genetics*
Nonsense Mediated mRNA Decay/immunology
Transcriptome/genetics
RNA-Binding Proteins/genetics*
Homozygote
RNA, Messenger/genetics

(all 18)

PubMed

32571908 Full text @ Proc. Natl. Acad. Sci. USA

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 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.

Genes / Markers

Figures

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Expression

Gene	Fish	Conditions	Stage	Anatomy	Assay	Figure
rag1	tnpo3^{t22074/t22074}	standard conditions	Day 5	thymus	ISH	Fig. 4
rag1	tnpo3^{t22074/t22074}; upf1^{t20450/t20450}	standard conditions	Day 5	thymus	ISH	Fig. 4
rag1	upf1^{t20450/t20450}	standard conditions	Day 5	thymus	ISH	Fig. 4
rag1	upf1^{t20450/t20450}	standard conditions	Day 5	thymus	ISH	Fig. 1
rag1	WT	standard conditions	Day 5	thymus	ISH	Fig. 4
rag1	WT	standard conditions	Day 5	thymus	ISH	Fig. 1
rag1	WT	standard conditions	Day 5	thymus	ISH	Fig. 5
rag1	WT + MO3-rpl10a	standard conditions	Day 5	thymus	ISH	Fig. 5
smg1	upf1^{t20450/t20450}	standard conditions	Day 5	whole organism	RNA-Seq	Fig. 1
smg1	WT	standard conditions	Day 5	whole organism	RNA-Seq	Fig. 1

1 - 10 of 20

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Phenotype

Fish	Conditions	Stage	Phenotype	Figure
WT + MO3-rpl10a	standard conditions	Day 5	thymus rag1 expression decreased amount, abnormal	Fig. 5
tnpo3^{t22074/t22074}	standard conditions	Day 5	T cell differentiation in thymus disrupted, abnormal	Fig. 4
tnpo3^{t22074/t22074}	standard conditions	Day 5	thymus rag1 expression decreased amount, abnormal	Fig. 4
tnpo3^{t22074/t22074}; upf1^{t20450/t20450}	standard conditions	Day 5	T cell differentiation in thymus disrupted, exacerbated	Fig. 4
tnpo3^{t22074/t22074}; upf1^{t20450/t20450}	standard conditions	Day 5	thymus rag1 expression decreased amount, abnormal	Fig. 4
upf1^{t20450/t20450}	standard conditions	Day 5	T cell differentiation in thymus disrupted, abnormal	Fig. 4
upf1^{t20450/t20450}	standard conditions	Day 5	thymus rag1 expression decreased amount, abnormal	Fig. 1
upf1^{t20450/t20450}	standard conditions	Day 5	thymus rag1 expression decreased amount, abnormal	Fig. 4
upf1^{t20450/t20450}	standard conditions	Day 5	whole organism smg1 expression increased amount, abnormal	Fig. 1
upf1^{t20450/t20450}	standard conditions	Day 5	whole organism smg5 expression increased amount, abnormal	Fig. 1

1 - 10 of 16

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Mutations / Transgenics

Allele	Type	Affected Genomic Region
fr100	Point Mutation	lsm8
t20450	Point Mutation	upf1
t22074	Point Mutation	tnpo3
t26426	Point Mutation	snapc3
t26683	Point Mutation	rag1
zdf1	Point Mutation	tp53

1 - 6 of 6

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Human Disease / Model

Sequence Targeting Reagents

Target	Reagent	Reagent Type
rpl10a	MO3-rpl10a	MRPHLNO
upf1	MO3-upf1	MRPHLNO

Fish

Fish
tnpo3^{t22074/t22074}
tnpo3^{t22074/t22074}; upf1^{t20450/t20450}
upf1^{t20450/t20450}
WT
WT + MO3-rpl10a

Antibodies

Name	Type	Antigen Genes	Isotypes	Host Organism
Ab1-upf1	polyclonal		IgG	Goat

Orthology

Engineered Foreign Genes

Mapping

Lawir et al., 2020 ZDB-PUB-200624-5 PMID:32571908

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

Lawir et al., 2020

ZDB-PUB-200624-5
PMID:32571908