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Effect of depletion of Sas10 on zebrafish gene expression at 5 days post fertilization

ABSTRACT: In yeast, Upt3 overexpression caused a de-repression of the silenced genes at different loci, suggesting Utp3 might be involved in regulating gene expression. To this end, we extracted total RNA from the WT and sas10 (zebrafish homolg of yeast utp3) embryos, three biological repeats each, at 5dpf and carried out an RNA-seq analysis. Comparing the gene expression between the WT and sas10 using DESeq2 identified a total of 8574 differentially expressed genes (DEGs), including 4457 downregulated and 4117 upregulated DEGs in the sas10 mutant (criteria adopted: TPM>5 in at least one replicate, fold-change more than 1.5, p-adjust <0.05). We found that 150 out of 308 liver- and 185 out of 385 intestine-specific genes were identified to be among the downregulated DEGs. GO analysi of upregulated genes showed that these genes are related to protein transport and ribosome biogenesis and function. 64 genes encoding the SSU processome proteins, including wdr36, utp6, tbl3, pwp2h, and utp18 of the UTP-B genes, together with 17 genes encoding the RNA exosome proteins essential for ribosome biogenesis, including mtr4 and dis3 of the RNA Mtr4-exosome genes, were among the upregulated genes in sas10 mutant. By salmon we compared the expression levle of different regions across pre-rRNA transcript, and found that 18S rRNA was significantly decreased, and no obvious difference was observed for ITS1, 5.8S rRNA and 28S rRNA, while 5’ETS and ITS2 was significantly and drastically elevated.

ORGANISM(S): Danio rerio

PROVIDER: GSE244191 | GEO | 2024/09/18

REPOSITORIES: GEO

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