Effects of cadmium and ifg-1 mutant on gene expression and mRNA splicing
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA764774 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR15988011_1.fastq.gz | Fastqsanger.gz | |||
| SRR15988011_2.fastq.gz | Fastqsanger.gz | |||
| SRR15988012_1.fastq.gz | Fastqsanger.gz | |||
| SRR15988012_2.fastq.gz | Fastqsanger.gz | |||
| SRR15988013_1.fastq.gz | Fastqsanger.gz |
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Project description:Splicing of pre-mRNA is an essential process for all eukaryotic dividing cells. Pre-mRNA splicing can be influenced by environmental factors and RNA splicing defects are implicated in numerous human diseases. To understand the genetic mechanism of RNA splicing regulation under environmental stress, we performed a genome-wide RNAi screen in C. elegans and identified suppression of protein synthesis leads to strong protection against cadmium-induced RNA splicing defects. Using a mutant with partial loss of function to the C. elegans ifg-1 gene (eIF4G), we performed RNA-sequencing and found that the levels of cadmium-induced alternative splicing observed in the wildtype is highly reduced in the ifg-1 mutant. Transcriptome analysis revealed ifg-1 mutant moderately up-regulate > 80 genes involved in RNA splicing regulation and depletion of core RNA splicing regulators abolish the ifg-1 long-lived phenotype. A secondary RNAi screen revealed depletion of sma-2 and sma-3 suppresses ifg-1’s protection against stress-induced RNA splicing protection, potentially via transcription of ifg-1 up-regulated RNA splicing regulating genes. Lastly, depletion of sma-2 and sma-3 reduces ifg-1’s long-lived phenotype. Our results propose a model where translation suppression via ifg-1 increases RNA splicing fidelity under stress by upregulating RNA splicing regulatory genes via the sma-2/3 pathway that contributes to its longevity phenotype.
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Project description:RNA undergoes numerous processing steps required for gene expression. Little is known about RNA homeostasis during environmental stress in metazoan cells. By studying regulation of a heavy metal-induced gene named numr-1 in C. elegans, we discovered that disruption of RNA processing acts as a signal for environmental stress. We find that NUMR-1 contains motifs common to RNA splicing factors and regulates RNA splicing in vivo. A genome-wide screen reveals that numr-1 is strongly and specifically induced by silencing of genes that function in basal RNA metabolism including subunits of the metazoan integrator complex. Human integrator processes snRNAs for functioning with splicing factors, and we find that silencing of C. elegans integrator subunits disrupts snRNA processing and causes aberrant pre-mRNA splicing. Cadmium, which also strongly induces numr-1, has the same effects on snRNA processing and pre-mRNA splicing. Lastly, we find that heat shock factor-1 is required for numr-1 induction by cadmium. Our results are consistent with a model in which disruption of integrator processing of RNA acts as a molecular damage signal initiating an adaptive stress response mediated by heat shock factor-1.
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Project description:Analysis of atsf1-2 mutant seedlings for pre-mRNA splicing defect. The atsf1-2 mutant is a homozygous T-DNA insertion line isolated from a SALK line, SALK_062177. Results identify transcripts with altered alternative splicing pattern in the atsf1-2 mutant. We used microarrays to examine the transcriptome profile in the atsf1-2 mutant and identified genes of which transcript levels were changed significantly. Arabidopsis seedlings were grown for 9 days under long day condition. They were then used for RNA extraction and hybridization on Affymetrix ATH1 Genome Array. Three replicates for Col-0 (control) and atsf1-2 (mutant) were compared respectively.
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