Effects of cadmium and ifg-1 mutant on gene expression and mRNA splicing

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. Total RNA was prepared from gravid young adult Caenorhabditis elegans with three biological replicates per group and sent to NovoGene for PE150 sequencing. Sequencing library were constructured with oligo-dT enrichment. Gene expression data were analyzed by DEGSeq with Alternative splicing data analyzed by rMATS.