Effects of cadmium and integrator complex knockdown on gene expression and mRNA splicing

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. Overall design: We report the use of mRNA sequencing to analyze the effects of cadmium exposure and integrator complex gene knockdown have on the transcriptome. 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.