Suppression of inositol pyrophosphate toxicosis and hyper-repression of the fission yeast regulon by loss-of-function mutations in chromatin remodelers Snf22 and Sol1.

Inositol pyrophosphates are signaling molecules that regulate cellular phosphate homeostasis in eukaryal taxa. In fission yeast, where the phosphate regulon (comprising phosphate acquisition genes , , and ) is repressed under phosphate-replete conditions by lncRNA-mediated transcriptional interference, mutations of inositol pyrophosphatases that increase IP levels derepress the regulon by eliciting precocious termination of lncRNA transcription. Asp1 pyrophosphatase mutations resulting in too much IP are cytotoxic in YES medium owing to overexpression of glycerophosphodiester transporter Tgp1. IP toxicosis is ameliorated by mutations in cleavage/polyadenylation and termination factors, perturbations of the Pol2 CTD code, and mutations in SPX domain proteins that act as inositol pyrophosphate sensors. Here, we show that IP toxicity is alleviated by deletion of , the gene encoding the ATPase subunit of the SWI/SNF chromatin remodeling complex, by an ATPase-inactivating () allele, and by deletion of the gene encoding SWI/SNF subunit Sol1. Deletion of hyper-repressed expression in phosphate-replete cells; suppressed the derepression elicited by mutations in Pol2 CTD, termination factor Seb1, Asp1 pyrophosphatase, and 14-3-3 protein Rad24 (that favor precocious lncRNA termination); and delayed induction during phosphate starvation. RNA analysis and lack of mutational synergies suggest that Snf22 is not impacting 3'-processing/termination. Using reporter assays, we find that Snf22 is important for the activity of the and promoters, but not for the promoters that drive the synthesis of the -repressive lncRNAs. Transcription profiling of ∆ and () cells identified an additional set of 66 protein-coding genes that were downregulated in both mutants.IMPORTANCERepression of the fission yeast genes , , and by lncRNA-mediated interference is sensitive to inositol pyrophosphate dynamics. Cytotoxic alleles derepress the genes via the action of IP as an agonist of precocious lncRNA 3'-processing/termination. IP toxicosis is alleviated by mutations of the Pol2 CTD and the 3'-processing/termination machinery that dampen the impact of toxic IP levels on termination. In this study, a forward genetic screen revealed that IP toxicity is suppressed by mutations of the Snf22 and Sol1 subunits of the SWI/SNF chromatin remodeling complex. Genetic and biochemical evidence indicates that the SWI/SNF is not affecting 3'-processing/termination or lncRNA promoter activity. Rather, SWI/SNF is critical for firing the mRNA promoters. Our results implicate the ATP-dependent nucleosome remodeling activity of SWI/SNF as necessary to ensure full access of -activating transcription factor Pho7 to its binding sites in the mRNA promoters.