Suppression of inositol pyrophosphate toxicosis and hyper-repression of the fission yeast
PHO
regulon by loss-of-function mutations in chromatin remodelers Snf22 and Sol1
Authors: Schwer Beate , Innokentev Aleksei , Sanchez Ana M. , Garg Angad , Shuman Stewart 
Published: June 2024

ABSTRACT

Inositol pyrophosphates are signaling molecules that regulate cellular phosphate homeostasis in eukaryal taxa. In fission yeast, where the phosphate regulon (comprising phosphate acquisition genes
pho1
,
pho84
, and
tgp1
) is repressed under phosphate-replete conditions by lncRNA-mediated transcriptional interference, mutations of inositol pyrophosphatases that increase IP
8
levels derepress the
PHO
regulon by eliciting precocious termination of lncRNA transcription. Asp1 pyrophosphatase mutations resulting in too much IP
8
are cytotoxic in YES medium owing to overexpression of glycerophosphodiester transporter Tgp1. IP
8
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
8
toxicity is alleviated by deletion of
snf22
+
, the gene encoding the ATPase subunit of the SWI/SNF chromatin remodeling complex, by an ATPase-inactivating
snf22-
(
D996A-E997A
) allele, and by deletion of the gene encoding SWI/SNF subunit Sol1. Deletion of

snf22
+

hyper-repressed
pho1
expression in phosphate-replete cells; suppressed the
pho1
derepression elicited by mutations in Pol2 CTD, termination factor Seb1, Asp1 pyrophosphatase, and 14-3-3 protein Rad24 (that favor precocious
prt
lncRNA termination); and delayed
pho1
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
tgp1
and
pho1
promoters, but not for the promoters that drive the synthesis of the
PHO
-repressive lncRNAs. Transcription profiling of
snf22
∆ and
snf22-
(
D996A-E997A
) cells identified an additional set of 66 protein-coding genes that were downregulated in both mutants.

IMPORTANCE

Repression of the fission yeast
PHO
genes
tgp1
,
pho1
, and
pho84
by lncRNA-mediated interference is sensitive to inositol pyrophosphate dynamics. Cytotoxic
asp1-STF
alleles derepress the
PHO
genes via the action of IP
8
as an agonist of precocious lncRNA 3′-processing/termination. IP
8
toxicosis is alleviated by mutations of the Pol2 CTD and the 3′-processing/termination machinery that dampen the impact of toxic IP
8
levels on termination. In this study, a forward genetic screen revealed that IP
8
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
PHO
mRNA promoters. Our results implicate the ATP-dependent nucleosome remodeling activity of SWI/SNF as necessary to ensure full access of
PHO
-activating transcription factor Pho7 to its binding sites in the
PHO
mRNA promoters.