Poly(A) site choice and Pol2 CTD Serine-5 status govern lncRNA control of phosphate-responsive gene expression in fission yeast.

Expression of fission yeast glycerophosphate transporter Tgp1 is repressed in phosphate-rich medium and induced during phosphate starvation. Repression is enforced by transcription of the locus upstream of to produce a long noncoding (lnc) RNA. Here we identify two essential elements of the promoter: a TATA box TATATATA and a HomolD box CAGTCACA, mutations of which inactivate the promoter and de-repress the downstream promoter under phosphate-replete conditions. The lncRNA poly(A) site maps to nucleotide +1636 of the transcription unit, which coincides with the binding site for Pho7 (TCGGACATTCAA), the transcription factor that drives expression. Overlap between the lncRNA template and the promoter points to transcriptional interference as the simplest basis for lncRNA repression. We identify a shorter RNA derived from the locus, polyadenylated at position +508, well upstream of the promoter. Mutating the RNA polyadenylation signal abolishes de-repression of the downstream promoter elicited by Pol2 CTD Ser5Ala phospho-site mutation. Ser5 mutation favors utilization of the short RNA poly(A) site, thereby diminishing transcription of the lncRNA that interferes with the promoter. Mutating the RNA polyadenylation signal attenuates induction of the promoter during phosphate starvation. Polyadenylation site choice governed by CTD Ser5 status adds a new level of lncRNA control of gene expression and reveals a new feature of the fission yeast CTD code.