Poly(A) site choice and Pol2 CTD Serine-5 status govern lncRNA control of phosphate-responsive  tgp1  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  nc-tgp1  locus upstream of  tgp1  to produce a long noncoding (lnc) RNA. Here we identify two essential elements of the  nc-tgp1  promoter: a TATA box  -30 TATATATA -23  and a HomolD box  -64 CAGTCACA -57 , mutations of which inactivate the  nc-tgp1  promoter and de-repress the downstream  tgp1  promoter under phosphate-replete conditions. The  nc-tgp1  lncRNA poly(A) site maps to nucleotide +1636 of the transcription unit, which coincides with the binding site for Pho7 ( 1632 TCGGACATTCAA 1643 ), the transcription factor that drives  tgp1  expression. Overlap between the lncRNA template and the  tgp1  promoter points to transcriptional interference as the simplest basis for lncRNA repression. We identify a shorter RNA derived from the  nc-tgp1  locus, polyadenylated at position +508, well upstream of the  tgp1  promoter. Mutating the  nc-tgp1-short  RNA polyadenylation signal abolishes de-repression of the downstream  tgp1  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  tgp1  promoter. Mutating the  nc-tgp1-short  RNA polyadenylation signal attenuates induction of the  tgp1  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.
Sanchez AM, Shuman S, Schwer B