RNA polymerase II CTD interactome with 3′ processing and termination factors in fission yeast and its impact on phosphate homeostasis

Abstract

The carboxy-terminal domain (CTD) code encrypted within the Y ¹S ²P ³T ⁴S ⁵P ⁶S ⁷heptad repeats of RNA polymerase II (Pol2) is deeply rooted in eukaryal biology. Key steps to deciphering the code are identifying the events in gene expression that are governed by individual “letters” and then defining a vocabulary of multiletter “words” and their meaning. Thr4 and Ser7 exert opposite effects on the fission yeast pho1gene, expression of which is repressed under phosphate-replete conditions by transcription of an upstream flanking long noncoding RNA (lncRNA). Here we attribute the derepression of pho1by a CTD -S7Amutation to precocious termination of lncRNA synthesis, an effect that is erased by mutations of cleavage-polyadenylation factor (CPF) subunits Ctf1, Ssu72, Ppn1, Swd22, and Dis2 and termination factor Rhn1. By contrast, a CTD -T4Amutation hyperrepresses pho1, as do CPF subunit and Rhn1 mutations, implying that T4Areduces lncRNA termination. Moreover, CTD -T4Ais synthetically lethal with ppn1∆ and swd22∆, signifying that Thr4 and the Ppn1•Swd22 module play important, functionally redundant roles in promoting Pol2 termination. We find that Ppn1 and Swd22 become essential for viability when the CTD array is curtailed and that S7Aovercomes the need for Ppn1•Swd22 in the short CTD context. Mutational synergies highlight redundant essential functions of ( i) Ppn1•Swd22 and Rhn1, ( ii) Ppn1•Swd22 and Ctf1, and ( iii) Ssu72 and Dis2 phosphatases. CTD alleles Y1F, S2A, and T4Ahave overlapping synthetic lethalities with ppn1∆ and swd22∆, suggesting that Tyr1-Ser2-Thr4 form a three-letter CTD word that abets termination, with Rhn1 being a likely “reader” of this word.