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The carboxyl-terminal domain (CTD) of RNA polymerase II consists of tandem repeats of heptapeptide Y 1 S 2 P 3 T 4 S 5 P 6 S 7 . The CTD recruits proteins that drive or regulate gene expression. The trafficking of CTD-interacting proteins is orchestrated by remodeling CTD primary structure via Ser/Thr/Tyr phosphorylation and proline  cis-trans  isomerization, which collectively inscribe a CTD code. The fission yeast CTD consists of 29 repeats. To decipher the output of the fission yeast CTD code, we manipulated CTD length and amino acid content and gauged effects of these changes on gene expression. Whereas deleting 11 heptads has no effect on yeast growth, RNA-seq revealed that 25% of protein-coding transcripts were dysregulated. We profiled the transcriptomes of full-length CTD mutants, in which: all Tyr1 residues were replaced by Phe; all Ser2, Thr4, or Ser7 positions were changed to Ala; and half of the essential CTD code “letters” Pro3, Ser5, and Pro6 were mutated to Ala. Overlapping RNA-seq profiles suggested that a quarter of the up-regulated mRNAs and half of the down-regulated mRNAs seen in full-length CTD mutants might be attributable to a decrement in wild-type heptad number. Concordant mutant-specific profiles were observed for  Y1F ,  S2A , and  T4A  cells, and for  P6•P6A  and  S5•S5A  cells, suggesting that Tyr1–Ser2–Thr4 and Ser5–Pro6 comprise distinct “words” in the CTD code. The phosphate regulon, which is repressed by lncRNA-mediated transcription interference, is de-repressed by CTD mutations  P6•P6A  and  S5•S5A.  De-repression of  pho1  in  P6•P6A  and  S5•S5A  cells depends on cleavage and polyadenylation factor subunits Swd22 and Ppn1 and termination factor Rhn1, signifying that Pro6 and Ser5 mutations elicit precocious lncRNA 3′-processing/termination.

Transcriptional profiling of fission yeast RNA polymerase II CTD mutants