Punctuation and syntax of the RNA polymerase II CTD code in fission yeast

Abstract

The primary structure and phosphorylation pattern of the tandem Y(1)S(2)P(3)T(4)S(5)P(6)S(7) repeats of the RNA polymerase II carboxyl-terminal domain (CTD) convey information about the transcription apparatus--a CTD code--to a large ensemble of CTD-binding receptor proteins. Four of the seven coding "letters" of the fission yeast CTD (Tyr1, Pro3, Ser5, Pro6) are essential in vivo, but the grammatical rules of the code are obscure. Here we show that the minimal fission yeast CTD coding unit is a decapeptide Y(1)S(2)P(3)T(4)S(5)P(6)S(7)Y(1)S(2)P(3) and the spacing between coding units is flexible; the coding unit must contain two Tyr1 residues and the spacing between consecutive tyrosines is important; Ser5-PO(4)-Pro6 comprises an essential two-letter code "word" that is read by the mRNA capping apparatus; and a threshold number of Ser5-PO(4)-Pro6 words are needed to comprise a readable "sentence" of CTD information. Bypassing the essentiality of the Ser5 and Pro6 letters by fusion of capping enzymes to the CTD helped reveal how CTD phosphorylation circuits are wired in vivo. We found that the Ser2-PO(4) mark is independent of Ser5, Pro6, Ser7, and Thr4, whereas the Ser5-PO(4) mark is independent of Ser2, Ser7, and Thr4. These results provide unique insights to the reading and writing of the CTD code.