The Ssu72 phosphatase mediates the RNA polymerase II initiation-elongation transition

Transitions between the different stages of the RNAPII transcription cycle involve the recruitment and exchange of factors, including mRNA capping enzymes, elongation factors, splicing factors, 3'-end-processing complexes, and termination factors. These transitions are coordinated by the dynamic phosphorylation of the C-terminal domain (CTD) of the largest subunit of RNAPII (Rpb1). The CTD is composed of reiterated heptapeptide repeats (Y(1)S(2)P(3)T(4)S(5)P(6)S(7)) that undergo phosphorylation and dephosphorylation as RNAPII transitions through the transcription cycle. An essential phosphatase in this process is Ssu72, which exhibits catalytic specificity for Ser(P)(5) and Ser(P)(7). Ssu72 is unique in that it is specific for Ser(P)(5) in one orientation of the CTD and for Ser(P)(7) when bound in the opposite orientation. Moreover, Ssu72 interacts with components of the initiation machinery and affects start site selection yet is an integral component of the CPF 3'-end-processing complex. Here we provide a comprehensive view of the effects of Ssu72 with respect to its Ser(P)(5) phosphatase activity. We demonstrate that Ssu72 dephosphorylates Ser(P)(5) at the initiation-elongation transition. Furthermore, Ssu72 indirectly affects the levels of Ser(P)(2) during the elongation stage of transcription but does so independent of its catalytic activity.