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 (Y¹S²P³T⁴S⁵P⁶S⁷) 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.Wedemonstrate 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.