Ssu72 associates with RNA polymerase II preinitiation and early elongation complexes but is inactivated when the transcript reaches 28 nt
The RNA polymerase II (Pol II) C-terminal domain (CTD) is composed of many imperfect repeats of the heptad YSPTSPS and is specifically modified by multiple kinases and phosphatases throughout the transcription cycle. These modifications are essential in the proper recruitment of transcription factors and for the proper transitions in the transcription cycle. During initiation Ser5 and Ser7 are heavily phosphorylated by CDK7 and these phosphates are gradually removed during transcription. There seems to be multiple phosphatases responsible for this removal, which indicates possible redundancies in its regulation. Here, we characterize an early acting phosphatase that we have previously shown to be associated with early elongation complexes as Ssu72. We show that Ssu72 is capable of associating with Pol II pre-initiation complexes (PICs) and that its dissociation is triggered by RNA strand extension prior to pausing. Thus, we show that Ssu72’s primary role in early transcription is to modulate the phosphorylation status of Pol II in the PIC.