RNA Polymerase II Holoenzymes and Subcomplexes*

The RNA polymerase II holoenzyme is the form of eukaryotic RNA polymerase II that is recruited to the promoters of proteincoding genes in living cells. The exact composition of the holoenzyme is not entirely established, due in part to technical difficulties associated with purifying intact megadalton size multiprotein complexes. Nonetheless, yeast and human holoenzyme preparations have been described that consist of near stoichiometric levels of most components known to be generally involved in initiation other than TATA-binding protein (TBP) and its associated factors. We review here the functions of five major components of yeast RNA polymerase II holoenzymes: core RNA polymerase II, the general transcription factors (GTFs), the core Srb-mediator complex, the Srb10 cyclin-dependent kinase (CDK) complex, and the Swi-Snf complex (Table I). The holoenzyme concept stems from the discovery that Srb proteins are critical for regulated transcription of protein coding genes and the observation that these proteins are tightly associated with a portion of core RNA polymerase II in yeast cells (1). The genes encoding the yeast Srb proteins were discovered through a genetic screen designed to identify components of the transcription apparatus that are involved in the response to transcriptional regulators (2, 3). Attempts to purify these proteins led to the isolation of a large complex containing core RNA polymerase II, a subset of the general transcription factors, and a variety of regulatory proteins (1). This holoenzyme complex had the capacity to initiate transcription and respond to activators when supplemented with additional purified general transcription factors in vitro. A subcomplex dissociated from the holoenzyme, which contains the Srb and additional proteins, reconstituted the response to activators in a defined in vitro transcription system (4). The response to activators is especially significant as in vitro systems reconstituted with yeast GTFs and polymerase alone are not activator-responsive (5, 6). Two of the yeast Srb proteins were found to be required for transcription of most protein-coding genes, and because they are found tightly associated with the holoenzyme, it seems likely that the Srb-containing holoenzyme is the form of RNA polymerase II that is recruited to most promoters in vivo (7). RNA polymerase II holoenzymes have been purified from many eukaryotic organisms (1, 4, 8–16). The subunit composition of these different preparations differs somewhat, and these differences involve the presence or absence of two types of components: GTFs and regulatory factors. Some protocols lead to the purification of RNA polymerase II holoenzymes containing all of the GTFs (8, 9, 14), whereas other protocols generate holoenzymes in which only a single GTF (TFIIF) remains associated (4). Some yeast holoenzyme preparations contain stoichiometric levels of Swi-Snf (17), whereas others lack any detectable Swi-Snf protein (18). In the present discussion, we will make the simplifying assumption that holoenzymes in living cells resemble the more complex preparations. Thus, the holoenzyme we discuss here is composed of core RNA polymerase II, all the GTFs other than TBP (and its associated proteins), the core Srb-mediator complex, the Srb10 cyclin-dependent kinase complex, and the Swi-Snf complex (Table I).