Transcription is regulated by myriad mechanisms, many of which affect RNA polymerase II (Pol II) preinitiation complex (PIC) assembly. Although there is an increasing appreciation of the diversity and specialization in PIC organization [
1], the general transcription factor (GTF) TATA-binding protein (TBP) has a widespread and crucial role in this process. TBP alone can support PIC formation on TATA-box-containing promoters, whereas TBP-associated factors (TAFs) are also typically required for TATA-less transcription [
1]. How is TBP distributed among different types of promoters? What factors regulate its distribution and activity? Two new papers [
2,
3] employ complementary approaches to advance our understanding of how the activity of this crucial transcription apparatus component is regulated.
TBP is a saddle-shaped molecule, the binding of which to TATA-box DNA establishes an extensive hydrophobic protein–DNA interface of exceptional stability [
4], thus, providing the protein–DNA platform required for assembly of a functional PIC. However, the extraordinarily long half-times for dissociation of TBP–DNA complexes measured
in vitro (15 min to 1 hr or more; [
5]) indicate that active mechanisms must be in place to ensure that TBP interacts with chromatin
in vivo on time scales appropriate for rapid gene regulation. The problem is potentially acute because TBP binds with high affinity to a variety of DNA sequences [
4] and, yet, numerous nonspecific sites would limit the available TBP pool. TBP binding to fortuitous sites within promoters could also inhibit PIC formation sterically.
Consistent with a role in initiating PIC assembly, many factors function by modulating TBP recruitment or activity. Although there are many interesting examples of transcriptional regulators that affect TBP function in gene-specific ways, here, I focus on modifier of transcription 1 (Mot1) and negative cofactor 2 (NC2), two regulators that have global effects on TBP activity. Mot1 is a member of the Snf2/Swi2 ATPase family that uses ATP hydrolysis to displace TBP from DNA [
6]. In yeast, the robust catalytic activity of Mot1 is responsible for the highly dynamic behavior of virtually the entire TBP pool [
7]. NC2 is a TBP-binding heterodimer with different activities. It was originally identified biochemically as a factor that blocks PIC assembly subsequent to TBP–DNA binding [
8]. More recently, it was discovered that NC2 permits TBP relocalization along the DNA contour, an activity consistent with the architecture of the NC2–TBP–DNA complex, which resembles a clamp encircling DNA [
9]. Individual NC2 subunits might also have separate functions, but this is not as well understood [
3].
The biochemical activities of Mot1 and NC2 indicate roles as global transcriptional repressors () and, indeed, genetic and genome-wide expression analyses in yeast support the notion that both factors can function in this way [
10–
14]. However, both factors also have global roles in gene activation that were unanticipated from biochemical analyses [
11–
16]. Two general models can explain how Mot1 and NC2 activate gene expression (). The first posits that the known biochemical activities of these factors can activate and repress transcription. Notably, Mot1-mediated TBP–DNA dissociation could ensure that a sufficient pool of free TBP is available for nucleating PIC formation; alternatively, removal of inactive, kinetically trapped forms of TBP might be essential to clear promoters for subsequent assembly of functional PICs [
17,
18]. NC2 might activate gene expression by transiently stabilizing weak TBP–DNA interactions [
19] or by funneling TBP to core promoters by catalyzing diffusion along DNA. All of these ideas posit that Mot1 and NC2 form transcriptionally inactive complexes with TBP and that they foster gene activation indirectly by modulating TBP dynamic behavior. A second general model is that Mot1 and NC2 have novel activities in gene activation. Intriguingly, some evidence points to direct roles for Mot1 in gene activation [
20,
21], although such mechanisms have not been elucidated in molecular detail.
The publisher's final edited version of this article is available at 
binding protein: linchpin of the RNA polymerase II preinitiation complex
