Activation and repression mechanisms in yeast.

In eukaryotes, gene expression depends on activator proteins that bind enhancer elements and stimulate transcription by RNA polymerase II (pol II) (Struhl 1995; Zawel and Reinberg 1995). This general requirement for activators is inferred from numerous observations in vivo that intact promoters are much more efficiently transcribed than core promoter derivatives containing only the TATA and initiator elements. The pol II transcript ion machinery is complex and has a molecular weight comparable to that of a ribosome. The pol II machinery is composed of two basic components, TFIID and the pol II holoenzyme. The TFIID complex. which contains the TATA-binding protein (TBP) and TBP-associated factors (TAFs). specifically binds the core promoter re-eion: TBP interacts with high affinity and specif ici tv for TATA elements, whereas certain TAFs can interact u' i th some specif ici ty for ini t iator and downstream elements (Burley and Roeder 1996; Verrijzer and Tjian 1996: Burke and Kadonaga 1997). The pol I I holoenzyme contains the core subunits of the enzyme, basic transcription factors (e.g., TFIIB). as well as Srb. Med, and a variety of other proteins (Koleske and Young 1995: Myers et al. 1998). Activator proteins generally bind their cognate prornoter elements with high specif ici ty and aff ini ty, and thel' can often bind their target sites in the context of nucleosolnal templates, the physiologically relevant substrate (Kingston et al. 1996;Polach and Widom 1996). In contrast, the TBP moiety of the TFIID complex is virtually unable to bind TATA elements in nucleosomal templates, although weak binding is observed when chromatin is disrupted by histone acetylat ion or by nucleosome remodeling (Imbalzano et al. 1994). The pol II holoenzyme does not appear to recognize specif ic DNA sequences, and its association with promoters reflects protein-protein interactions with TFIID and/or activators. Activators contain a DNA-binding domain that specifically recognizes enhancer elements and a physically separate activation domain that stimulates transcription (Struhl 1996; Ptashne and Gann 1991). Activation domains are functional ly autonomous; they retain their functional activity when fused at different positions to a wide variety of heterologous DNA-binding domains and when tethered at different positions in the promoter region. Activation domains can interact directly with many components of the pol II machinery, and they can affect multiple steps in the assembly of an active transcription complex. However, the molecular mechanisms of transcriptional activation in vivo, particularly the physiological significance and relative importance of specific protein-protein interactions and mechanistic steps. remain to be clari f ied. For example, act ivators can interact with TBP or isolated TAFs, but there is no evidence for activator-TAF interactions in the context of TFIID or for activator-TBP interactions when TBP is bound to TATA elements. This paper reviews our efforts to understand the molecular mechanism of transcript ional act ivat ion in yeast. These studies take advantage of the power of yeast genetics and molecular biology. and the experiments are typically performed under conditions where all proteins are present at physiological concentrations, and the DNA template is in the form of chromatin. In addition, we discuss activation and repression mechanisms in which changes in chromatin structure have a direct and active role in transcriptional regulation.