Recent work elucidating nucleosome positioning in yeast has revealed a common chromatin architecture around TSS’s consisting of a nucleosome covering the TSS, an immediate upstream nucleosome-free region (NFR) of ~140 bp, and a well-positioned nucleosome (‘−1’ nucleosome) on the upstream border of the NFR (7
). Veners et al.
) demonstrated that the −1 nucleosome is evicted upon recruitment of RNA polymerase II. Additionally they showed that a number of chromatin remodeling complexes were selectively associated with the −1 nucleosome. Furthermore, a number of sequence-specific experimentally determined binding sites overlapped the −1 nucleosome. These results support the idea that the positioning of the −1 nucleosome may be strongly regulated.
Here we show that sequence motifs with a strong positional bias within promoter regions cluster almost exclusively ~100–300 bp upstream of the TSS (C). This localization places them in a prime location to regulate or be regulated by the −1 nucleosome, further supporting the idea that positioning of the −1 nucleosome is important in transcriptional regulation.
If CRFs with sequence motifs that exhibit strong positional preferences are modifying the chromatin structure in part to provide specificity to other DBPs, what is the mechanism of action? One possibility is that CRFs remove and/or shift nucleosomes to open up binding sites for other transcriptional regulators. For example, Rap1p, Abf1p and Reb1p are all highly abundant sequence-specific general regulatory factors that bind motifs with a strong preference for promoter regions. There is good evidence that all three play a role in influencing chromatin structure (10
). Additionally, these proteins appear to act in part by creating bubbles of open chromatin (8
). In the case of Rap1p and Abf1p, creating a region of open chromatin appears to facilitate the binding of additional regulatory factors, leading to transcription enhancement (31
). In many cases, Rap1p and Abf1p are unable to activate robust transcription alone (34
) and require additional regulatory factors. Further support is provided by the observation that Rap1p- and Abf1p-binding sites can be substituted for one another without a loss in function (31
However, both Rap1p and Abf1p are involved in many functions, including repression (36–38
). Rap1p initiates a repressive chromatin structure by interacting directly with the chromatin modifying factors Sir3p and Sir4p (37
). Therefore, in addition to making binding sites accessible, it is likely that DBPs whose sequence motifs show a strong positional preference can increase specificity by directly interacting with chromatin modifiers or transcriptional regulators.
A question that immediately presents itself is whether or not the pronounced preference for promoter regions is sufficient to determine specificity. Is the positional distribution sufficient to fully explain binding in vivo
? In a genome-wide location analysis, Lieb et al.
) noted the strongly skewed positional preference of Rap1p-binding motifs and concluded that the positional distribution of potential Rap1p-binding sites may account for much of the specificity in Rap1p binding. However, the skewed positional distribution of these potential binding sites was insufficient in fully explaining the pattern of Rap1p binding. For the case of Rap1p, additional genome-wide mechanisms also appear to be at work.