Preferential accessibility of the yeast his3 promoter is determined by a general property of the DNA sequence, not by specific elements

Yeast promoter regions are often more accessible to nuclear proteins than a re nonpromoter regions. As assayed by HinfI endonuclease cleavage in living yeast cells, HinfI sites located in the promoters of all seven genes teste d were 5- to 20-fold more accessible than sites in adjacent nonpromoter reg ions. HinfI hypersensitivity within the his3 promoter region is locally det ermined, since it was observed when this region a-as translocated to the mi ddle of the ade2 structural gene. Detailed analysis of the his3 promoter in dicated that preferential accessibility is not determined by specific eleme nts such as the Gcn4 binding site, poly(dA-dT) sequences, TATA elements, or initiator elements or by transcriptional activity. However, progressive de letion of the promoter region in either direction resulted in a progressive loss of HinfI accessibility. Preferential accessibility is independent of the Swi-Snf chromatin remodeling complex, Gcn5 histone acetylase complexes Ada and SAGA and Rad6, which ubiquitinates histone H2B. These results sugge st that preferential accessibility of the his3 (and presumably other) promo ter regions is determined by a general property of the DNA sequence (e.g., base composition or a related feature) rather than by defined sequence elem ents. The organization of the compact yeast genome into inherently distinct promoter and nonpromoter regions may ensure that transcription factors bin d preferentially to appropriate sites in promoters rather than to the exces s of irrelevant but equally high-affinity sites in nonpromoter regions.