Activation of Saccharomyces cerevisiae HIS3 Results in Gcn4p-Dependent, SWI/SNF-Dependent Mobilization of Nucleosomes over the Entire Gene

Abstract

The effects of transcriptional activation on the chromatin structure of the Saccharomyces cerevisiae HIS3 gene were addressed by mapping the precise positions of nucleosomes in uninduced and induced chromatin. In the absence of the Gcn4p activator, the HIS3 gene is organized into a predominant nucleosomal array. In wild-type chromatin, this array is disrupted, and several alternative overlapping nucleosomal arrays are formed. The disruption of the predominant array also requires the SWI/SNF remodeling machine, indicating that the SWI/SNF complex plays an important role in nucleosome mobilization over the entire HIS3 gene. The Isw1 remodeling complex plays a more subtle role in determining nucleosome positions on HIS3, favoring positions different from those preferred by the SWI/SNF complex. Both the SWI/SNF and Isw1 complexes are constitutively present in HIS3 chromatin, although Isw1 tends to be excluded from the HIS3 promoter. Despite the apparent disorder of HIS3 chromatin generated by the formation of multiple nucleosomal arrays, nucleosome density profiles indicate that some long-range order is always present. We propose that Gcn4p stimulates nucleosome mobilization over the entire HIS3 gene by the SWI/SNF complex. We suggest that the net effect of interplay among remodeling machines at HIS3 is to create a highly dynamic chromatin structure.The central role of chromatin structure in gene regulation is currently the subject of intense interest. Much has been learned about the ATP-dependent chromatin remodeling machines, which use the free energy of ATP hydrolysis to move nucleosomes along DNA and alter nucleosome conformation (31), and the histone-modifying enzymes and their complexes. There is also a great deal of information available concerning changes in chromatin structure occurring at various gene promoters (3,20). Because most of the obvious changes in chromatin structure occur at gene promoters, emphasis has been placed on these events, which are clearly of major importance. However, in our high-resolution studies of the chromatin structure of the CUP1 and HIS3 genes of Saccharomyces cerevisiae, we have obtained evidence pointing to more widespread changes in chromatin structure resulting from induction; these changes involve the entire gene and flanking sequences (9, 29). Our observations indicate that, at least for these genes, chromatin remodeling is not confined to the promoter but occurs on the scale of a chromatin domain.It is now apparent that ATP-dependent chromatin remodeling machines can be grouped into several functional classes (2). One class includes the SWI/SNF and RSC complexes, which are capable of mobilizing nucleosomes and driving a conformational change in the nucleosome to create the remodeled state (24,31). A second class is defined by the ISWI group of complexes, exemplified in budding yeast by the Isw1 and Isw2 complexes, which are capable of mobilizing nucleosomes to create arrays with characteristic spacing but cannot remodel nucleosome structure (19,39). A third class of com...

A SWI/SNF- and INO80-dependent nucleosome movement at the INO1 promoter

“…The INO1 ORF and its promoter are organized into a set of well-positioned overlapping nucleosomes during repressing conditions. Such overlapping chromatin structures were also observed in other genes such as CUP1 (28,35) and HIS3 (36). It is interesting to observe overlapping positions under repressing conditions.…”

“…This differs from previous observations in other genes. For example, in HIS3, both SWI/SNF and ISW1 act synergistically in induction (36). The ISW1 complex plays a more subtle role in nucleosome mobilization over HIS3, favoring positions different from those preferred by SWI/SNF.…”

Chromatin-dependent Transcription Factor Accessibility Rather than Nucleosome Remodeling Predominates during Global Transcriptional Restructuring in Saccharomyces cerevisiae

“…Consistent with this notion, several examples have been reported in which gene induction involves recruitment to a promoter of chromatin remodeling factors and histone modifying activities designed to remove or reposition a nucleosome to allow access to an otherwise masked transcription factor binding site (Li et al, 2007;Williams and Tyler, 2007). For example, remodeling factors act at the above-mentioned promoters for PHO5, GAL1, CUP1, and SUC2 to facilitate nucleosome loss on transcriptional activation and conversely to assemble or stabilize nucleosomes on the gene promoter during transcriptional repression (Almer et al, 1986;Fedor and Kornberg, 1989;Shen et al, 2001;Kim et al, 2006).…”

“…Consistent with this notion, several examples have been reported in which gene induction involves recruitment to a promoter of chromatin remodeling factors and histone modifying activities designed to remove or reposition a nucleosome to allow access to an otherwise masked transcription factor binding site (Li et al, 2007;Williams and Tyler, 2007). For example, remodeling factors act at the above-mentioned promoters for PHO5, GAL1, CUP1, and SUC2 to facilitate nucleosome loss on transcriptional activation and conversely to assemble or stabilize nucleosomes on the gene promoter during transcriptional repression (Almer et al, 1986;Fedor and Kornberg, 1989;Shen et al, 2001;Kim et al, 2006).Chromatin can also play a more passive role in gene regulation by simply controlling which transcription factor binding sites are available for participation in gene regulation. Recent genome-wide studies of nucleosome positioning found that most yeast promoters contain an extended nucleosome-depleted region (NDR) that is enriched for transcription factor binding sites (Lee et al, 2004;Yuan et al, 2005;Lee et al, 2007;Mavrich et al, 2008;Shivaswamy et al, 2008).…”

Activator-dependent recruitment of SWI/SNF and INO80 during INO1 activation

“…These remodelers hydrolyze ATP to alter the contacts between histone octamers and DNA, resulting in nucleosome movement. The effects of individual remodelers on certain genes have been extensively characterized [5][6][7][8]. However, it is becoming clear that the regulation of some, if not all yeast genes, including HIS3 [7] and INO1 [8], requires more than one remodeler.…”