Within the genomes of metazoans, nucleosomes are highly organised adjacent to the binding sites for a subset of transcription factors. Here we have sought to investigate which chromatin remodelling enzymes are responsible for this. We find that the ATP-dependent chromatin remodelling enzyme SNF2H plays a major role organising arrays of nucleosomes adjacent to the binding sites for the architectural transcription factor CTCF sites and acts to promote CTCF binding. At many other factor binding sites SNF2H and the related enzyme SNF2L contribute to nucleosome organisation. The action of SNF2H at CTCF sites is functionally important as depletion of CTCF or SNF2H affects transcription of a common group of genes. This suggests that chromatin remodelling ATPase’s most closely related to the Drosophila ISWI protein contribute to the function of many human gene regulatory elements.

Regulation of the Saccharomyces cerevisiae HO promoter has been shown to require the recruitment of chromatin-modifying and -remodeling enzymes. Despite this, relatively little is known about what changes to chromatin structure occur during the course of regulation at HO. Here, we used indirect end labeling in synchronized cultures to show that the chromatin structure is disrupted in a region that spans bp ؊600 to ؊1800 relative to the transcriptional start site. Across this region, there is a loss of canonical nucleosomes and a reduction in histone DNA cross-linking, as monitored by chromatin immunoprecipitation. The ATPase Snf2 is required for these alterations, but the histone acetyltransferase Gcn5 is not. This suggests that the SWI/SNF complex is directly involved in nucleosome removal at HO. We also present evidence indicating that the histone chaperone Asf1 assists in this. These observations suggest that SWI/SNF-related complexes in concert with histone chaperones act to remove histone octamers from DNA during the course of gene regulation.The Saccharomyces cerevisiae HO gene encodes an endonuclease that generates a double-stranded break at the matingtype locus that allows the yeast to switch between a and ␣ mating types (53). HO is transcribed transiently during the late G 1 phase only in mother cells, but not in daughter cells (40). As such, it has been considered a paradigm for a developmentally and cell cycle-regulated gene in a relatively simple eukaryote.Considerable progress has been made in defining the order of events that result in HO transcription. They are triggered by the dephosphorylation of the transcription factor Swi5 during late anaphase, which allows it to enter the nucleus (56). The HO promoter contains two binding sites for Swi5 1,300 and 1,800 bp upstream of the transcriptional start site within a region referred to as URS1. Binding of Swi5 and Pho2 to URS1 (8,38) results in the recruitment of the SWI/SNF complex in mother cells (14). In daughter cells, the presence of the repressor Ash1 prevents SWI/SNF recruitment and subsequent stages in the activation of HO (14; reviewed in reference 12). The SAGA histone acetyltransferase complex is also recruited to URS1 and is required for HO transcription (14, 34). Chromatin immunoprecipitation (ChIP) studies suggest that both the SAGA complex itself and histone acetylation spread from URS1 to a second regulatory region,URS2, where the transcription factor SBF is recruited to a series of binding sites in the region from 100 to 700 bp upstream of the transcription start site (14,34). SBF is in turn required for recruitment of the mediator complex and, subsequently, following reactivation of Cdk1, RNA polymerase II (13).The involvement of chromatin-modifying and -remodeling enzymes in the activation of HO raises the possibility that the chromatin structure may be altered. In vitro, SWI/SNF-related complexes have been found to be capable of generating a range of different transitions in chromatin structure. These can involve nucleosome sliding,...

Highlights► The passage of RNA polymerase is intricately coupled with chromatin alterations. ► These include the action of histone chaperones, modifying and remodelling enzymes. ► The interplay between these events is complex involving parallel pathways and feedback loops. ► Overall the process acts to ensure disruption of chromatin during transcription is transient.