Also, as for our UL3 cell analysis, this effect was only seen at promoters and not at other regions of low nucleosome density. Taken together with our observations from UL3 cells, these observations suggest that genomewide changes in nucleosome occupancy near TSSes can occur in response to at least two different stimuli. Furthermore, these changes are unlikely to be artifacts of the nucleosome mapping method, since they can be seen by both microarray and sequencing approaches. At the outset of this study we hypothesized that the recruitment of hSWI/SNF to GR binding sites and GR-regulated promoters might result in discrete changes in nucleosome positions that would activate or repress transcription by allowing or blocking the binding of transcription factors to DNA. By contrast, in UL3 cells we found almost no clear cases of nucleosomes shifting from one position to another after addition of Dex and/or after knock down of the hSWI/SNF ATPase, BRG1. Instead, the most frequently (+)-JQ1 1268524-70-4 observed effect, after 1 hr of Dex treatment, was an increase in the apparent occupancy at already existing nucleosome peaks within,2 kb of transcription start sites. This effect could be seen for specific nucleosomes on individual promoters, as well as on average across all Dex repressed or Dex activated promoters. Surprisingly, a strong increase in average nucleosome occupancy was also seen over the promoters of genes that were not regulated by Dex, an effect that was reproducible in independent samples and could not be explained by differences in MNase digestion or any systematic bias in the microarray analysis. Accordingly, these results suggest that the most prominent effect of GR and Dex on chromatin is to rapidly increase measured nucleosome occupancy on a large fraction of Pol II promoters, apparently genomewide. Given that this effect is seen after only 1 hour of dex treatment, it seems unlikely that it would be due to GR-directed transcriptional activation or repression of a second wave of transcription factors. This is also consistent with studies showing that inhibition of translation via cyclohexamide does not alter the distribution of genes that are upregulated, unregulated and downregulated by a two or four hour incubation with Dex. For Dex-unregulated genes, while there are no known or expected GR binding sites near their promoters, the increased nucleosome occupancy that is observed could potentially be mediated by very long range influences, in cis or even in trans, of GR bound to chromatin. Indeed, recent studies have indicated that more than half of all functional GRBSes are located over 10 kb away from the start site of genes they regulate, and GR and Dex can SAR131675 VEGFR/PDGFR inhibitor mediate dramatic unfolding of large chromatin domains in fluorescence microscopy studies.