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DamID chromatin profiling in Kc cells ( Greil et?al., 2006; Orian et?al., 2009) revealed that UpSET binds to??3,500 regions genome-wide and overlaps with gene-rich regions ( Figures 2A�C2C, and S2A), corresponding to ?6,000 genes. These results are consistent with the broad presence of UpSET observed on polytene chromosomes ( Figures 1F�C1H). Recently, several different chromatin states have been characterized in the Drosophila genome by profiling the binding of 53 [http://en.wikipedia.org/wiki/Bumetanide Bumetanide] different proteins ( Filion et?al., 2010), as well as histone modifications, transcription factor binding, and/or gene expression ( modENCODE Consortium et?al., 2010). To determine whether UpSET associates with specific chromatin states, we examined the UpSET DamID-signal distribution for each regulatory region described by the modENCODE consortium. DamID signal distribution over each chromatin state showed a preferential recruitment of UpSET to TSS/promoter regions (p?[http://www.selleckchem.com/products/abt-199.html selleck chemicals llc] see Extended Experimental Procedures). Analyses of UpSET enrichment in five chromatin types defined by Filion et?al. revealed a similarly high overlap with active regions ( Figure?S2B). Thus, UpSET is preferentially targeted to active promoter regions. To determine whether UpSET binding correlates with gene expression, we performed an end analysis to correlate UpSET binding relative to the 5�� and 3�� ends of genes arranged by expression-based quintiles (Deal et?al., 2010). Our results show that a peak of UpSET binding mainly occurs 25�C50?bp downstream of the TSS. This binding is dependent on gene expression, as quintiles with highly expressed genes have higher upSET signal ( Figure?2E). As active TSS regions are marked by active chromatin marks (i.e., H3K4m3), as well as with high levels of RNA pol II, we performed an end analysis of RNA pol II- and H3K4m3-enriched sites from S2 cells ( Muse et?al., 2007). Consistent with UpSET enrichment at active TSSs, we observed high UpSET signal in [http://www.selleckchem.com/products/ABT-263.html Navitoclax purchase] regions enriched for RNA pol II and H3K4m3 ( Figure?2F). This overlap is not due to polymerase pausing, as promoters demonstrating high or low pausing indexes show similar enrichment for UpSET ( Figure?S2C) ( Gilchrist et?al., 2010). Together, our results suggest that UpSET targets promoter/TSS regions of transcriptionally active genes independently of the pausing features of the promoters. The histone deacetylase Rpd3 and its accessory subunit Sin3 can be recruited to transcriptionally active regions (Filion et?al., 2010).