The development, growth, and survival of eukaryotic organisms require the proper regulation of tens of thousands of genes. By complex formulae that have yet to be solved, the expression of each of these thousands of genes is controlled by a wide variety of mechanisms (e.g., see Lefstin and

To investigate the basis for enhancer-promoter specificity, we compared the ability of enhancers to activate transcription in vivo from core promoters containing either downstream promoter element (DPE) or TATA box motifs. To eliminate position effects, we generated and analyzed pairs of sister Drosophila lines that contain a DPE-or TATA-dependent reporter gene at precisely the same genomic position relative to each enhancer. These studies revealed transcriptional enhancers that are specific for promoters that contain either DPE or TATA box elements. Thus, the core promoter not only mediates the initiation of transcription, but also functions as a regulatory element. The regulation of gene expression at the level of transcription is a key control point for many cellular processes. In eukaryotes, there are tens of thousands of protein-coding genes, each of which has its unique program of transcription. The cis-acting DNA sequences that encode these transcriptional programs include transcriptional enhancers, proximal promoters, and core promoters. Enhancers and proximal promoters are recognized by sequence-specific DNA-binding proteins that regulate transcription (see, e.g., Blackwood and Kadonaga 1998;Lee and Young 2000;Lemon and Tjian 2000;Malik and Roeder 2000). Enhancers are often located many kilobase pairs (kbp) upstream or downstream of the transcription start site, whereas proximal promoters are typically within a couple hundred base pairs (bp) of the start site. Core promoters encompass the transcription start site and specify the site of transcription initiation by the basal transcriptional machinery (see, e.g., Orphanides et al. 1996;Smale 1997;White 2001).The core promoter is at a unique and important position in the transcription process, as it is the eventual target of the action of the many sequence-specific factors and coregulators that control the transcriptional activity of each gene. There are several core promoter elements, including the TATA box, TFIIB recognition element (BRE), Initiator (Inr), and downstream promoter element (DPE). The TATA box is an A/T-rich region that is located about 30 nucleotides (nt) upstream of the transcription start site and is recognized by the TATA-binding protein (TBP) subunit of the TFIID complex. The BRE is located immediately upstream of the TATA box of some TATA-containing promoters, and it increases the affinity of TFIIB for the core promoter (Lagrange et al. 1998). The Inr is a conserved sequence, encompassing the transcription start site, that functions to direct accurate transcription initiation either by itself or in conjunction with a TATA or DPE motif (Smale and Baltimore 1989). The DPE is located about 30 nt downstream of the start site and is recognized by TBP-associated factor (TAF) subunits of TFIID (Burke andKadonaga 1996, 1997).There are some intriguing similarities and differences between TATA and DPE elements. Both the TATA and DPE are recognition sites for the binding of TFIID. Core promoters that contain either a TATA or a DPE motif are typi...

Many hormones activate transcription by raising the level of cAMP within cells. In one well studied pathway, cAMP induces protein kinase A to phosphorylate the transcription factor CREB, which binds to a consensus sequence, the cAMP-regulated enhancer, found in many target genes. A generally accepted model suggests that phosphorylated CREB recruits the histone acetyltransferase CBP to activate transcription. In contrast, histone deacetylases have been linked to the cessation of CREB-dependent transcription. Here we tested this model in the regulation of endogenous CREB target genes. We used a constitutively active CREB mutant and microarray analysis to identify target genes in PC12 cells. We then tested the role of histone deacetylase activity in cAMP activation of four of these genes (c-FOS, ICER, NOR-1, and NUR77) by treating cells with the histone deacetylase inhibitor trichostatin A. Consistent with the generally accepted model, trichostatin A enhanced activation of c-FOS and NUR77 by cAMP. Surprisingly, trichostatin A blocked activation of ICER and NOR-1. The block of ICER and NOR-1 activation persisted in the presence of cycloheximide, indicating that the trichostatin A effect did not depend on new protein synthesis. This unexpected role of histone deacetylases in transcriptional activation of certain endogenous CREB target genes was not apparent in transfected reporter genes. Chromatin immunoprecipitation analysis indicated that the differential roles of histone deacetylases in activating or repressing CREB target genes was manifested at the level of preinitiation complex recruitment. These data indicate that histone deacetylases differentially regulate CREB target genes by contributing to either activation or cessation of transcription.

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