GCN5 is a histone acetyltransferase (HAT) originally identified inIn eukaryotes, genomic DNA is packaged by histones into nucleosomes that further fold to form higher-order chromatin structures. Eukaryotic cells have evolved two major enzymatic mechanisms to modify chromatin structure: (i) ATP-dependent nucleosome remodeling by multiprotein complexes that use the energy of ATP hydrolysis to alter the association of core histones with DNA and (ii) covalent modifications of core histones, including acetylation, that regulate core histone interactions with either DNA, adjacent nucleosomes, or other regulatory proteins (reviewed in references 7, 39, 64, and 74).Reversible acetylation of specific lysine residues within the N-terminal tails of nucleosomal core histones has long been correlated with changes in chromatin that occur during transcription, replication, and DNA repair in vivo (reviewed in references 7, 61, and 65). Significant progress in understanding the role of nuclear histone acetylation came from the findings that the Saccharomyces cerevisiae transcription coactivator GCN5, and more recently other yeast and metazoan transcription cofactors, are histone acetyltransferases (HATs) and that several transcription corepressor complexes have histone deacetylases as integral subunits (reviewed in references 4 and 10). HATs differ in substrate specificity and may also modify nonhistone regulatory proteins, as originally demonstrated for p53 acetylation by p300 (27). Many nuclear HATs are also part of large multiprotein assemblies. These include yeast SAGA (SPT-ADA-GCN5 acetylase), ADA, NuA3, NuA4, and Elongator complexes, yeast and metazoan TFIID complexes, and human TFTC (TATA-binding protein [TBP]-free TBP-associated factor II [TAF II ]-containing complex), PCAF, STAGA (SPT3-TAF II 31-GCN5L acetylase), TIP60, and TFIIIC complexes (reviewed in references 10 and 24).In yeast, GCN5 is an integral subunit of at least two distinct multiprotein HAT complexes, the ADA and SAGA complexes, that acetylate histones H3 and H2B within nucleosomes (25). The yeast SAGA complex is composed of (i) ADA adapter (coactivator) proteins (ADA1, ADA2, ADA3, ADA4 [GCN5], and ADA5 [SPT20]), (ii) SPT proteins (SPT3, SPT7, SPT8, and SPT20 [ADA5]), (iii) a subset of the yeast TAF II s (yTAF II s) (yTAF II 17/20, yTAF II 25, yTAF II 60, yTAF II 61/68, and yTAF II 90), and (iv) a protein, Tra1, that is structurally related to members of the ATM/DNA-PK/phosphatidylinositol 3-kinase family (reviewed in references 10, 24, and 78). The ADA complex shares GCN5, ADA2, and ADA3 with SAGA but lacks all other SAGA subunits and has ADA-specific components (20). The SAGA complex, but not the ADA complex,

The core promoter of eukaryotic genes is the minimal DNA region that recruits the basal transcription machinery to direct efficient and accurate transcription initiation. The fraction of human and yeast genes that contain specific core promoter elements such as the TATA box and the initiator (INR) remains unclear and core promoter motifs specific for TATA-less genes remain to be identified. Here, we present genome-scale computational analyses indicating that ∼76% of human core promoters lack TATA-like elements, have a high GC content, and are enriched in Sp1 binding sites. We further identify two motifs -M3 (SCGGAAGY) and M22 (TGCGCANK) -that occur preferentially in human TATA-less core promoters. About 24% of human genes have a TATA-like element and their promoters are generally AT-rich; however, only ∼10% of these TATA-containing promoters have the canonical TATA box (TATAWAWR). In contrast, ∼46% of human core promoters contain the consensus INR (YYANWYY) and ∼30% are INR-containing TATA-less genes. Significantly, ∼46% of human promoters lack both TATA-like and consensus INR elements. Surprisingly, mammalian-type INR sequences are present -and tend to cluster -in the transcription start site (TSS) region of ∼40% of yeast core promoters and the frequency of specific core promoter types appears to be conserved in yeast and human genomes. Gene Ontology analyses reveal that TATA-less genes in humans, as in yeast, are frequently involved in basic "housekeeping" processes, while TATAcontaining genes are more often highly regulated, such as by biotic or stress stimuli. These results reveal unexpected similarities in the occurrence of specific core promoter types and in their associated biological processes in yeast and humans and point to novel vertebrate-specific DNA motifs that might play a selective role in TATA-independent transcription.

Eukaryotic GCN5 acetyltransferases influence diverse biological processes by acetylating histones and non-histone proteins and regulating chromatin and gene-specific transcription as part of multiprotein complexes. In lower eukaryotes and invertebrates, these complexes include the yeast ADA complex that is still incompletely understood; the SAGA (Spt-Ada-Gcn5 acetylase) complexes from yeast to Drosophila that are mostly coactivators; and the ATAC (Ada Two-A containing) complex, only known in Drosophila and still poorly characterized. In contrast, vertebrate organisms, express two paralogous GCN5-like acetyltransferases (GCN5 and PCAF), which have been found so far only in SAGA-type complexes referred to hereafter as the STAGA (SPT3-TAF9-GCN5/PCAF acetylase) complexes. We now report the purification and characterization of vertebrate (human) ATAC-type complexes and identify novel components of STAGA. We show that human ATAC complexes incorporate in addition to GCN5 or PCAF (GCN5/PCAF), other epigenetic coregulators (ADA2-A, ADA3, STAF36, and WDR5), cofactors of chromatin assembly/remodeling and DNA replication machineries (POLE3/CHRAC17 and POLE4), the stress-and TGF␤-activated protein kinase (TAK1/MAP3K7) and MAP3-kinase regulator (MBIP), additional cofactors of unknown function, and a novel YEATS2-NC2␤ histone fold module that interacts with the TATA-binding protein (TBP) and negatively regulates transcription when recruited to a promoter. We further identify the p38 kinase-interacting protein (p38IP/ FAM48A) as a novel component of STAGA with distant similarity to yeast Spt20. These results suggest that vertebrate ATACtype and STAGA-type complexes link specific extracellular signals to modification of chromatin structure and regulation of the basal transcription machinery.Epigenetic information carried in the form of histone posttranslational modifications (or "marks") is essential for the proper expression, maintenance, and replication of eukaryotic genomes. These covalent modifications are deposited (or removed) by a variety of enzymes that are often part of large multiprotein "coregulator" complexes. These complexes are targeted to specific chromosomal loci by DNA-binding regulators and/or via direct docking to predeposited epigenetic marks (1

The transcription factor TFII-I has been shown to bind independently to two distinct promoter elements, a pyrimidine-rich initiator (Inr) and a recognition site (E-box) for upstream stimulatory factor 1 (USF1), and to stimulate USF1 binding to both of these sites. Here we describe the isolation of a cDNA encoding TFII-I and demonstrate that the corresponding 120 kDa polypeptide, when expressed ectopically, is capable of binding to both Inr and E-box elements. The primary structure of TFII-I reveals novel features that include six directly repeated 90 residue motifs that each possess a potential helix-loop/span-helix homology. These unique structural features suggest that TFII-I may have the capacity for multiple protein-protein and, potentially, multiple protein-DNA interactions. Consistent with this hypothesis and with previous in vitro studies, we further demonstrate that ectopic TFII-I and USF1 can act synergistically, and in some cases independently, to activate transcription in vivo through both Inr and the E-box elements of the adenovirus major late promoter. We also describe domains of USF1 that are necessary for its independent and synergistic activation functions.

The c-Myc oncoprotein (Myc) controls cell fate by regulating gene transcription in association with a DNA-binding partner, Max. While Max lacks a transcription regulatory domain, the N terminus of Myc contains a transcription activation domain (TAD) that recruits cofactor complexes containing the histone acetyltransferases (HATs) GCN5 and Tip60. Here, we report a novel functional interaction between Myc TAD and the p300 coactivator-acetyltransferase. We show that p300 associates with Myc in mammalian cells and in vitro through direct interactions with Myc TAD residues 1 to 110 and acetylates Myc in a TAD-dependent manner in vivo at several lysine residues located between the TAD and DNA-binding domain. Moreover, the Myc:Max complex is differentially acetylated by p300 and GCN5 and is not acetylated by Tip60 in vitro, suggesting distinct functions for these acetyltransferases. Whereas p300 and CBP can stabilize Myc independently of acetylation, p300-mediated acetylation results in increased Myc turnover. In addition, p300 functions as a coactivator that is recruited by Myc to the promoter of the human telomerase reverse transcriptase gene, and p300/CBP stimulates Myc TAD-dependent transcription in a HAT domain-dependent manner. Our results suggest dual roles for p300/CBP in Myc regulation: as a Myc coactivator that stabilizes Myc and as an inducer of Myc instability via direct Myc acetylation.The c-Myc oncoprotein (Myc) is the ubiquitous member of a small family of highly related DNA-binding transcription factors (including L-Myc and N-Myc) that regulate a wide variety of genes involved in the control of cell growth, proliferation, differentiation, and apoptotic cell death. Myc is essential for embryonic development and both Myc expression and activity are tightly regulated by mitogens and other physiological stimuli in normal somatic cells. Notably, unregulated Myc expression is tumorigenic in mice and has been associated with most types of cancer in humans. Myc binds to E-box DNA elements having the core consensus sequence CACGTG as a heterodimer with an obligatory partner protein called Max. Myc and Max dimerize and bind DNA via their respective basic-helix-loop-helix-leucine zipper (bHLHZip) domains. While Max does not have a transcription regulatory domain, Myc has a phylogenetically conserved N-terminal transcription activation domain (TAD) that is also essential for oncogenic cellular transformation (reviewed in reference 10).Several proteins have been shown to interact with Myc N-terminal TAD and are potential regulators or mediators of Myc transactivating and transforming activities (10,30). Among these, the TRRAP protein has been shown to contribute to the transformation activity of Myc through interactions with the conserved Myc box 1 (MB1) and MB2 regions within the TAD (23) and is a subunit of various transcription regulatory cofactors complexes that have histone acetyltransferase (HAT) activity. These TRRAP-HAT complexes include the GCN5 HAT-containing complexes STAGA (21, 22) and TFTC (3), the rela...