Despite high levels of homology, transcription coactivators p300 and CREB binding protein (CBP) are both indispensable during embryogenesis. They are largely known to regulate the same genes. To identify genes preferentially regulated by p300 or CBP, we performed an extensive genome-wide survey using the ChIP-seq on cell-cycle synchronized cells. We found that 57% of the tags were within genes or proximal promoters, with an overall preference for binding to transcription start and end sites. The heterogeneous binding patterns possibly reflect the divergent roles of CBP and p300 in transcriptional regulation. Most of the 16 103 genes were bound by both CBP and p300. However, after stimulation 89 and 1944 genes were preferentially bound by CBP or p300, respectively. Target genes were found to be primarily involved in the regulation of metabolic and developmental processes, and transcription, with CBP showing a stronger preference than p300 for genes active in negative regulation of transcription. Analysis of transcription factor binding sites suggest that CBP and p300 have many partners in common, but AP-1 and Serum Response Factor (SRF) appear to be more prominent in CBP-specific sequences, whereas AP-2 and SP1 are enriched in p300-specific targets. Taken together, our findings further elucidate the distinct roles of coactivators p300 and CBP in transcriptional regulation.

Gene activation in eukaryotes requires chromatin remodeling, in part via histone modifications. To study the events at the promoter of a mitogen-inducible gene, we examined the induction of expression of the collagenase gene. It has been established that the collagenase gene can be activated by c-Jun and c-Fos and that the transcriptional coactivator p300 is involved in the activation. As expected, we found histone acetyltransferase activity at the collagenase promoter during activation. Interestingly, we also found histone methyltransferase and kinase activity. Strikingly, the first modification observed is methylation of histone H3 lysine 4, which correlates with the binding of the SET9 methyltransferase and the assembly of a complex consisting of c-Jun, c-Fos, TATA binding protein, and RNA polymerase II. The assembly of the preinitiation complex also shows an ordered binding of the acetyltransferase p300, the RSK2 kinase, and the SWI/SNF component Brg-1. Our results suggest that collagenase gene activation involves a dynamic recruitment of different factors and that in addition to acetylation, histone H3 lysine 4 di-and trimethylation and histone H3 serine 10 phosphorylation are important steps in the activation of this gene.In eukaryotic cells, genomic DNA is packaged into nucleosomes, the basic unit of chromatin structure. The packaging of DNA into chromatin has a repressive effect on gene expression, and therefore, reconfiguration of chromatin has been postulated as mandatory for transcriptional initiation (24,34,45). One of the central questions in this process is how RNA polymerase and associated proteins gain access to chromatin templates. Increasing evidence indicates that gene expression is regulated by means of facilitating access of DNA-binding factors to DNA via chromatin-remodeling factors and covalent histone modifications (14).The major chromatin-remodeling factors are the SWI/SNF ATP-dependent remodeling complexes. Upon recruitment, these complexes are thought to alter the structure of the promoter-bound nucleosome in an ATP-dependent manner (34).The covalent-histone modifications are brought about by proteins that, upon recruitment, can phosphorylate, acetylate, and methylate histone tails (5, 41). The best-studied histone modification involved in transcriptional activation is acetylation. Levels of acetylated histones H3 and H4 have been correlated with the transcription status of many genes: transcriptionally active euchromatin regions of the genome are often associated with hyperacetylated histones, whereas transcriptionally silent regions are associated with hypoacetylated histones (17). In vivo, the steady-state levels of histone acetylation are maintained by the balance of the opposing histone acetyltransferase (HAT) and histone deacetylase activities, and these enzymes are associated with gene activation and repression, respectively (21, 44). Besides acetylation, phosphorylation of histone H3 on serine 10 is also associated with gene activation. Phosphorylation, mediated via ERK or p38 ...

The adenovirus E1A protein regulates transcription of cellular genes via its interaction with the transcriptional coactivators p300/CBP. The collagenase promoter activated by the c-Jun protein is repressed by E1A. Here we show that E1A repression is specific for c-Jun, as E1A does not repress the collagenase promoter activated by the homologous transcription factor EB1. Using chimeras of c-Jun and EB1, we demonstrate that a 12 amino acid region in the basic region of the c-Jun DNA-binding domain is essential for repression by E1A. Since repression requires the binding of p300 to E1A, we studied the involvement of p300 acetyltransferase activity in the repression mechanism. We demonstrate that c-Jun is acetylated in vivo, and mutational analysis identified Lys271 in the c-Jun basic region to be essential for repression of the collagenase promoter by E1A. In addition, Lys271 is acetylated both in vitro and in vivo. These results suggest that the specific repression of the collagenase promoter by E1A involves acetylation of c-Jun.

The transcriptional coactivator p300 regulates transcription by binding to proteins involved in transcription and by acetylating histones and other proteins. These transcriptional effects are mainly at promoter and enhancer elements. Regulation of transcription also occurs through scaffold/matrix attachment regions (S/MARs), the chromatin regions that bind the nuclear matrix. Here we show that p300 binds to the S/MAR binding protein scaffold attachment factor A (SAF-A), a major constituent of the nuclear matrix. Using chromatin immunoprecipitations, we established that both p300 and SAF-A bind to S/MAR elements in the transiently silent topoisomerase I gene prior to its activation at G 1 during cell cycle. This binding is accompanied by local acetylation of nucleosomes, suggesting that p300-SAF-A interactions at S/MAR elements of nontranscribed genes might poise these genes for transcription.Activation of gene expression is thought to be a multistep process involving changes in chromatin structure, as well as site-specific events such as the acetylation of histones (20). An important factor in higher-order organization is the nuclear matrix, a proteinaceous structure that consists of a network of RNPs and other nonhistone proteins and that serves as a scaffold for loops of chromatin (reviewed in reference 5). This matrix has been associated with the regulation of transcription, DNA replication, and RNA processing (44). The DNA regions anchoring the chromosomal DNA to the nuclear matrix (called matrix-associated regions [MARs] or scaffold-attachment regions [SARs] [8]) are composed of AT-rich sequences. They have a unique structure characterized by a narrow minor groove, a high unwinding potential and the formation of hairpin structures (5). S/MARs are located in the introns of several large genes (32, 53) and also at borders of transcription units (23,47).

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