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Basal core promoters control the equilibrium between negative cofactor 2 and preinitiation complexes in human cells.

ABSTRACT: BACKGROUND: The general transcription factor TFIIB and its antagonist negative cofactor 2 (NC2) are hallmarks of RNA polymerase II (RNAPII) transcription. Both factors bind TATA box-binding protein (TBP) at promoters in a mutually exclusive manner. Dissociation of NC2 is thought to be followed by TFIIB association and subsequent preinitiation complex formation. TFIIB dissociates upon RNAPII promoter clearance, thereby providing a specific measure for steady-state preinitiation complex levels. As yet, genome-scale promoter mapping of human TFIIB has not been reported. It thus remains elusive how human core promoters contribute to preinitiation complex formation in vivo. RESULTS: We compare target genes of TFIIB and NC2 in human B cells and analyze associated core promoter architectures. TFIIB occupancy is positively correlated with gene expression, with the vast majority of promoters being GC-rich and lacking defined core promoter elements. TATA elements, but not the previously in vitro defined TFIIB recognition elements, are enriched in some 4 to 5% of the genes. NC2 binds to a highly related target gene set. Nonetheless, subpopulations show strong variations in factor ratios: whereas high TFIIB/NC2 ratios select for promoters with focused start sites and conserved core elements, high NC2/TFIIB ratios correlate to multiple start-site promoters lacking defined core elements. CONCLUSIONS: TFIIB and NC2 are global players that occupy active genes. Preinitiation complex formation is independent of core elements at the majority of genes. TATA and TATA-like elements dictate TFIIB occupancy at a subset of genes. Biochemical data support a model in which preinitiation complex but not TBP-NC2 complex formation is regulated.

SUBMITTER: Albert TK

PROVIDER: S-EPMC2864573 | biostudies-literature | 2010

REPOSITORIES: biostudies-literature

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Basal core promoters control the equilibrium between negative cofactor 2 and preinitiation complexes in human cells.

Albert Thomas K TK Grote Korbinian K Boeing Stefan S Meisterernst Michael M

Genome biology 20100315 3

<h4>Background</h4>The general transcription factor TFIIB and its antagonist negative cofactor 2 (NC2) are hallmarks of RNA polymerase II (RNAPII) transcription. Both factors bind TATA box-binding protein (TBP) at promoters in a mutually exclusive manner. Dissociation of NC2 is thought to be followed by TFIIB association and subsequent preinitiation complex formation. TFIIB dissociates upon RNAPII promoter clearance, thereby providing a specific measure for steady-state preinitiation complex lev ...[more]

PMID: 20230619

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Project description:In this study, we investigate three oxabicyclic compounds, 3,6-dioxabicyclo[3. 1.0]hexane (C4H6O2, ETHF), 7-oxabicyclo[2.2.1]heptane (C6H10O, 14ECH), and 7-oxabicyclo[4.1.0]heptane (C6H10O, 12ECH) as novel promoters for gas hydrates. According to the outcomes of powder X-ray diffraction (PXRD) and synchrotron high-resolution powder diffraction (HRPD), all CH4 hydrates formed with ETHF, 14ECH, and 12ECH were identified to be sII (Fd-3m) hydrates with corresponding lattice parameters of 17.195, 17.330, and 17.382 Å, respectively. It was also clearly demonstrated that CH4 molecules are accommodated in the sII-S cages through solid-state 13C NMR and Raman spectra. Consequently, we clarified that the three compounds observed are large guest molecules (LGMs) that occupy the sII-L cages. Moreover, the thermodynamic stability of each LGM + CH4 (and N2) hydrate system was remarkably improved compared to that of the simple CH4 (and N2) hydrate. In particular, 14ECH manifested several unique features compared to the other two promoters. First, the 14ECH + CH4 hydrate did not dissociate up to room temperature (298 K), even at a moderate pressure of approximately 60 bar. At a given pressure, 14ECH increased the dissociation temperature of the CH4 hydrate by ~18 K, indicating that its promotion capability is as strong as that of tetrahydrofuran (THF), currently considered to be the most powerful promoter. Second, more interestingly, it was revealed by further PXRD, NMR, and Raman analyses that 14ECH forms a simple sII hydrate in the absence of help gases. According to differential scanning calorimetry (DSC) outcomes, we revealed that the simple 14ECH hydrate dissociates at 270~278 K under ambient pressure. In addition to the thermodynamic stability, we also note that the 14ECH + CH4 hydrate presented a sufficiently high temperature of formation, requiring little additional cooling. Given these promising features, we expect that the 14ECH hydrate system can be adopted to realize hydrate-based technologies. We also believe that the LGMs introduced here have considerable potential to serve as alternates to conventional promoters and that they can be widely utilized in both engineering and scientific research fields.

Dataset Information

Basal core promoters control the equilibrium between negative cofactor 2 and preinitiation complexes in human cells.

Publications

Basal core promoters control the equilibrium between negative cofactor 2 and preinitiation complexes in human cells.

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