Three Key Subregions Contribute to the Function of the Downstream RNA Polymerase II Core Promoter

REFERENCES

• Ahsan, B., T. L. Saito, S. Hashimoto, K. Muramatsu, M. Tsuda, A. Sasaki, K. Matsushima, T. Aigaki, and S. Morishita. 2009. Machibase: a Drosophila melanogaster 5′-end mRNA transcription database. Nucleic Acids Res. 37:D49–D53.
   PubMedGoogle Scholar
• Bartholomew, B., G. A. Kassavetis, B. R. Braun, and E. P. Geiduschek. 1990. The subunit structure of Saccharomyces cerevisiae transcription factor IIIC probed with a novel photocrosslinking reagent. EMBO J. 9:2197–2205.
   PubMedGoogle Scholar
• Bartholomew, B., G. A. Kassavetis, and E. P. Geiduschek. 1991. Two components of Saccharomyces cerevisiae transcription factor IIIB (TFIIIB) are stereospecifically located upstream of a tRNA gene and interact with the second-largest subunit of TFIIIC. Mol. Cell. Biol. 11:5181–5189.
   PubMedGoogle Scholar
• Burke, T. W., and J. T. Kadonaga. 1996. Drosophila TFIID binds to a conserved downstream basal promoter element that is present in many TATA-box-deficient promoters. Genes Dev. 10:711–724.
   PubMed Web of Science ®Google Scholar
• Burke, T. W., and J. T. Kadonaga. 1997. The downstream core promoter element, DPE, is conserved from Drosophila to humans and is recognized by TAFII60 of Drosophila. Genes Dev. 11:3020–3031.
   PubMed Web of Science ®Google Scholar
• Burley, S. K., and R. G. Roeder. 1996. Biochemistry and structural biology of transcription factor IID (TFIID). Annu. Rev. Biochem. 65:769–799.
   PubMed Web of Science ®Google Scholar
• D'Alessio, J. A., K. J. Wright, and R. Tjian. 2009. Shifting players and paradigms in cell-specific transcription. Mol. Cell 36:924–931.
   PubMedGoogle Scholar
• Dynlacht, B. D., T. Hoey, and R. Tjian. 1991. Isolation of coactivators associated with the TATA-binding protein that mediate transcriptional activation. Cell 66:563–576.
   PubMedGoogle Scholar
• Hoey, T., R. O. Weinzierl, G. Gill, J. L. Chen, B. D. Dynlacht, and R. Tjian. 1993. Molecular cloning and functional analysis of Drosophila TAF110 reveal properties expected of coactivators. Cell 72:247–260.
   PubMedGoogle Scholar
• Juven-Gershon, T., S. Cheng, and J. T. Kadonaga. 2006. Rational design of a super core promoter that enhances gene expression. Nat. Methods. 3:917–922.
   PubMed Web of Science ®Google Scholar
• Juven-Gershon, T., J.-Y. Hsu, and J. T. Kadonaga. 2008. Caudal, a key developmental regulator, is a DPE-specific transcription factor. Genes Dev. 22:2823–2830.
   PubMed Web of Science ®Google Scholar
• Juven-Gershon, T., and J. T. Kadonaga. 2010. Regulation of gene expression via the core promoter and the basal transcriptional machinery. Dev. Biol. 339:225–229.
   PubMed Web of Science ®Google Scholar
• Kadonaga, J. T. 1991. Purification of sequence-specific DNA binding proteins by DNA affinity chromatography. Methods Enzymol. 208:10–23.
   PubMed Web of Science ®Google Scholar
• Kokubo, T., D.-W. Gong, J. C. Wootton, M. Horikoshi, R. G. Roeder, and Y. Nakatani. 1994. Molecular cloning of Drosophila TFIID subunits. Nature 367:484–487.
   PubMed Web of Science ®Google Scholar
• Kutach, A. K., and J. T. Kadonaga. 2000. The downstream promoter element DPE appears to be as widely used as the TATA box in Drosophila core promoters. Mol. Cell. Biol. 20:4754–4764.
   PubMed Web of Science ®Google Scholar
• Lee, D. H., N. Gershenzon, M. Gupta, I. P. Ioshikhes, D. Reinberg, and B. A. Lewis. 2005. Functional characterization of core promoter elements: the downstream core element is recognized by TAF1. Mol. Cell. Biol. 25:9674–9686.
   PubMed Web of Science ®Google Scholar
• Lewis, B. A., T. K. Kim, and S. H. Orkin. 2000. A downstream element in the human beta-globin promoter: evidence of extended sequence-specific transcription factor IID contacts. Proc. Natl. Acad. Sci. U. S. A. 97:7172–7177.
   PubMed Web of Science ®Google Scholar
• Lim, C. Y., B. Santoso, T. Boulay, E. Dong, U. Ohler, and J. T. Kadonaga. 2004. The MTE, a new core promoter element for transcription by RNA polymerase II. Genes Dev. 18:1606–1617.
   PubMed Web of Science ®Google Scholar
• Ohler, U., G. C. Liao, H. Niemann, and G. M. Rubin. 2002. Computational analysis of core promoters in the Drosophila genome. Genome Biol. 3:RESEARCH0087. http://genomebiology.com/2002/3/12/RESEARCH/0087.
   Google Scholar
• Shao, H., M. Revach, S. Moshonov, Y. Tzuman, K. Gazit, S. Albeck, T. Unger, and R. Dikstein. 2005. Core promoter binding by histone-like TAF complexes. Mol. Cell Biol. 25:206–219.
   PubMed Web of Science ®Google Scholar
• Smale, S. T., and J. T. Kadonaga. 2003. The RNA polymerase II core promoter. Annu. Rev. Biochem. 72:449–479.
   PubMed Web of Science ®Google Scholar
• Soeller, W. C., S. J. Poole, and T. Kornberg. 1988. In vitro transcription of the Drosophila engrailed gene. Genes Dev. 2:68–81.
   PubMedGoogle Scholar
• Thomas, M. C., and C. M. Chiang. 2006. The general transcription machinery and general cofactors. Crit. Rev. Biochem. Mol. Biol. 41:105–178.
   PubMed Web of Science ®Google Scholar
• Wampler, S. L., C. M. Tyree, and J. T. Kadonaga. 1990. Fractionation of the general RNA polymerase II transcription factors from Drosophila embryos. J. Biol. Chem. 265:21223–21231.
   PubMedGoogle Scholar