Regulation of gene expression via the core promoter and the basal transcriptional machinery

Bártfai, 2004, TBP2, a vertebrate-specific member of the TBP family, is required in embryonic development of zebrafish, Curr. Biol., 14, 593, 10.1016/j.cub.2004.03.034 Burke, 1996, Drosophila TFIID binds to a conserved downstream basal promoter element that is present in many TATA-box-deficient promoters, Genes Dev., 10, 711, 10.1101/gad.10.6.711 Burke, 1997, The downstream core promoter element, DPE, is conserved from Drosophila to humans and is recognized by TAFII60 of Drosophila, Genes Dev., 11, 3020, 10.1101/gad.11.22.3020 Butler, 2001, Enhancer–promoter specificity mediated by DPE or TATA core promoter motifs, Genes Dev., 15, 2515, 10.1101/gad.924301 Butler, 2002, The RNA polymerase II core promoter: a key component in the regulation of gene expression, Genes Dev., 16, 2583, 10.1101/gad.1026202 Carninci, 2006, Genome-wide analysis of mammalian promoter architecture and evolution, Nat. Genet., 38, 626, 10.1038/ng1789 Chalkley, 1999, DNA binding site selection by RNA polymerase II TAFs: a TAF(II)250–TAF(II)150 complex recognizes the initiator, EMBO J., 18, 4835, 10.1093/emboj/18.17.4835 Cooper, 2006, Comprehensive analysis of transcriptional promoter structure and function in 1% of the human genome, Genome Res., 16, 1, 10.1101/gr.4222606 Deato, 2007, Switching of the core transcription machinery during myogenesis, Genes Dev., 21, 2137, 10.1101/gad.1583407 Deato, 2008, MyoD targets TAF3/TRF3 to activate myogenin transcription, Mol. Cell, 32, 96, 10.1016/j.molcel.2008.09.009 Deng, 2005, A core promoter element downstream of the TATA box that is recognized by TFIIB, Genes Dev., 19, 2418, 10.1101/gad.342405 Deng, 2007, TFIIB and the regulation of transcription by RNA polymerase II, Chromosoma, 116, 417, 10.1007/s00412-007-0113-9 Evans, 2001, Activator-mediated disruption of sequence-specific DNA contacts by the general transcription factor TFIIB, Genes Dev., 15, 2945, 10.1101/gad.206901 FitzGerald, 2006, Comparative genomics of Drosophila and human core promoters, Genome Biol., 7, R53, 10.1186/gb-2006-7-7-r53 Frith, 2008, A code for transcription initiation in mammalian genomes, Genome Res., 18, 1, 10.1101/gr.6831208 Gershenzon, 2006, The features of Drosophila core promoters revealed by statistical analysis, BMC Genomics, 7, 161, 10.1186/1471-2164-7-161 Goldberg, M.L., 1979. Ph.D. Thesis, Stanford University, Stanford, CA, U.S.A. Hart, 2007, Initiation of zebrafish haematopoiesis by the TATA-box-binding protein-related factor Trf3, Nature, 450, 1082, 10.1038/nature06349 Heintzman, 2007, The gateway to transcription: identifying, characterizing and understanding promoters in the eukaryotic genome, Cell. Mol. Life Sci., 64, 386, 10.1007/s00018-006-6295-0 Hsu, 2008, TBP, Mot1, and NC2 establish a regulatory circuit that controls DPE-dependent versus TATA-dependent transcription, Genes Dev., 22, 2353, 10.1101/gad.1681808 Isogai, 2007, Transcription of histone gene cluster by differential core-promoter factors, Genes Dev., 21, 2936, 10.1101/gad.1608807 Jallow, 2004, Specialized and redundant roles of TBP and a vertebrate-specific TBP paralog in embryonic gene regulation in Xenopus, Proc. Natl. Acad. Sci. U. S. A., 101, 13525, 10.1073/pnas.0405536101 Jones, 2007, Transcription strategies in terminally differentiated cells: shaken to the core, Genes Dev., 21, 2113, 10.1101/gad.1598007 Juven-Gershon, 2006, Perspectives on the RNA polymerase II core promoter, Biochem. Soc. Trans., 34, 1047, 10.1042/BST0341047 Juven-Gershon, 2006, Rational design of a super core promoter that enhances gene expression, Nat. Methods, 3, 917, 10.1038/nmeth937 Juven-Gershon, 2008, Caudal, a key developmental regulator, is a DPE-specific transcriptional factor, Genes Dev., 22, 2823, 10.1101/gad.1698108 Juven-Gershon, 2008, The RNA polymerase II core promoter – the gateway to transcription, Curr. Opin. Cell Biol., 20, 253, 10.1016/j.ceb.2008.03.003 Kim, 2005, A high-resolution map of active promoters in the human genome, Nature, 436, 876, 10.1038/nature03877 Kutach, 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, 10.1128/MCB.20.13.4754-4764.2000 Lagrange, 1998, New core promoter element in RNA polymerase II-dependent transcription: sequence-specific DNA binding by transcription factor IIB, Genes Dev., 12, 34, 10.1101/gad.12.1.34 Levine, 2003, Transcription regulation and animal diversity, Nature, 424, 147, 10.1038/nature01763 Lewis, 2005, Functional characterization of core promoter elements: DPE-specific transcription requires the protein kinase CK2 and the PC4 coactivator, Mol. Cell, 18, 471, 10.1016/j.molcel.2005.04.005 Lim, 2004, The MTE, a new core promoter element for transcription by RNA polymerase II, Genes Dev., 18, 1606, 10.1101/gad.1193404 Molina, 2005, Genome wide analysis of Arabidopsis core promoters, BMC Genomics, 6, 25, 10.1186/1471-2164-6-25 Müller, 2007, New problems in RNA polymerase II transcription initiation: matching the diversity of core promoters with a variety of promoter recognition factors, J. Biol. Chem., 282, 14685, 10.1074/jbc.R700012200 Ohler, 2002, Computational analysis of core promoters in the Drosophila genome, Genome Biol., 3, 10.1186/gb-2002-3-12-research0087 Ohtsuki, 1998, Different core promoters possess distinct regulatory activities in the Drosophila embryo, Genes Dev., 12, 547, 10.1101/gad.12.4.547 Pfeiffer, 2008, Tools for neuroanatomy and neurogenetics in Drosophila, Proc. Natl. Acad. Sci. U. S. A., 105, 9715, 10.1073/pnas.0803697105 Ponjavic, 2006, Transcriptional and structural impact of TATA-initiation site spacing in mammalian core promoters, Genome Biol., 7, R78, 10.1186/gb-2006-7-8-r78 Purnell, 1994, TFIID sequence recognition of the initiator and sequences farther downstream in Drosophila class II genes, Genes Dev., 8, 830, 10.1101/gad.8.7.830 Reeve, 2003, Archaeal chromatin and transcription, Mol. Microbiol., 48, 587, 10.1046/j.1365-2958.2003.03439.x Reina, 2007, On a roll for new TRF targets, Genes Dev., 21, 2855, 10.1101/gad.1623207 Sandelin, 2007, Mammalian RNA polymerase II core promoters: insights from genome-wide studies, Nat. Rev. Genet., 8, 424, 10.1038/nrg2026 Smale, 2001, Core promoters: active contributors to combinatorial gene regulation, Genes Dev., 15, 2503, 10.1101/gad.937701 Smale, 1989, The “initiator” as a transcription control element, Cell, 57, 103, 10.1016/0092-8674(89)90176-1 Smale, 2003, The RNA polymerase II core promoter, Annu. Rev. Biochem., 72, 449, 10.1146/annurev.biochem.72.121801.161520 Takada, 2000, A TRF1:BRF complex directs Drosophila RNA polymerase III transcription, Cell, 101, 459, 10.1016/S0092-8674(00)80857-0 Thomas, 2006, The general transcription machinery and general cofactors, Crit. Rev. Biochem. Mol. Biol., 41, 105, 10.1080/10409230600648736 Torres-Padilla, 2007, TBP homologues in embryo transcription: who does what?, EMBO Rep., 8, 1016, 10.1038/sj.embor.7401093 van Werven, 2008, Cooperative action of NC2 and Mot1p to regulate TATA-binding protein function across the genome, Genes Dev., 22, 2359, 10.1101/gad.1682308 Willy, 2000, A basal transcription factor that activates or represses transcription, Science, 290, 982, 10.1126/science.290.5493.982 Yamamoto, 2007, Differentiation of core promoter architecture between plants and mammals revealed by LDSS analysis, Nucleic Acids Res., 35, 6219, 10.1093/nar/gkm685 Yamamoto, 2007, Identification of plant promoter constituents by analysis of local distribution of short sequences, BMC Genomics, 8, 67, 10.1186/1471-2164-8-67 Yang, 2007, Prevalence of the initiator over the TATA box in human and yeast genes and identification of DNA motifs enriched in human TATA-less core promoters, Gene, 389, 52, 10.1016/j.gene.2006.09.029