Regulatory interplay between TFIID’s conformational transitions and its modular interaction with core promoter DNA

References

• Näär AM, Lemon BD, Tjian R. Transcriptional coactivator complexes. Annu Rev Biochem 2001; 70:475 - 501; http://dx.doi.org/10.1146/annurev.biochem.70.1.475; PMID: 11395415
   PubMed Web of Science ®Google Scholar
• Albright SR, Tjian R. TAFs revisited: more data reveal new twists and confirm old ideas. Gene 2000; 242:1 - 13; http://dx.doi.org/10.1016/S0378-1119(99)00495-3; PMID: 10721692
   PubMed Web of Science ®Google Scholar
• Burley SK, Roeder RG. Biochemistry and structural biology of transcription factor IID (TFIID). Annu Rev Biochem 1996; 65:769 - 99; http://dx.doi.org/10.1146/annurev.bi.65.070196.004005; PMID: 8811195
   PubMed Web of Science ®Google Scholar
• Smale ST, Baltimore D. The “initiator” as a transcription control element. Cell 1989; 57:103 - 13; http://dx.doi.org/10.1016/0092-8674(89)90176-1; PMID: 2467742
   PubMed Web of Science ®Google Scholar
• Theisen JW, Lim CY, Kadonaga JT. Three key subregions contribute to the function of the downstream RNA polymerase II core promoter. Mol Cell Biol 2010; 30:3471 - 9; http://dx.doi.org/10.1128/MCB.00053-10; PMID: 20457814
   PubMed Web of Science ®Google Scholar
• Burke TW, Kadonaga JT. The downstream core promoter element, DPE, is conserved from Drosophila to humans and is recognized by TAFII60 of Drosophila. Genes Dev 1997; 11:3020 - 31; http://dx.doi.org/10.1101/gad.11.22.3020; PMID: 9367984
   PubMed Web of Science ®Google Scholar
• Lee DH, Gershenzon N, Gupta M, Ioshikhes IP, Reinberg D, Lewis BA. Functional characterization of core promoter elements: the downstream core element is recognized by TAF1. Mol Cell Biol 2005; 25:9674 - 86; http://dx.doi.org/10.1128/MCB.25.21.9674-9686.2005; PMID: 16227614
   PubMed Web of Science ®Google Scholar
• Bieniossek C, Papai G, Schaffitzel C, Garzoni F, Chaillet M, Scheer E, et al. The architecture of human general transcription factor TFIID core complex. Nature 2013; 493:699 - 702; http://dx.doi.org/10.1038/nature11791; PMID: 23292512
   PubMed Web of Science ®Google Scholar
• Leschziner AE, Nogales E. Visualizing flexibility at molecular resolution: analysis of heterogeneity in single-particle electron microscopy reconstructions. Annu Rev Biophys Biomol Struct 2007; 36:43 - 62; http://dx.doi.org/10.1146/annurev.biophys.36.040306.132742; PMID: 17201674
   PubMedGoogle Scholar
• Cianfrocco MA, Kassavetis GA, Grob P, Fang J, Juven-Gershon T, Kadonaga JT, et al. Human TFIID binds to core promoter DNA in a reorganized structural state. Cell 2013; 152:120 - 31; http://dx.doi.org/10.1016/j.cell.2012.12.005; PMID: 23332750
   PubMed Web of Science ®Google Scholar
• Liu WL, Coleman RA, Ma E, Grob P, Yang JL, Zhang Y, et al. Structures of three distinct activator-TFIID complexes. Genes Dev 2009; 23:1510 - 21; http://dx.doi.org/10.1101/gad.1790709; PMID: 19571180
   PubMed Web of Science ®Google Scholar
• Liu WL, Coleman RA, Grob P, King DS, Florens L, Washburn MP, et al. Structural changes in TAF4b-TFIID correlate with promoter selectivity. Mol Cell 2008; 29:81 - 91; http://dx.doi.org/10.1016/j.molcel.2007.11.003; PMID: 18206971
   PubMed Web of Science ®Google Scholar
• Grob P, Cruse MJ, Inouye C, Peris M, Penczek PA, Tjian R, et al. Cryo-electron microscopy studies of human TFIID: conformational breathing in the integration of gene regulatory cues. Structure 2006; 14:511 - 20; http://dx.doi.org/10.1016/j.str.2005.11.020; PMID: 16531235
   PubMed Web of Science ®Google Scholar
• Andel F 3rd, Ladurner AG, Inouye C, Tjian R, Nogales E. Three-dimensional structure of the human TFIID-IIA-IIB complex. Science 1999; 286:2153 - 6; http://dx.doi.org/10.1126/science.286.5447.2153; PMID: 10591646
   PubMed Web of Science ®Google Scholar
• Juven-Gershon T, Cheng S, Kadonaga JT. Rational design of a super core promoter that enhances gene expression. Nat Methods 2006; 3:917 - 22; http://dx.doi.org/10.1038/nmeth937; PMID: 17124735
   PubMed Web of Science ®Google Scholar
• Oelgeschläger T, Chiang CM, Roeder RG. Topology and reorganization of a human TFIID-promoter complex. Nature 1996; 382:735 - 8; http://dx.doi.org/10.1038/382735a0; PMID: 8751448
   PubMed Web of Science ®Google Scholar
• Van Dyke MW, Roeder RG, Sawadogo M. Physical analysis of transcription preinitiation complex assembly on a class II gene promoter. Science 1988; 241:1335 - 8; http://dx.doi.org/10.1126/science.3413495; PMID: 3413495
   PubMed Web of Science ®Google Scholar
• Sawadogo M, Roeder RG. Interaction of a gene-specific transcription factor with the adenovirus major late promoter upstream of the TATA box region. Cell 1985; 43:165 - 75; http://dx.doi.org/10.1016/0092-8674(85)90021-2; PMID: 4075392
   PubMed Web of Science ®Google Scholar
• Hoffmann A, Chiang CM, Oelgeschläger T, Xie X, Burley SK, Nakatani Y, et al. A histone octamer-like structure within TFIID. Nature 1996; 380:356 - 9; http://dx.doi.org/10.1038/380356a0; PMID: 8598932
   PubMed Web of Science ®Google Scholar
• Xie X, Kokubo T, Cohen SL, Mirza UA, Hoffmann A, Chait BT, et al. Structural similarity between TAFs and the heterotetrameric core of the histone octamer. Nature 1996; 380:316 - 22; http://dx.doi.org/10.1038/380316a0; PMID: 8598927
   PubMed Web of Science ®Google Scholar
• Selleck W, Howley R, Fang Q, Podolny V, Fried MG, Buratowski S, et al. A histone fold TAF octamer within the yeast TFIID transcriptional coactivator. Nat Struct Biol 2001; 8:695 - 700; http://dx.doi.org/10.1038/90408; PMID: 11473260
   PubMedGoogle Scholar
• Shao H, Revach M, Moshonov S, Tzuman Y, Gazit K, Albeck S, et al. Core promoter binding by histone-like TAF complexes. Mol Cell Biol 2005; 25:206 - 19; http://dx.doi.org/10.1128/MCB.25.1.206-219.2005; PMID: 15601843
   PubMed Web of Science ®Google Scholar
• Bleichenbacher M, Tan S, Richmond TJ. Novel interactions between the components of human and yeast TFIIA/TBP/DNA complexes. J Mol Biol 2003; 332:783 - 93; http://dx.doi.org/10.1016/S0022-2836(03)00887-8; PMID: 12972251
   PubMed Web of Science ®Google Scholar
• Tan S, Hunziker Y, Sargent DF, Richmond TJ. Crystal structure of a yeast TFIIA/TBP/DNA complex. Nature 1996; 381:127 - 51; http://dx.doi.org/10.1038/381127a0; PMID: 8610010
   PubMed Web of Science ®Google Scholar
• Chalkley GE, Verrijzer CP. DNA binding site selection by RNA polymerase II TAFs: a TAF(II)250-TAF(II)150 complex recognizes the initiator. EMBO J 1999; 18:4835 - 45; http://dx.doi.org/10.1093/emboj/18.17.4835; PMID: 10469661
   PubMed Web of Science ®Google Scholar
• Dosztányi Z, Csizmok V, Tompa P, Simon I. IUPred: web server for the prediction of intrinsically unstructured regions of proteins based on estimated energy content. Bioinformatics 2005; 21:3433 - 4; http://dx.doi.org/10.1093/bioinformatics/bti541; PMID: 15955779
   PubMed Web of Science ®Google Scholar
• Ozer J, Mitsouras K, Zerby D, Carey M, Lieberman PM. Transcription factor IIA derepresses TATA-binding protein (TBP)-associated factor inhibition of TBP-DNA binding. J Biol Chem 1998; 273:14293 - 300; http://dx.doi.org/10.1074/jbc.273.23.14293; PMID: 9603936
   PubMed Web of Science ®Google Scholar
• Wright KJ, Marr MT 2nd, Tjian R. TAF4 nucleates a core subcomplex of TFIID and mediates activated transcription from a TATA-less promoter. Proc Natl Acad Sci U S A 2006; 103:12347 - 52; http://dx.doi.org/10.1073/pnas.0605499103; PMID: 16895980
   PubMed Web of Science ®Google Scholar
• Martinez E, Kundu TK, Fu J, Roeder RG. A human SPT3-TAFII31-GCN5-L acetylase complex distinct from transcription factor IID. J Biol Chem 1998; 273:23781 - 5; http://dx.doi.org/10.1074/jbc.273.37.23781; PMID: 9726987
   PubMed Web of Science ®Google Scholar
• Grant PA, Schieltz D, Pray-Grant MG, Steger DJ, Reese JC, Yates JR 3rd, et al. A subset of TAF(II)s are integral components of the SAGA complex required for nucleosome acetylation and transcriptional stimulation. Cell 1998; 94:45 - 53; http://dx.doi.org/10.1016/S0092-8674(00)81220-9; PMID: 9674426
   PubMed Web of Science ®Google Scholar
• Ogryzko VV, Kotani T, Zhang X, Schiltz RL, Howard T, Yang XJ, et al. Histone-like TAFs within the PCAF histone acetylase complex. Cell 1998; 94:35 - 44; http://dx.doi.org/10.1016/S0092-8674(00)81219-2; PMID: 9674425
   PubMed Web of Science ®Google Scholar
• Wieczorek E, Brand M, Jacq X, Tora L. Function of TAF(II)-containing complex without TBP in transcription by RNA polymerase II. Nature 1998; 393:187 - 91; http://dx.doi.org/10.1038/30283; PMID: 9603525
   PubMed Web of Science ®Google Scholar
• Tse C, Sera T, Wolffe AP, Hansen JC. Disruption of higher-order folding by core histone acetylation dramatically enhances transcription of nucleosomal arrays by RNA polymerase III. Mol Cell Biol 1998; 18:4629 - 38; PMID: 9671473
   PubMed Web of Science ®Google Scholar
• He Y, Fang J, Taatjes DJ, Nogales E. Structural visualization of key steps in human transcription initiation. Nature 2013; 495:481 - 6; http://dx.doi.org/10.1038/nature11991; PMID: 23446344
   PubMed Web of Science ®Google Scholar
• Ohtsuki S, Levine M, Cai HN. Different core promoters possess distinct regulatory activities in the Drosophila embryo. Genes Dev 1998; 12:547 - 56; http://dx.doi.org/10.1101/gad.12.4.547; PMID: 9472023
   PubMed Web of Science ®Google Scholar
• Juven-Gershon T, Hsu JY, Kadonaga JT. Caudal, a key developmental regulator, is a DPE-specific transcriptional factor. Genes Dev 2008; 22:2823 - 30; http://dx.doi.org/10.1101/gad.1698108; PMID: 18923080
   PubMed Web of Science ®Google Scholar
• Liu D, Ishima R, Tong KI, Bagby S, Kokubo T, Muhandiram DR, et al. Solution structure of a TBP-TAF(II)230 complex: protein mimicry of the minor groove surface of the TATA box unwound by TBP. Cell 1998; 94:573 - 83; http://dx.doi.org/10.1016/S0092-8674(00)81599-8; PMID: 9741622
   PubMed Web of Science ®Google Scholar
• Bagby S, Mal TK, Liu D, Raddatz E, Nakatani Y, Ikura M. TFIIA-TAF regulatory interplay: NMR evidence for overlapping binding sites on TBP. FEBS Lett 2000; 468:149 - 54; http://dx.doi.org/10.1016/S0014-5793(00)01213-8; PMID: 10692576
   PubMed Web of Science ®Google Scholar
• Carninci P, Sandelin A, Lenhard B, Katayama S, Shimokawa K, Ponjavic J, et al. Genome-wide analysis of mammalian promoter architecture and evolution. Nat Genet 2006; 38:626 - 35; http://dx.doi.org/10.1038/ng1789; PMID: 16645617
   PubMed Web of Science ®Google Scholar
• Patikoglou GA, Kim JL, Sun L, Yang SH, Kodadek T, Burley SK. TATA element recognition by the TATA box-binding protein has been conserved throughout evolution. Genes Dev 1999; 13:3217 - 30; http://dx.doi.org/10.1101/gad.13.24.3217; PMID: 10617571
   PubMed Web of Science ®Google Scholar
• Goodrich JA, Tjian R. Unexpected roles for core promoter recognition factors in cell-type-specific transcription and gene regulation. Nat Rev Genet 2010; 11:549 - 58; PMID: 20628347
   PubMed Web of Science ®Google Scholar
• Vermeulen M, Mulder KW, Denissov S, Pijnappel WW, van Schaik FM, Varier RA, et al. Selective anchoring of TFIID to nucleosomes by trimethylation of histone H3 lysine 4. Cell 2007; 131:58 - 69; http://dx.doi.org/10.1016/j.cell.2007.08.016; PMID: 17884155
   PubMed Web of Science ®Google Scholar
• Lauberth SM, Nakayama T, Wu X, Ferris AL, Tang Z, Hughes SH, et al. H3K4me3 interactions with TAF3 regulate preinitiation complex assembly and selective gene activation. Cell 2013; 152:1021 - 36; http://dx.doi.org/10.1016/j.cell.2013.01.052; PMID: 23452851
   PubMed Web of Science ®Google Scholar
• Rhee HS, Pugh BF. Genome-wide structure and organization of eukaryotic pre-initiation complexes. Nature 2012; 483:295 - 301; http://dx.doi.org/10.1038/nature10799; PMID: 22258509
   PubMed Web of Science ®Google Scholar
• Lomvardas S, Thanos D. Nucleosome sliding via TBP DNA binding in vivo. Cell 2001; 106:685 - 96; http://dx.doi.org/10.1016/S0092-8674(01)00490-1; PMID: 11572775
   PubMed Web of Science ®Google Scholar