[1] Stadhouders R, Vidal E, Serra F, Di Stefano B, Le Dily F, Quilez J, et al. Transcription factors orchestrate dynamic interplay between genome topology and gene regulation during cell reprogramming. Nat Genet. 2018;50:238–49. [PMC free article] [PubMed] [Google Scholar]
[2] Vihervaara A, Mahat DB, Guertin MJ, Chu T, Danko CG, Lis JT, et al. Transcriptional response to stress is pre-wired by promoter and enhancer architecture. Nat Commun. 2017;8:255. [PMC free article] [PubMed] [Google Scholar]
[3] Reja R, Vinayachandran V, Ghosh S, Pugh BF. Molecular mechanisms of ribosomal protein gene coregulation. Genes Dev. 2015;29:1942–54. [PMC free article] [PubMed] [Google Scholar]
[4] Weingarten-Gabbay S, Nir R, Lubliner S, Sharon E, Kalma Y, Weinberger A, et al. Systematic interrogation of human promoters. Genome Res. 2019;29:171–83. [PMC free article] [PubMed] [Google Scholar]
[5] Plank JL, Dean A. Enhancer function: mechanistic and genome-wide insights come together. Mol Cell. 2014;55:5–14. [PMC free article] [PubMed] [Google Scholar]
[6] Vo Ngoc L, Huang CY, Cassidy CJ, Medrano C, Kadonaga JT. Identification of the human DPR core promoter element using machine learning. Nature. 2020;585:459–63. [PMC free article] [PubMed] [Google Scholar]
[7] Consortium EP. An integrated encyclopedia of DNA elements in the human genome. Nature. 2012;489:57–74. [PMC free article] [PubMed] [Google Scholar]
[8] Sanyal A, Lajoie BR, Jain G, Dekker J. The long-range interaction landscape of gene promoters. Nature. 2012;489:109–13. [PMC free article] [PubMed] [Google Scholar]
[9] Roeder RG. The role of general initiation factors in transcription by RNA polymerase II. Trends Biochem Sci. 1996;21:327–35. [PubMed] [Google Scholar]
[10] Lifton RP, Goldberg ML, Karp RW, Hogness DS. The organization of the histone genes in Drosophila melanogaster: functional and evolutionary implications. Cold Spring Harb Symp Quant Biol. 1978;42Pt 2:1047–51. [PubMed] [Google Scholar]
[11] Mitchell PJ, Tjian R. Transcriptional regulation in mammalian cells by sequence-specific DNA binding proteins. Science. 1989;245:371–8. [PubMed] [Google Scholar]
[12] Buratowski S, Hahn S, Sharp PA, Guarente L. Function of a yeast TATA element-binding protein in a mammalian transcription system. Nature. 1988;334:37–42. [PubMed] [Google Scholar]
[13] Vo Ngoc L, Kassavetis GA, Kadonaga JT. The RNA Polymerase II Core Promoter in Drosophila. Genetics. 2019;212:13–24. [PMC free article] [PubMed] [Google Scholar]
[14] Roadmap Epigenomics C, Kundaje A, Meuleman W, Ernst J, Bilenky M, Yen A, et al. Integrative analysis of 111 reference human epigenomes. Nature. 2015;518:317–30. [PMC free article] [PubMed] [Google Scholar]
[15] Tippens ND, Liang J, Leung AK, Wierbowski SD, Ozer A, Booth JG, et al. Transcription imparts architecture, function and logic to enhancer units. Nat Genet. 2020;52:1067–75. [PMC free article] [PubMed] [Google Scholar]
[16] Andersson R, Sandelin A. Determinants of enhancer and promoter activities of regulatory elements. Nat Rev Genet. 2020;21:71–87. [PubMed] [Google Scholar]
[17] O’Neill LP, Turner BM. Immunoprecipitation of native chromatin: NChIP. Methods. 2003;31:76–82. [PubMed] [Google Scholar]
[18] Collas P, Dahl JA. Chop it, ChIP it, check it: the current status of chromatin immunoprecipitation. Front Biosci. 2008;13:929–43. [PubMed] [Google Scholar]
[19] Cao Y, Yao Z, Sarkar D, Lawrence M, Sanchez GJ, Parker MH, et al. Genome-wide MyoD binding in skeletal muscle cells: a potential for broad cellular reprogramming. Dev Cell. 2010;18:662–74. [PMC free article] [PubMed] [Google Scholar]
[20] Lin YC, Jhunjhunwala S, Benner C, Heinz S, Welinder E, Mansson R, et al. A global network of transcription factors, involving E2A, EBF1 and Foxo1, that orchestrates B cell fate. Nat Immunol. 2010;11:635–43. [PMC free article] [PubMed] [Google Scholar]
[21] Pilon AM, Ajay SS, Kumar SA, Steiner LA, Cherukuri PF, Wincovitch S, et al. Genome-wide ChIP-Seq reveals a dramatic shift in the binding of the transcription factor erythroid Kruppel-like factor during erythrocyte differentiation. Blood. 2011;118:e139–48. [PMC free article] [PubMed] [Google Scholar]
[22] Spitz F, Furlong EE. Transcription factors: from enhancer binding to developmental control. Nat Rev Genet. 2012;13:613–26. [PubMed] [Google Scholar]
[23] Chang LH, Ghosh S, Noordermeer D. TADs and Their Borders: Free Movement or Building a Wall?J Mol Biol. 2020;432:643–52. [PubMed] [Google Scholar]
[24] Lupianez DG, Kraft K, Heinrich V, Krawitz P, Brancati F, Klopocki E, et al. Disruptions of topological chromatin domains cause pathogenic rewiring of gene-enhancer interactions. Cell. 2015;161:1012–25. [PMC free article] [PubMed] [Google Scholar]
[25] Arzate-Mejia RG, Recillas-Targa F, Corces VG. Developing in 3D: the role of CTCF in cell differentiation. Development. 2018;145. [PMC free article] [PubMed] [Google Scholar]
[26] Szabo Q, Bantignies F, Cavalli G. Principles of genome folding into topologically associating domains. Sci Adv. 2019;5:eaaw1668. [PMC free article] [PubMed] [Google Scholar]
[27] Li Y, Haarhuis JHI, Sedeno Cacciatore A, Oldenkamp R, van Ruiten MS, Willems L, et al. The structural basis for cohesin-CTCF-anchored loops. Nature. 2020;578:472–6. [PMC free article] [PubMed] [Google Scholar]
[28] Barrington C, Georgopoulou D, Pezic D, Varsally W, Herrero J, Hadjur S. Enhancer accessibility and CTCF occupancy underlie asymmetric TAD architecture and cell type specific genome topology. Nat Commun. 2019;10:2908. [PMC free article] [PubMed] [Google Scholar]
[29] Banani SF, Lee HO, Hyman AA, Rosen MK. Biomolecular condensates: organizers of cellular biochemistry. Nat Rev Mol Cell Biol. 2017;18:285–98. [PMC free article] [PubMed] [Google Scholar]
[30] Boehning M, Dugast-Darzacq C, Rankovic M, Hansen AS, Yu T, Marie-Nelly H, et al. RNA polymerase II clustering through carboxy-terminal domain phase separation. Nat Struct Mol Biol. 2018;25:833–40. [PubMed] [Google Scholar]
[31] Boija A, Klein IA, Sabari BR, Dall’Agnese A, Coffey EL, Zamudio AV, et al. Transcription Factors Activate Genes through the Phase-Separation Capacity of Their Activation Domains. Cell. 2018;175:1842–55 e16. [PMC free article] [PubMed] [Google Scholar]
[32] Whyte WA, Orlando DA, Hnisz D, Abraham BJ, Lin CY, Kagey MH, et al. Master transcription factors and mediator establish super-enhancers at key cell identity genes. Cell. 2013;153:307–19. [PMC free article] [PubMed] [Google Scholar]
[33] Cho WK, Spille JH, Hecht M, Lee C, Li C, Grube V, et al. Mediator and RNA polymerase II clusters associate in transcription-dependent condensates. Science. 2018;361:412–5. [PMC free article] [PubMed] [Google Scholar]
[34] Sabari BR, Dall’Agnese A, Boija A, Klein IA, Coffey EL, Shrinivas K, et al. Coactivator condensation at super-enhancers links phase separation and gene control. Science. 2018;361. [PMC free article] [PubMed] [Google Scholar]
[35] Hnisz D, Shrinivas K, Young RA, Chakraborty AK, Sharp PA. A Phase Separation Model for Transcriptional Control. Cell. 2017;169:13–23. [PMC free article] [PubMed] [Google Scholar]
[36] Hahn SPhase Separation, Protein Disorder, and Enhancer Function. Cell. 2018;175:1723–5. [PubMed] [Google Scholar]
[37] McSwiggen DT, Mir M, Darzacq X, Tjian R. Evaluating phase separation in live cells: diagnosis, caveats, and functional consequences. Genes Dev. 2019;33:1619–34. [PMC free article] [PubMed] [Google Scholar]
[38] Peng Y, Zhang Y. Enhancer and super-enhancer: Positive regulators in gene transcription. Animal Model Exp Med. 2018;1:169–79. [PMC free article] [PubMed] [Google Scholar]
[39] Chambers I, Smith A. Self-renewal of teratocarcinoma and embryonic stem cells. Oncogene. 2004;23:7150–60. [PubMed] [Google Scholar]
[40] Zamudio AV, Dall’Agnese A, Henninger JE, Manteiga JC, Afeyan LK, Hannett NM, et al. Mediator Condensates Localize Signaling Factors to Key Cell Identity Genes. Mol Cell. 2019;76:753–66 e6. [PMC free article] [PubMed] [Google Scholar]
[41] Wilflingseder J, Willi M, Lee HK, Olauson H, Jankowski J, Ichimura T, et al. Enhancer and super-enhancer dynamics in repair after ischemic acute kidney injury. Nat Commun. 2020;11:3383. [PMC free article] [PubMed] [Google Scholar]
[42] Chen T, Dent SY. Chromatin modifiers and remodellers: regulators of cellular differentiation. Nat Rev Genet. 2014;15:93–106. [PMC free article] [PubMed] [Google Scholar]
[43] 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. [PubMed] [Google Scholar]
[44] 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. [PubMed] [Google Scholar]
[45] 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. [PubMed] [Google Scholar]
[46] Allen BL, Taatjes DJ. The Mediator complex: a central integrator of transcription. Nat Rev Mol Cell Biol. 2015;16:155–66. [PMC free article] [PubMed] [Google Scholar]
[47] Ptashne M, Gann A. Transcriptional activation by recruitment. Nature. 1997;386:569–77. [PubMed] [Google Scholar]
[48] Green MR. Eukaryotic transcription activation: right on target. Mol Cell. 2005;18:399–402. [PubMed] [Google Scholar]
[49] Rossi MJ, Lai WKM, Pugh BF. Simplified ChIP-exo assays. Nat Commun. 2018;9:2842. [PMC free article] [PubMed] [Google Scholar]
[50] Rhee HS, Pugh BF. Genome-wide structure and organization of eukaryotic pre-initiation complexes. Nature. 2012;483:295–301. [PMC free article] [PubMed] [Google Scholar]
[51] Rhee HS, Pugh BF. Comprehensive genome-wide protein-DNA interactions detected at single-nucleotide resolution. Cell. 2011;147:1408–19. [PMC free article] [PubMed] [Google Scholar]
[52] Rhee HS, Bataille AR, Zhang L, Pugh BF. Subnucleosomal structures and nucleosome asymmetry across a genome. Cell. 2014;159:1377–88. [PMC free article] [PubMed] [Google Scholar]
[53] Vinayachandran V, Reja R, Rossi MJ, Park B, Rieber L, Mittal C, et al. Widespread and precise reprogramming of yeast protein-genome interactions in response to heat shock. Genome Res. 2018. [PMC free article] [PubMed] [Google Scholar]
[54] Badjatia N, Rossi MJ, Bataille AR, Mittal C, Lai WKM, Pugh BF. Acute stress drives global repression through two independent RNA polymerase II stalling events in Saccharomyces. Cell Rep. 2021;in press. [PMC free article] [PubMed] [Google Scholar]
[55] Krietenstein N, Wal M, Watanabe S, Park B, Peterson CL, Pugh BF, et al. Genomic Nucleosome Organization Reconstituted with Pure Proteins. Cell. 2016;167:709–21 e12. [PMC free article] [PubMed] [Google Scholar]
[56] Geiman TM, Robertson KD. Chromatin remodeling, histone modifications, and DNA methylation-how does it all fit together?J Cell Biochem. 2002;87:117–25. [PubMed] [Google Scholar]
[57] Visel A, Blow MJ, Li Z, Zhang T, Akiyama JA, Holt A, et al. ChIP-seq accurately predicts tissue-specific activity of enhancers. Nature. 2009;457:854–8. [PMC free article] [PubMed] [Google Scholar]
[58] Raisner R, Kharbanda S, Jin L, Jeng E, Chan E, Merchant M, et al. Enhancer Activity Requires CBP/P300 Bromodomain-Dependent Histone H3K27 Acetylation. Cell Rep. 2018;24:1722–9. [PubMed] [Google Scholar]
[59] Calo E, Wysocka J. Modification of enhancer chromatin: what, how, and why?Mol Cell. 2013;49:825–37. [PMC free article] [PubMed] [Google Scholar]
[60] Bedford DC, Kasper LH, f*ckuyama T, Brindle PK. Target gene context influences the transcriptional requirement for the KAT3 family of CBP and p300 histone acetyltransferases. Epigenetics. 2010;5:9–15. [PMC free article] [PubMed] [Google Scholar]
[61] Zhang JJ, Vinkemeier U, Gu W, Chakravarti D, Horvath CM, Darnell JE, Jr. Two contact regions between Stat1 and CBP/p300 in interferon gamma signaling. Proc Natl Acad Sci U S A. 1996;93:15092–6. [PMC free article] [PubMed] [Google Scholar]
[62] Qin BY, Liu C, Srinath H, Lam SS, Correia JJ, Derynck R, et al. Crystal structure of IRF-3 in complex with CBP. Structure. 2005;13:1269–77. [PubMed] [Google Scholar]
[63] Wojciak JM, Martinez-Yamout MA, Dyson HJ, Wright PE. Structural basis for recruitment of CBP/p300 coactivators by STAT1 and STAT2 transactivation domains. EMBO J. 2009;28:948–58. [PMC free article] [PubMed] [Google Scholar]
[64] Ortega E, Rengachari S, Ibrahim Z, Hoghoughi N, Gaucher J, Holehouse AS, et al. Transcription factor dimerization activates the p300 acetyltransferase. Nature. 2018;562:538–44. [PMC free article] [PubMed] [Google Scholar]
[65] Yudkovsky N, Logie C, Hahn S, Peterson CL. Recruitment of the SWI/SNF chromatin remodeling complex by transcriptional activators. Genes Dev. 1999;13:2369–74. [PMC free article] [PubMed] [Google Scholar]
[66] West JA, Cook A, Alver BH, Stadtfeld M, Deaton AM, Hochedlinger K, et al. Nucleosomal occupancy changes locally over key regulatory regions during cell differentiation and reprogramming. Nat Commun. 2014;5:4719. [PMC free article] [PubMed] [Google Scholar]
[67] You JS, Kelly TK, De Carvalho DD, Taberlay PC, Liang G, Jones PA. OCT4 establishes and maintains nucleosome-depleted regions that provide additional layers of epigenetic regulation of its target genes. Proc Natl Acad Sci U S A. 2011;108:14497–502. [PMC free article] [PubMed] [Google Scholar]
[68] Ding J, Xu H, Faiola F, Ma’ayan A, Wang J. Oct4 links multiple epigenetic pathways to the pluripotency network. Cell Res. 2012;22:155–67. [PMC free article] [PubMed] [Google Scholar]
[69] King HW, Klose RJ. The pioneer factor OCT4 requires the chromatin remodeller BRG1 to support gene regulatory element function in mouse embryonic stem cells. Elife. 2017;6. [PMC free article] [PubMed] [Google Scholar]
[70] Wu T, Kamikawa YF, Donohoe ME. Brd4’s Bromodomains Mediate Histone H3 Acetylation and Chromatin Remodeling in Pluripotent Cells through P300 and Brg1. Cell Rep. 2018;25:1756–71. [PubMed] [Google Scholar]
[71] Wu T, Pinto HB, Kamikawa YF, Donohoe ME. The BET family member BRD4 interacts with OCT4 and regulates pluripotency gene expression. Stem Cell Reports. 2015;4:390–403. [PMC free article] [PubMed] [Google Scholar]
[72] Wang YL, Faiola F, Martinez E. Purification of multiprotein histone acetyltransferase complexes. Methods Mol Biol. 2012;809:427–43. [PMC free article] [PubMed] [Google Scholar]
[73] Thomas MC, Chiang CM. The general transcription machinery and general cofactors. Crit Rev Biochem Mol Biol. 2006;41:105–78. [PubMed] [Google Scholar]
[74] Grant PA, Duggan L, Cote J, Roberts SM, Brownell JE, Candau R, et al. Yeast Gcn5 functions in two multisubunit complexes to acetylate nucleosomal histones: characterization of an Ada complex and the SAGA (Spt/Ada) complex. Genes Dev. 1997;11:1640–50. [PubMed] [Google Scholar]
[75] Henry KW, Wyce A, Lo WS, Duggan LJ, Emre NC, Kao CF, et al. Transcriptional activation via sequential histone H2B ubiquitylation and deubiquitylation, mediated by SAGA-associated Ubp8. Genes Dev. 2003;17:2648–63. [PMC free article] [PubMed] [Google Scholar]
[76] Sermwittayawong D, Tan S. SAGA binds TBP via its Spt8 subunit in competition with DNA: implications for TBP recruitment. Embo J. 2006;25:3791–800. [PMC free article] [PubMed] [Google Scholar]
[77] Huisinga KL, Pugh BF. A genome-wide housekeeping role for TFIID and a highly regulated stress-related role for SAGA in Saccharomyces cerevisiae. Mol Cell. 2004;13:573–85. [PubMed] [Google Scholar]
[78] Chen XF, Lehmann L, Lin JJ, Vashisht A, Schmidt R, Ferrari R, et al. Mediator and SAGA have distinct roles in Pol II preinitiation complex assembly and function. Cell Rep. 2012;2:1061–7. [PMC free article] [PubMed] [Google Scholar]
[79] Basehoar AD, Zanton SJ, Pugh BF. Identification and distinct regulation of yeast TATA box-containing genes. Cell. 2004;116:699–709. [PubMed] [Google Scholar]
[80] Donczew R, Warfield L, Pacheco D, Erijman A, Hahn S. Two roles for the yeast transcription coactivator SAGA and a set of genes redundantly regulated by TFIID and SAGA. Elife. 2020;9. [PMC free article] [PubMed] [Google Scholar]
[81] Bhaumik SR, Raha T, Aiello DP, Green MR. In vivo target of a transcriptional activator revealed by fluorescence resonance energy transfer. Genes Dev. 2004;18:333–43. [PMC free article] [PubMed] [Google Scholar]
[82] Reeves WM, Hahn S. Targets of the Gal4 transcription activator in functional transcription complexes. Mol Cell Biol. 2005;25:9092–102. [PMC free article] [PubMed] [Google Scholar]
[83] Lang SE, Hearing P. The adenovirus E1A oncoprotein recruits the cellular TRRAP/GCN5 histone acetyltransferase complex. Oncogene. 2003;22:2836–41. [PubMed] [Google Scholar]
[84] McMahon SB, Van Buskirk HA, Dugan KA, Copeland TD, Cole MD. The novel ATM-related protein TRRAP is an essential cofactor for the c-Myc and E2F oncoproteins. Cell. 1998;94:363–74. [PubMed] [Google Scholar]
[85] Ard PG, Chatterjee C, Kunjibettu S, Adside LR, Gralinski LE, McMahon SB. Transcriptional regulation of the mdm2 oncogene by p53 requires TRRAP acetyltransferase complexes. Mol Cell Biol. 2002;22:5650–61. [PMC free article] [PubMed] [Google Scholar]
[86] Allard S, Utley RT, Savard J, Clarke A, Grant P, Brandl CJ, et al. NuA4, an essential transcription adaptor/histone H4 acetyltransferase complex containing Esa1p and the ATM-related cofactor Tra1p. Embo J. 1999;18:5108–19. [PMC free article] [PubMed] [Google Scholar]
[87] Liu X, Tesfai J, Evrard YA, Dent SY, Martinez E. c-Myc transformation domain recruits the human STAGA complex and requires TRRAP and GCN5 acetylase activity for transcription activation. J Biol Chem. 2003;278:20405–12. [PMC free article] [PubMed] [Google Scholar]
[88] Zhang N, Ichikawa W, Faiola F, Lo SY, Liu X, Martinez E. MYC interacts with the human STAGA coactivator complex via multivalent contacts with the GCN5 and TRRAP subunits. Biochim Biophys Acta. 2014;1839:395–405. [PMC free article] [PubMed] [Google Scholar]
[89] Gamper AM, Roeder RG. Multivalent binding of p53 to the STAGA complex mediates coactivator recruitment after UV damage. Mol Cell Biol. 2008;28:2517–27. [PMC free article] [PubMed] [Google Scholar]
[90] Papadopoulos P, Gutierrez L, Demmers J, Scheer E, Pourfarzad F, Papageorgiou DN, et al. TAF10 Interacts with the GATA1 Transcription Factor and Controls Mouse Erythropoiesis. Mol Cell Biol. 2015;35:2103–18. [PMC free article] [PubMed] [Google Scholar]
[91] Sengupta T, Cohet N, Morle F, Bieker JJ. Distinct modes of gene regulation by a cell-specific transcriptional activator. Proc Natl Acad Sci U S A. 2009;106:4213–8. [PMC free article] [PubMed] [Google Scholar]
[92] Uesugi M, Verdine GL. The alpha-helical FXXPhiPhi motif in p53: TAF interaction and discrimination by MDM2. Proc Natl Acad Sci U S A. 1999;96:14801–6. [PMC free article] [PubMed] [Google Scholar]
[93] Uesugi M, Nyanguile O, Lu H, Levine AJ, Verdine GL. Induced alpha helix in the VP16 activation domain upon binding to a human TAF. Science. 1997;277:1310–3. [PubMed] [Google Scholar]
[94] Yoon JW, Lamm M, Iannaccone S, Higashiyama N, Leong KF, Iannaccone P, et al. p53 modulates the activity of the GLI1 oncogene through interactions with the shared coactivator TAF9. DNA Repair (Amst). 2015;34:9–17. [PMC free article] [PubMed] [Google Scholar]
[95] Garbett KA, Tripathi MK, Cencki B, Layer JH, Weil PA. Yeast TFIID serves as a coactivator for Rap1p by direct protein-protein interaction. Mol Cell Biol. 2007;27:297–311. [PMC free article] [PubMed] [Google Scholar]
[96] Layer JH, Miller SG, Weil PA. Direct transactivator-transcription factor IID (TFIID) contacts drive yeast ribosomal protein gene transcription. J Biol Chem. 2010;285:15489–99. [PMC free article] [PubMed] [Google Scholar]
[97] Papai G, Tripathi MK, Ruhlmann C, Layer JH, Weil PA, Schultz P. TFIIA and the transactivator Rap1 cooperate to commit TFIID for transcription initiation. Nature. 2010;465:956–60. [PMC free article] [PubMed] [Google Scholar]
[98] Rossi MJ, Kuntala PK, Lai WKM, Yamada N, Badjatia N, Mittal C, et al. High resolution protein architecture of the budding yeast genome. Nature. 2021;in press. [PMC free article] [PubMed] [Google Scholar]
[99] 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. [PMC free article] [PubMed] [Google Scholar]
[100] Saluja D, Vassallo MF, Tanese N. Distinct subdomains of human TAFII130 are required for interactions with glutamine-rich transcriptional activators. Mol Cell Biol. 1998;18:5734–43. [PMC free article] [PubMed] [Google Scholar]
[101] Tanese N, Saluja D, Vassallo MF, Chen JL, Admon A. Molecular cloning and analysis of two subunits of the human TFIID complex: hTAFII130 and hTAFII100. Proc Natl Acad Sci U S A. 1996;93:13611–6. [PMC free article] [PubMed] [Google Scholar]
[102] Hibino E, Inoue R, Sugiyama M, Kuwahara J, Matsuzaki K, Hoshino M. Interaction between intrinsically disordered regions in transcription factors Sp1 and TAF4. Protein Sci. 2016;25:2006–17. [PMC free article] [PubMed] [Google Scholar]
[103] Gill G, Pascal E, Tseng ZH, Tjian R. A glutamine-rich hydrophobic patch in transcription factor Sp1 contacts the dTAFII110 component of the Drosophila TFIID complex and mediates transcriptional activation. Proc Natl Acad Sci U S A. 1994;91:192–6. [PMC free article] [PubMed] [Google Scholar]
[104] Wang X, Truckses DM, Takada S, Matsumura T, Tanese N, Jacobson RH. Conserved regionI of human coactivator TAF4 binds to a short hydrophobic motif present in transcriptional regulators. Proc Natl Acad Sci U S A. 2007;104:7839–44. [PMC free article] [PubMed] [Google Scholar]
[105] Chen WY, Zhang J, Geng H, Du Z, Nakadai T, Roeder RG. A TAF4 coactivator function for E proteins that involves enhanced TFIID binding. Genes Dev. 2013;27:1596–609. [PMC free article] [PubMed] [Google Scholar]
[106] Bhattacharya S, Lou X, Hwang P, Rajashankar KR, Wang X, Gustafsson JA, et al. Structural and functional insight into TAF1-TAF7, a subcomplex of transcription factor II D. Proc Natl Acad Sci U S A. 2014;111:9103–8. [PMC free article] [PubMed] [Google Scholar]
[107] Wang H, Curran EC, Hinds TR, Wang EH, Zheng N. Crystal structure of a TAF1-TAF7 complex in human transcription factor IID reveals a promoter binding module. Cell Res. 2014;24:1433–44. [PMC free article] [PubMed] [Google Scholar]
[108] Li HH, Li AG, Sheppard HM, Liu X. Phosphorylation on Thr-55 by TAF1 mediates degradation of p53: a role for TAF1 in cell G1 progression. Mol Cell. 2004;13:867–78. [PubMed] [Google Scholar]
[109] Li AG, Piluso LG, Cai X, Gadd BJ, Ladurner AG, Liu X. An acetylation switch in p53 mediates holo-TFIID recruitment. Mol Cell. 2007;28:408–21. [PubMed] [Google Scholar]
[110] Allende-Vega N, Saville MK, Meek DW. Transcription factor TAFII250 promotes Mdm2-dependent turnover of p53. Oncogene. 2007;26:4234–42. [PMC free article] [PubMed] [Google Scholar]
[111] Coleman RA, Qiao Z, Singh SK, Peng CS, Cianfrocco M, Zhang Z, et al. p53 Dynamically Directs TFIID Assembly on Target Gene Promoters. Mol Cell Biol. 2017;37. [PMC free article] [PubMed] [Google Scholar]
[112] Wei Y, Resetca D, Li Z, Johansson-Akhe I, Ahlner A, Helander S, et al. Multiple direct interactions of TBP with the MYC oncoprotein. Nat Struct Mol Biol. 2019;26:1035–43. [PubMed] [Google Scholar]
[113] Anandapadamanaban M, Andresen C, Helander S, Ohyama Y, Siponen MI, Lundstrom P, et al. High-resolution structure of TBP with TAF1 reveals anchoring patterns in transcriptional regulation. Nat Struct Mol Biol. 2013;20:1008–14. [PMC free article] [PubMed] [Google Scholar]
[114] Kotani T, Miyake T, Tsukihashi Y, Hinnebusch AG, Nakatani Y, Kawaichi M, et al. Identification of highly conserved amino-terminal segments of dTAFII230 and yTAFII145 that are functionally interchangeable for inhibiting TBP-DNA interactions in vitro and in promoting yeast cell growth in vivo. J Biol Chem. 1998;273:32254–64. [PubMed] [Google Scholar]
[115] Patel AB, Louder RK, Greber BJ, Grunberg S, Luo J, Fang J, et al. Structure of human TFIID and mechanism of TBP loading onto promoter DNA. Science. 2018;362. [PMC free article] [PubMed] [Google Scholar]
[116] Poss ZC, Ebmeier CC, Taatjes DJ. The Mediator complex and transcription regulation. Crit Rev Biochem Mol Biol. 2013;48:575–608. [PMC free article] [PubMed] [Google Scholar]
[117] Borggrefe T, Yue X. Interactions between subunits of the Mediator complex with gene-specific transcription factors. Semin Cell Dev Biol. 2011;22:759–68. [PubMed] [Google Scholar]
[118] Verger A, Monte D, Villeret V. Twenty years of Mediator complex structural studies. Biochem Soc Trans. 2019;47:399–410. [PMC free article] [PubMed] [Google Scholar]
[119] Plaschka C, Lariviere L, Wenzeck L, Seizl M, Hemann M, Tegunov D, et al. Architecture of the RNA polymerase II-Mediator core initiation complex. Nature. 2015;518:376–80. [PubMed] [Google Scholar]
[120] Quevedo M, Meert L, Dekker MR, Dekkers DHW, Brandsma JH, van den Berg DLC, et al. Mediator complex interaction partners organize the transcriptional network that defines neural stem cells. Nat Commun. 2019;10:2669. [PMC free article] [PubMed] [Google Scholar]
[121] Fondell JD, Ge H, Roeder RG. Ligand induction of a transcriptionally active thyroid hormone receptor coactivator complex. Proc Natl Acad Sci U S A. 1996;93:8329–33. [PMC free article] [PubMed] [Google Scholar]
[122] Sever R, Glass CK. Signaling by nuclear receptors. Cold Spring Harb Perspect Biol. 2013;5:a016709. [PMC free article] [PubMed] [Google Scholar]
[123] Yuan CX, Ito M, Fondell JD, Fu ZY, Roeder RG. The TRAP220 component of a thyroid hormone receptor- associated protein (TRAP) coactivator complex interacts directly with nuclear receptors in a ligand-dependent fashion. Proc Natl Acad Sci U S A. 1998;95:7939–44. [PMC free article] [PubMed] [Google Scholar]
[124] Belorusova AY, Bourguet M, Hessmann S, Chalhoub S, Kieffer B, Cianferani S, et al. Molecular determinants of MED1 interaction with the DNA bound VDR-RXR heterodimer. Nucleic Acids Res. 2020;48:11199–213. [PMC free article] [PubMed] [Google Scholar]
[125] Ren Y, Behre E, Ren Z, Zhang J, Wang Q, Fondell JD. Specific structural motifs determine TRAP220 interactions with nuclear hormone receptors. Mol Cell Biol. 2000;20:5433–46. [PMC free article] [PubMed] [Google Scholar]
[126] Liu Z, Yao X, Yan G, Xu Y, Yan J, Zou W, et al. Mediator MED23 cooperates with RUNX2 to drive osteoblast differentiation and bone development. Nat Commun. 2016;7:11149. [PMC free article] [PubMed] [Google Scholar]
[127] Wang G, Balamotis MA, Stevens JL, Yamaguchi Y, Handa H, Berk AJ. Mediator requirement for both recruitment and postrecruitment steps in transcription initiation. Mol Cell. 2005;17:683–94. [PubMed] [Google Scholar]
[128] Stevens JL, Cantin GT, Wang G, Shevchenko A, Shevchenko A, Berk AJ. Transcription control by E1A and MAP kinase pathway via Sur2 mediator subunit. Science. 2002;296:755–8. [PubMed] [Google Scholar]
[129] Yin JW, Liang Y, Park JY, Chen D, Yao X, Xiao Q, et al. Mediator MED23 plays opposing roles in directing smooth muscle cell and adipocyte differentiation. Genes Dev. 2012;26:2192–205. [PMC free article] [PubMed] [Google Scholar]
[130] Chu Y, Gomez Rosso L, Huang P, Wang Z, Xu Y, Yao X, et al. Liver Med23 ablation improves glucose and lipid metabolism through modulating FOXO1 activity. Cell Res. 2014;24:1250–65. [PMC free article] [PubMed] [Google Scholar]
[131] Yang X, Zhao M, Xia M, Liu Y, Yan J, Ji H, et al. Selective requirement for Mediator MED23 in Ras-active lung cancer. Proc Natl Acad Sci U S A. 2012;109:E2813–22. [PMC free article] [PubMed] [Google Scholar]
[132] Sun Y, Zhu X, Chen X, Liu H, Xu Y, Chu Y, et al. The mediator subunit Med23 contributes to controlling T-cell activation and prevents autoimmunity. Nat Commun. 2014;5:5225. [PubMed] [Google Scholar]
[133] Fant CB, Taatjes DJ. Regulatory functions of the Mediator kinases CDK8 and CDK19. Transcription. 2019;10:76–90. [PMC free article] [PubMed] [Google Scholar]
[134] Poss ZC, Ebmeier CC, Odell AT, Tangpeerachaikul A, Lee T, Pelish HE, et al. Identification of Mediator Kinase Substrates in Human Cells using Cortistatin A and Quantitative Phosphoproteomics. Cell Rep. 2016;15:436–50. [PMC free article] [PubMed] [Google Scholar]
[135] Pelish HE, Liau BB, Nitulescu II, Tangpeerachaikul A, Poss ZC, Da Silva DH, et al. Mediator kinase inhibition further activates super-enhancer-associated genes in AML. Nature. 2015;526:273–6. [PMC free article] [PubMed] [Google Scholar]
[136] Steinparzer I, Sedlyarov V, Rubin JD, Eislmayr K, Galbraith MD, Levandowski CB, et al. Transcriptional Responses to IFN-gamma Require Mediator Kinase-Dependent Pause Release and Mechanistically Distinct CDK8 and CDK19Functions. Mol Cell2019;76:485–99 e8. [PMC free article] [PubMed] [Google Scholar]
[137] Lai F, Orom UA, Cesaroni M, Beringer M, Taatjes DJ, Blobel GA, et al. Activating RNAs associate with Mediator to enhance chromatin architecture and transcription. Nature. 2013;494:497–501. [PMC free article] [PubMed] [Google Scholar]
[138] Hsieh CL, Fei T, Chen Y, Li T, Gao Y, Wang X, et al. Enhancer RNAs participate in androgen receptor-driven looping that selectively enhances gene activation. Proc Natl Acad Sci U S A. 2014;111:7319–24. [PMC free article] [PubMed] [Google Scholar]
[139] Tuttle LM, Pacheco D, Warfield L, Luo J, Ranish J, Hahn S, et al. Gcn4-Mediator Specificity Is Mediated by a Large and Dynamic Fuzzy Protein-Protein Complex. Cell Rep. 2018;22:3251–64. [PMC free article] [PubMed] [Google Scholar]
[140] Brzovic PS, Heikaus CC, Kisselev L, Vernon R, Herbig E, Pacheco D, et al. The acidic transcription activator Gcn4 binds the mediator subunit Gal11/Med15 using a simple protein interface forming a fuzzy complex. Mol Cell. 2011;44:942–53. [PMC free article] [PubMed] [Google Scholar]
[141] Taatjes DJ, Naar AM, Andel F 3rd, Nogales E, Tjian RStructure, function, and activator-induced conformations of the CRSP coactivator. Science. 2002;295:1058–62. [PubMed] [Google Scholar]
