Regulation of hepatocyte cell cycle re-entry by RNA polymerase II-associated Gdown1

References

• Budirahardja Y, Gonczy P. Coupling the cell cycle to development. Development. 2009;136:2861–2872.
   PubMed Web of Science ®Google Scholar
• Murray AW. Recycling the cell cycle: cyclins revisited. Cell. 2004;116:221–234.
   PubMed Web of Science ®Google Scholar
• He S, Nakada D, Morrison SJ. Mechanisms of stem cell self-renewal. Annu Rev Cell Dev Biol. 2009;25:377–406.
   PubMed Web of Science ®Google Scholar
• Bahler J. Cell-cycle control of gene expression in budding and fission yeast. Annu Rev Genet. 2005;39:69–94.
   PubMed Web of Science ®Google Scholar
• Bertoli C, Skotheim JM, de Bruin RA. Control of cell cycle transcription during G1 and S phases. Nat Rev Mol Cell Biol. 2013;14:518–528.
   PubMed Web of Science ®Google Scholar
• Smith ZD, Sindhu C, Meissner A. Molecular features of cellular reprogramming and development. Nat Rev Mol Cell Biol. 2016;17:139–154.
   PubMed Web of Science ®Google Scholar
• Hirschi KK, Li S, Roy K. Induced pluripotent stem cells for regenerative medicine. Annu Rev Biomed Eng. 2014;16:277–294.
   PubMed Web of Science ®Google Scholar
• Bradner JE, Hnisz D, Young RA. Transcriptional addiction in cancer. Cell. 2017;168:629–643.
   PubMed Web of Science ®Google Scholar
• Kastenhuber ER, Lowe SW. Putting p53 in context. Cell. 2017;170:1062–1078.
   PubMed Web of Science ®Google Scholar
• Grunberg S, Hahn S. Structural insights into transcription initiation by RNA polymerase II. Trends Biochem Sci. 2013;38:603–611.
   PubMed Web of Science ®Google Scholar
• Cramer P. Organization and regulation of gene transcription. Nature. 2019;573:45–54.
   PubMed Web of Science ®Google Scholar
• Haberle V, Stark A. Eukaryotic core promoters and the functional basis of transcription initiation. Nat Rev Mol Cell Biol. 2018;19:621–637.
   PubMed Web of Science ®Google Scholar
• Chen HT, Warfield L, Hahn S. The positions of TFIIF and TFIIE in the RNA polymerase II transcription preinitiation complex. Nat Struct Mol Biol. 2007;14:696–703.
   PubMed Web of Science ®Google Scholar
• He Y, Fang J, Taatjes DJ, et al. Structural visualization of key steps in human transcription initiation. Nature. 2013;495:481–486.
   PubMed Web of Science ®Google Scholar
• Pan G, Greenblatt J. Initiation of transcription by RNA polymerase II is limited by melting of the promoter DNA in the region immediately upstream of the initiation site. J Biol Chem. 1994;269:30101–30104.
   PubMed Web of Science ®Google Scholar
• Chen HT, Hahn S. Mapping the location of TFIIB within the RNA polymerase II transcription preinitiation complex: a model for the structure of the PIC. Cell. 2004;119:169–180.
   PubMed Web of Science ®Google Scholar
• Hahn S. Structure and mechanism of the RNA polymerase II transcription machinery. Nat Struct Mol Biol. 2004;11:394–403.
   PubMed Web of Science ®Google Scholar
• Bjorklund S, Kim YJ. Mediator of transcriptional regulation. Trends Biochem Sci. 1996;21:335–337.
   PubMed Web of Science ®Google Scholar
• Soutourina J. Transcription regulation by the Mediator complex. Nat Rev Mol Cell Biol. 2018;19:262–274.
   PubMed Web of Science ®Google Scholar
• Malik S, Roeder RG. The metazoan mediator co-activator complex as an integrative hub for transcriptional regulation. Nat Rev Genet. 2010;11:761–772.
   PubMed Web of Science ®Google Scholar
• Allen BL, Taatjes DJ. The Mediator complex: a central integrator of transcription. Nat Rev Mol Cell Biol. 2015;16:155–166.
   PubMed Web of Science ®Google Scholar
• Malik S, Roeder RG. Mediator: a drawbridge across the enhancer-promoter divide. Mol Cell. 2016;64:433–434.
   PubMed Web of Science ®Google Scholar
• Plaschka C, Lariviere L, Wenzeck L, et al. Architecture of the RNA polymerase II-mediator core initiation complex. Nature. 2015;518:376–380.
   PubMed Web of Science ®Google Scholar
• Robinson PJ, Trnka MJ, Bushnell DA, et al. Structure of a complete mediator-RNA polymerase II pre-initiation complex. Cell. 2016;166:1411–1422 e1416.
   PubMed Web of Science ®Google Scholar
• Jeronimo C, Robert F. The mediator complex: at the nexus of RNA polymerase II transcription. Trends Cell Biol. 2017;27:765–783.
   PubMed Web of Science ®Google Scholar
• Hu X, Malik S, Negroiu CC, et al. A Mediator-responsive form of metazoan RNA polymerase II. Proc Natl Acad Sci U S A. 2006;103:9506–9511.
   PubMed Web of Science ®Google Scholar
• Roginski RS, Mohan Raj BK, Birditt B, et al. The human GRINL1A gene defines a complex transcription unit, an unusual form of gene organization in eukaryotes. Genomics. 2004;84:265–276.
   PubMed Web of Science ®Google Scholar
• Malik S, Roeder RG. Isolation and functional characterization of the TRAP/mediator complex. Methods Enzymol. 2003;364:257–284.
   PubMed Web of Science ®Google Scholar
• Tyree CM, George CP, Lira-DeVito LM, et al. Identification of a minimal set of proteins that is sufficient for accurate initiation of transcription by RNA polymerase II. Genes Dev. 1993;7:1254–1265.
   PubMed Web of Science ®Google Scholar
• Cheng B, Li T, Rahl PB, et al. Functional association of Gdown1 with RNA polymerase II poised on human genes. Mol Cell. 2012;45:38–50.
   PubMed Web of Science ®Google Scholar
• Wu YM, Chang JW, Wang CH, et al. Regulation of mammalian transcription by Gdown1 through a novel steric crosstalk revealed by cryo-EM. Embo J. 2012;31:3575–3587.
   PubMed Web of Science ®Google Scholar
• Jishage M, Yu X, Shi Y, et al. Architecture of Pol II(G) and molecular mechanism of transcription regulation by Gdown1. Nat Struct Mol Biol. 2018;25:859–867.
   PubMed Web of Science ®Google Scholar
• Eichner J, Chen HT, Warfield L, et al. Position of the general transcription factor TFIIF within the RNA polymerase II transcription preinitiation complex. Embo J. 2010;29:706–716.
   PubMed Web of Science ®Google Scholar
• Tan S, Conaway RC, Conaway JW. Dissection of transcription factor TFIIF functional domains required for initiation and elongation. Proc Natl Acad Sci U S A. 1995;92:6042–6046.
   PubMed Web of Science ®Google Scholar
• He Y, Yan C, Fang J, et al. Near-atomic resolution visualization of human transcription promoter opening. Nature. 2016;533:359–365.
   PubMed Web of Science ®Google Scholar
• Sainsbury S, Niesser J, Cramer P. Structure and function of the initially transcribing RNA polymerase II-TFIIB complex. Nature. 2013;493:437–440.
   PubMed Web of Science ®Google Scholar
• Kostrewa D, Zeller ME, Armache KJ, et al. RNA polymerase II-TFIIB structure and mechanism of transcription initiation. Nature. 2009;462:323–330.
   PubMed Web of Science ®Google Scholar
• Sali A, Berman HM, Schwede T, et al. Outcome of the first wwPDB hybrid/integrative methods task force workshop. Structure. 2015;23:1156–1167.
   PubMed Web of Science ®Google Scholar
• Russel D, Lasker K, Webb B, et al. Putting the pieces together: integrative modeling platform software for structure determination of macromolecular assemblies. PLoS Biol. 2012;10:e1001244.
   PubMed Web of Science ®Google Scholar
• Fagerberg L, Hallstrom BM, Oksvold P, et al. Analysis of the human tissue-specific expression by genome-wide integration of transcriptomics and antibody-based proteomics. Mol Cell Proteomics. 2014;13:397–406.
   PubMed Web of Science ®Google Scholar
• Yue F, Cheng Y, Breschi A, et al. A comparative encyclopedia of DNA elements in the mouse genome. Nature. 2014;515:355–364.
   PubMed Web of Science ®Google Scholar
• Jishage M, Ito K, Chu CS, et al. Transcriptional down-regulation of metabolic genes by Gdown1 ablation induces quiescent cell re-entry into the cell cycle. Genes Dev. 2020;34:767–784.
   PubMed Web of Science ®Google Scholar
• Hirota K, Fukamizu A. Transcriptional regulation of energy metabolism in the liver. J Recept Signal Transduct Res. 2010;30:403–409.
   PubMed Web of Science ®Google Scholar
• Michalopoulos GK. Hepatostat: liver regeneration and normal liver tissue maintenance. Hepatology. 2017;65:1384–1392.
   PubMed Web of Science ®Google Scholar
• Michalopoulos GK. Advances in liver regeneration. Expert Rev Gastroenterol Hepatol. 2014;8:897–907.
   PubMed Web of Science ®Google Scholar
• Fausto N, Campbell JS, Riehle KJ. Liver regeneration. Hepatology. 2006;43:S45–S53.
   PubMed Web of Science ®Google Scholar
• Taub R. Liver regeneration: from myth to mechanism. Nat Rev Mol Cell Bio. 2004;5:836–847.
   PubMed Web of Science ®Google Scholar
• Forbes SJ, Newsome PN. Liver regeneration - mechanisms and models to clinical application. Nat Rev Gastroenterol Hepatol. 2016;13:473–485.
   PubMed Web of Science ®Google Scholar
• Yin C, Evason KJ, Asahina K, et al. Hepatic stellate cells in liver development, regeneration, and cancer. J Clin Invest. 2013;123:1902–1910.
   PubMed Web of Science ®Google Scholar
• DeLaney E, Luse DS, Huang X. Gdown1 associates efficiently with RNA polymerase II after promoter clearance and displaces TFIIF during transcript elongation. PLoS One. 2016;11:e0163649.
   PubMed Web of Science ®Google Scholar
• Chen FX, Smith ER, Shilatifard A. Born to run: control of transcription elongation by RNA polymerase II. Nat Rev Mol Cell Biol. 2018;19:464–478.
   PubMed Web of Science ®Google Scholar
• Liu XL, Kraus WL, Bai XY. Ready, pause, go: regulation of RNA polymerase II pausing and release by cellular signaling pathways. Trends Biochem Sci. 2015;40:516–525.
   PubMed Web of Science ®Google Scholar
• Thompson NL, Mead JE, Braun L, et al. Sequential protooncogene expression during rat liver regeneration. Cancer Res. 1986;46:3111–3117.
   PubMed Web of Science ®Google Scholar
• Mohn KL, Laz TM, Melby AE, et al. Immediate-early gene expression differs between regenerating liver, insulin-stimulated H-35 cells, and mitogen-stimulated Balb/c 3T3 cells. Liver-specific induction patterns of gene 33, phosphoenolpyruvate carboxykinase, and the jun, fos, and egr families. J Biol Chem. 1990;265:21914–21921.
   PubMed Web of Science ®Google Scholar
• Core L, Adelman K. Promoter-proximal pausing of RNA polymerase II: a nexus of gene regulation. Genes Dev. 2019;33:960–982.
   PubMed Web of Science ®Google Scholar
• Pinkert CA, Ornitz DM, Brinster RL, et al. An albumin enhancer located 10 kb upstream functions along with its promoter to direct efficient, liver-specific expression in transgenic mice. Genes Dev. 1987;1:268–276.
   PubMed Web of Science ®Google Scholar
• Hnisz D, Shrinivas K, Young RA, et al. A phase separation model for transcriptional control. Cell. 2017;169:13–23.
   PubMed Web of Science ®Google Scholar
• Fujimoto A, Furuta M, Totoki Y, et al. Whole-genome mutational landscape and characterization of noncoding and structural mutations in liver cancer. Nat Genet. 2016;48:500–+.
   Web of Science ®Google Scholar
• Cancer Genome Atlas Research Network. Electronic address, w. b. e., and Cancer Genome Atlas Research, N. Ally A, Balasundaram M, Carlsen R. Comprehensive and integrative genomic characterization of hepatocellular Carcinoma. Cell. 2017;169(7):1327–1341 e1323. DOI:10.1016/j.cell.2017.05.046.
   PubMed Web of Science ®Google Scholar
• Schulze K, Imbeaud S, Letouze E, et al. Exome sequencing of hepatocellular carcinomas identifies new mutational signatures and potential therapeutic targets. Nat Genet. 2015;47:505–U106.
   PubMed Web of Science ®Google Scholar
• Fernandez-Banet J, Lee NP, Chan KT, et al. Decoding complex patterns of genomic rearrangement in hepatocellular carcinoma. Genomics. 2014;103:189–203.
   PubMed Web of Science ®Google Scholar