Promoter Occupancy of STAT1 in Interferon Responses Is Regulated by Processive Transcription

REFERENCES

• Stark GR, Darnell JE, Jr. 2012. The JAK-STAT pathway at twenty. Immunity 36:503–514. http://dx.doi.org/10.1016/j.immuni.2012.03.013.
   PubMed Web of Science ®Google Scholar
• O'Shea JJ, Plenge R. 2012. JAK and STAT signaling molecules in immunoregulation and immune-mediated disease. Immunity 36:542–550. http://dx.doi.org/10.1016/j.immuni.2012.03.014.
   PubMed Web of Science ®Google Scholar
• Casanova JL, Holland SM, Notarangelo LD. 2012. Inborn errors of human JAKs and STATs. Immunity 36:515–528. http://dx.doi.org/10.1016/j.immuni.2012.03.016.
   PubMed Web of Science ®Google Scholar
• Ungureanu D, Vanhatupa S, Kotaja N, Yang J, Aittomaki S, Janne OA, Palvimo JJ, Silvennoinen O. 2003. PIAS proteins promote SUMO-1 conjugation to STAT1. Blood 102:3311–3313. http://dx.doi.org/10.1182/blood-2002-12-3816.
   PubMedGoogle Scholar
• Bancerek J, Poss ZC, Steinparzer I, Sedlyarov V, Pfaffenwimmer T, Mikulic I, Dolken L, Strobl B, Muller M, Taatjes DJ, Kovarik P. 2013. CDK8 kinase phosphorylates transcription factor STAT1 to selectively regulate the interferon response. Immunity 38:250–262. http://dx.doi.org/10.1016/j.immuni.2012.10.017.
   PubMed Web of Science ®Google Scholar
• Tenoever BR, Ng SL, Chua MA, McWhirter SM, Garcia-Sastre A, Maniatis T. 2007. Multiple functions of the IKK-related kinase IKKε in interferon-mediated antiviral immunity. Science 315:1274–1278. http://dx.doi.org/10.1126/science.1136567.
   PubMed Web of Science ®Google Scholar
• Donnelly RP, Kotenko SV. 2010. Interferon-lambda: a new addition to an old family. J Interferon Cytokine Res 30:555–564. http://dx.doi.org/10.1089/jir.2010.0078.
   PubMed Web of Science ®Google Scholar
• ten Hoeve J, de Jesus Ibarra-Sanchez M, Fu Y, Zhu W, Tremblay M, David M, Shuai K. 2002. Identification of a nuclear Stat1 protein tyrosine phosphatase. Mol Cell Biol 22:5662–5668. http://dx.doi.org/10.1128/MCB.22.16.5662-5668.2002.
   PubMed Web of Science ®Google Scholar
• Krämer OH, Knauer SK, Greiner G, Jandt E, Reichardt S, Guhrs KH, Stauber RH, Bohmer FD, Heinzel T. 2009. A phosphorylation-acetylation switch regulates STAT1 signaling. Genes Dev 23:223–235. http://dx.doi.org/10.1101/gad.479209.
   PubMed Web of Science ®Google Scholar
• Antunes F, Marg A, Vinkemeier U. 2011. STAT1 signaling is not regulated by a phosphorylation-acetylation switch. Mol Cell Biol 31:3029–3037. http://dx.doi.org/10.1128/MCB.05300-11.
   PubMedGoogle Scholar
• Meyer T, Marg A, Lemke P, Wiesner B, Vinkemeier U. 2003. DNA binding controls inactivation and nuclear accumulation of the transcription factor Stat1. Genes Dev 17:1992–2005. http://dx.doi.org/10.1101/gad.268003.
   PubMed Web of Science ®Google Scholar
• Mertens C, Zhong M, Krishnaraj R, Zou W, Chen X, Darnell JE, Jr. 2006. Dephosphorylation of phosphotyrosine on STAT1 dimers requires extensive spatial reorientation of the monomers facilitated by the N-terminal domain. Genes Dev 20:3372–3381. http://dx.doi.org/10.1101/gad.1485406.
   PubMedGoogle Scholar
• Sadzak I, Schiff M, Gattermeier I, Glinitzer R, Sauer I, Saalmuller A, Yang E, Schaljo B, Kovarik P. 2008. Recruitment of Stat1 to chromatin is required for interferon-induced serine phosphorylation of Stat1 transactivation domain. Proc Natl Acad Sci U S A 105:8944–8949. http://dx.doi.org/10.1073/pnas.0801794105.
   PubMed Web of Science ®Google Scholar
• Kimura T, Kadokawa Y, Harada H, Matsumoto M, Sato M, Kashiwazaki Y, Tarutani M, Tan RS, Takasugi T, Matsuyama T, Mak TW, Noguchi S, Taniguchi T. 1996. Essential and non-redundant roles of p48 (ISGF3γ) and IRF-1 in both type I and type II interferon responses, as revealed by gene targeting studies. Genes Cells 1:115–124. http://dx.doi.org/10.1046/j.1365-2443.1996.08008.x.
   PubMed Web of Science ®Google Scholar
• Semper C, Leitner NR, Lassnig C, Parrini M, Mahlakoiv T, Rammerstorfer M, Lorenz K, Rigler D, Muller S, Kolbe T, Vogl C, Rulicke T, Staeheli P, Decker T, Muller M, Strobl B. 2014. STAT1β is not dominant negative and is capable of contributing to gamma interferon-dependent innate immunity. Mol Cell Biol 34:2235–2248. http://dx.doi.org/10.1128/MCB.00295-14.
   PubMedGoogle Scholar
• Donehower LA, Harvey M, Slagle BL, McArthur MJ, Montgomery CA, Jr, Butel JS, Bradley A. 1992. Mice deficient for p53 are developmentally normal but susceptible to spontaneous tumours. Nature 356:215–221. http://dx.doi.org/10.1038/356215a0.
   PubMed Web of Science ®Google Scholar
• Kovarik P, Stoiber D, Novy M, Decker T. 1998. Stat1 combines signals derived from IFN-γ and LPS receptors during macrophage activation. EMBO J 17:3660–3668. (Erratum, 17:4210.)
   PubMed Web of Science ®Google Scholar
• Dolken L, Ruzsics Z, Radle B, Friedel CC, Zimmer R, Mages J, Hoffmann R, Dickinson P, Forster T, Ghazal P, Koszinowski UH. 2008. High-resolution gene expression profiling for simultaneous kinetic parameter analysis of RNA synthesis and decay. RNA (New York, NY) 14:1959–1972. http://dx.doi.org/10.1261/rna.1136108.
   PubMed Web of Science ®Google Scholar
• Alexander WS, Starr R, Fenner JE, Scott CL, Handman E, Sprigg NS, Corbin JE, Cornish AL, Darwiche R, Owczarek CM, Kay TW, Nicola NA, Hertzog PJ, Metcalf D, Hilton DJ. 1999. SOCS1 is a critical inhibitor of interferon gamma signaling and prevents the potentially fatal neonatal actions of this cytokine. Cell 98:597–608. http://dx.doi.org/10.1016/S0092-8674(00)80047-1.
   PubMed Web of Science ®Google Scholar
• Thompson JE, Cubbon RM, Cummings RT, Wicker LS, Frankshun R, Cunningham BR, Cameron PM, Meinke PT, Liverton N, Weng Y, DeMartino JA. 2002. Photochemical preparation of a pyridone containing tetracycle: a Jak protein kinase inhibitor. Bioorg Med Chem Lett 12:1219–1223. http://dx.doi.org/10.1016/S0960-894X(02)00106-3.
   PubMed Web of Science ®Google Scholar
• Bensaude O. 2011. Inhibiting eukaryotic transcription: which compound to choose? How to evaluate its activity? Transcription 2:103–108. http://dx.doi.org/10.4161/trns.2.3.16172.
   PubMedGoogle Scholar
• Chao SH, Price DH. 2001. Flavopiridol inactivates P-TEFb and blocks most RNA polymerase II transcription in vivo. J Biol Chem 276:31793–31799. http://dx.doi.org/10.1074/jbc.M102306200.
   PubMed Web of Science ®Google Scholar
• Rickert P, Corden JL, Lees E. 1999. Cyclin C/CDK8 and cyclin H/CDK7/p36 are biochemically distinct CTD kinases. Oncogene 18:1093–1102. http://dx.doi.org/10.1038/sj.onc.1202399.
   PubMed Web of Science ®Google Scholar
• Nelson WG, Kastan MB. 1994. DNA strand breaks: the DNA template alterations that trigger p53-dependent DNA damage response pathways. Mol Cell Biol 14:1815–1823.
   PubMed Web of Science ®Google Scholar
• Choong ML, Yang H, Lee MA, Lane DP. 2009. Specific activation of the p53 pathway by low dose actinomycin D: a new route to p53 based cyclotherapy. Cell Cycle (Georgetown, Tex) 8:2810–2818. http://dx.doi.org/10.4161/cc.8.17.9503.
   PubMed Web of Science ®Google Scholar
• Youlyouz-Marfak I, Gachard N, Le Clorennec C, Najjar I, Baran-Marszak F, Reminieras L, May E, Bornkamm GW, Fagard R, Feuillard J. 2008. Identification of a novel p53-dependent activation pathway of STAT1 by antitumour genotoxic agents. Cell Death Differ 15:376–385. http://dx.doi.org/10.1038/sj.cdd.4402270.
   PubMedGoogle Scholar
• O'Connell RM, Taganov KD, Boldin MP, Cheng G, Baltimore D. 2007. MicroRNA-155 is induced during the macrophage inflammatory response. Proc Natl Acad Sci U S A 104:1604–1609. http://dx.doi.org/10.1073/pnas.0610731104.
   PubMed Web of Science ®Google Scholar
• Gantier MP, McCoy CE, Rusinova I, Saulep D, Wang D, Xu D, Irving AT, Behlke MA, Hertzog PJ, Mackay F, Williams BR. 2011. Analysis of microRNA turnover in mammalian cells following Dicer1 ablation. Nucleic Acids Res 39:5692–5703. http://dx.doi.org/10.1093/nar/gkr148.
   PubMed Web of Science ®Google Scholar
• Zhou C, Yu Q, Chen L, Wang J, Zheng S, Zhang J. 2012. A miR-1231 binding site polymorphism in the 3′UTR of IFNAR1 is associated with hepatocellular carcinoma susceptibility. Gene 507:95–98. http://dx.doi.org/10.1016/j.gene.2012.06.073.
   PubMedGoogle Scholar
• Gough DJ, Messina NL, Hii L, Gould JA, Sabapathy K, Robertson AP, Trapani JA, Levy DE, Hertzog PJ, Clarke CJ, Johnstone RW. 2010. Functional crosstalk between type I and II interferon through the regulated expression of STAT1. PLoS Biol 8:e1000361. http://dx.doi.org/10.1371/journal.pbio.1000361.
   PubMedGoogle Scholar
• Toshchakov V, Jones BW, Perera PY, Thomas K, Cody MJ, Zhang S, Williams BR, Major J, Hamilton TA, Fenton MJ, Vogel SN. 2002. TLR4, but not TLR2, mediates IFN-β-induced STAT1α/β-dependent gene expression in macrophages. Nat Immunol 3:392–398. http://dx.doi.org/10.1038/ni774.
   PubMed Web of Science ®Google Scholar
• Mancebo HS, Lee G, Flygare J, Tomassini J, Luu P, Zhu Y, Peng J, Blau C, Hazuda D, Price D, Flores O. 1997. P-TEFb kinase is required for HIV Tat transcriptional activation in vivo and in vitro. Genes Dev 11:2633–2644. http://dx.doi.org/10.1101/gad.11.20.2633.
   PubMed Web of Science ®Google Scholar
• Haspel RL, Darnell JE, Jr. 1999. A nuclear protein tyrosine phosphatase is required for the inactivation of Stat1. Proc Natl Acad Sci U S A 96:10188–10193. http://dx.doi.org/10.1073/pnas.96.18.10188.
   PubMedGoogle Scholar
• Rateitschak K, Karger A, Fitzner B, Lange F, Wolkenhauer O, Jaster R. 2010. Mathematical modelling of interferon-gamma signalling in pancreatic stellate cells reflects and predicts the dynamics of STAT1 pathway activity. Cell Signal 22:97–105. http://dx.doi.org/10.1016/j.cellsig.2009.09.019.
   PubMedGoogle Scholar
• Swameye I, Muller TG, Timmer J, Sandra O, Klingmüller U. 2003. Identification of nucleocytoplasmic cycling as a remote sensor in cellular signaling by databased modeling. Proc Natl Acad Sci U S A 100:1028–1033. http://dx.doi.org/10.1073/pnas.0237333100.
   PubMed Web of Science ®Google Scholar
• Gerhold CB, Gasser SM. 2014. INO80 and SWR complexes: relating structure to function in chromatin remodeling. Trends Cell Biol 24:619–631. http://dx.doi.org/10.1016/j.tcb.2014.06.004.
   PubMed Web of Science ®Google Scholar
• Petty E, Pillus L. 2013. Balancing chromatin remodeling and histone modifications in transcription. Trends Genet 29:621–629. http://dx.doi.org/10.1016/j.tig.2013.06.006.
   PubMed Web of Science ®Google Scholar
• Saccani S, Pantano S, Natoli G. 2001. Two waves of nuclear factor κB recruitment to target promoters. J Exp Med 193:1351–1359. http://dx.doi.org/10.1084/jem.193.12.1351.
   PubMed Web of Science ®Google Scholar
• Barozzi I, Simonatto M, Bonifacio S, Yang L, Rohs R, Ghisletti S, Natoli G. 2014. Coregulation of transcription factor binding and nucleosome occupancy through DNA features of mammalian enhancers. Mol Cell 54:844–857. http://dx.doi.org/10.1016/j.molcel.2014.04.006.
   PubMed Web of Science ®Google Scholar
• Zupkovitz G, Tischler J, Posch M, Sadzak I, Ramsauer K, Egger G, Grausenburger R, Schweifer N, Chiocca S, Decker T, Seiser C. 2006. Negative and positive regulation of gene expression by mouse histone deacetylase 1. Mol Cell Biol 26:7913–7928. http://dx.doi.org/10.1128/MCB.01220-06.
   PubMed Web of Science ®Google Scholar
• Nusinzon I, Horvath CM. 2003. Interferon-stimulated transcription and innate antiviral immunity require deacetylase activity and histone deacetylase 1. Proc Natl Acad Sci U S A 100:14742–14747. http://dx.doi.org/10.1073/pnas.2433987100.
   PubMed Web of Science ®Google Scholar
• Chang HM, Paulson M, Holko M, Rice CM, Williams BR, Marié I, Levy DE. 2004. Induction of interferon-stimulated gene expression and antiviral responses require protein deacetylase activity. Proc Natl Acad Sci U S A 101:9578–9583. http://dx.doi.org/10.1073/pnas.0400567101.
   PubMed Web of Science ®Google Scholar
• Gnatovskiy L, Mita P, Levy DE. 2013. The human RVB complex is required for efficient transcription of type I interferon-stimulated genes. Mol Cell Biol 33:3817–3825. http://dx.doi.org/10.1128/MCB.01562-12.
   PubMedGoogle Scholar
• Pattenden SG, Klose R, Karaskov E, Bremner R. 2002. Interferon-gamma-induced chromatin remodeling at the CIITA locus is BRG1 dependent. EMBO J 21:1978–1986. http://dx.doi.org/10.1093/emboj/21.8.1978.
   PubMedGoogle Scholar
• Yen K, Vinayachandran V, Pugh BF. 2013. SWR-C and INO80 chromatin remodelers recognize nucleosome-free regions near +1 nucleosomes. Cell 154:1246–1256. http://dx.doi.org/10.1016/j.cell.2013.08.043.
   PubMed Web of Science ®Google Scholar
• Rosowski EE, Nguyen QP, Camejo A, Spooner E, Saeij JP. 2014. Toxoplasma gondii inhibits gamma interferon (IFN-γ)- and IFN-β-induced host cell STAT1 transcriptional activity by increasing the association of STAT1 with DNA. Infect Immun 82:706–719. http://dx.doi.org/10.1128/IAI.01291-13.
   PubMedGoogle Scholar