Antagonistic Controls of Chromatin and mRNA Start Site Selection by Tup Family Corepressors and the CCAAT-Binding Factor

REFERENCES

• Wolffe AP. 1997. Histones, nucleosomes and the roles of chromatin structure in transcriptional control. Biochem Soc Trans 25:354–358.
   PubMedGoogle Scholar
• Wolffe AP. 1994. Nucleosome positioning and modification: chromatin structures that potentiate transcription. Trends Biochem Sci 19:240–244. http://dx.doi.org/10.1016/0968-0004(94)90148-1.
   PubMed Web of Science ®Google Scholar
• Bannister AJ, Kouzarides T. 2011. Regulation of chromatin by histone modifications. Cell Res 21:381–395. http://dx.doi.org/10.1038/cr.2011.22.
   PubMed Web of Science ®Google Scholar
• Clapier CR, Cairns BR. 2009. The biology of chromatin remodeling complexes. Annu Rev Biochem 78:273–304. http://dx.doi.org/10.1146/annurev.biochem.77.062706.153223.
   PubMed Web of Science ®Google Scholar
• Mannervik M. 1999. Target genes of homeodomain proteins. Bioessays 21:267–270. http://dx.doi.org/10.1002/(SICI)1521-1878(199904)21:4<267::AID-BIES1>3.0.CO;2-C.
   PubMedGoogle Scholar
• Ptashne M, Gann A. 1997. Transcriptional activation by recruitment. Nature 386:569–577. http://dx.doi.org/10.1038/386569a0.
   PubMed Web of Science ®Google Scholar
• Struhl K. 1995. Yeast transcriptional regulatory mechanisms. Annu Rev Genet 29:651–674. http://dx.doi.org/10.1146/annurev.ge.29.120195.003251.
   PubMed Web of Science ®Google Scholar
• Malave TM, Dent SY. 2006. Transcriptional repression by Tup1-Ssn6. Biochem Cell Biol 84:437–443. http://dx.doi.org/10.1139/o06-073.
   PubMedGoogle Scholar
• Naar AM, Lemon BD, Tjian R. 2001. Transcriptional coactivator complexes. Annu Rev Biochem 70:475–501. http://dx.doi.org/10.1146/annurev.biochem.70.1.475.
   PubMed Web of Science ®Google Scholar
• Courey AJ, Jia S. 2001. Transcriptional repression: the long and the short of it. Genes Dev 15:2786–2796. http://dx.doi.org/10.1101/gad.939601.
   PubMed Web of Science ®Google Scholar
• Liu Z, Karmarkar V. 2008. Groucho/Tup1 family co-repressors in plant development. Trends Plant Sci 13:137–144. http://dx.doi.org/10.1016/j.tplants.2007.12.005.
   PubMed Web of Science ®Google Scholar
• Roth SY. 1995. Chromatin-mediated transcriptional repression in yeast. Curr Opin Genet Dev 5:168–173. http://dx.doi.org/10.1016/0959-437X(95)80004-2.
   PubMedGoogle Scholar
• Wahi M, Komachi K, Johnson AD. 1998. Gene regulation by the yeast Ssn6-Tup1 corepressor. Cold Spring Harbor Symp Quant Biol 63:447–457. http://dx.doi.org/10.1101/sqb.1998.63.447.
   PubMedGoogle Scholar
• Davie JK, Edmondson DG, Coco CB, Dent SY. 2003. Tup1-Ssn6 interacts with multiple class I histone deacetylases in vivo. J Biol Chem 278:50158–50162. http://dx.doi.org/10.1074/jbc.M309753200.
   PubMedGoogle Scholar
• Gromoller A, Lehming N. 2000. Srb7p is a physical and physiological target of Tup1p. EMBO J 19:6845–6852. http://dx.doi.org/10.1093/emboj/19.24.6845.
   PubMedGoogle Scholar
• Mukai Y, Davie JK, Dent SY. 2003. Physical and functional interaction of the yeast corepressor Tup1 with mRNA 5′-triphosphatase. J Biol Chem 278:18895–18901. http://dx.doi.org/10.1074/jbc.M302155200.
   PubMedGoogle Scholar
• Zhang Z, Reese JC. 2004. Redundant mechanisms are used by Ssn6-Tup1 in repressing chromosomal gene transcription in Saccharomyces cerevisiae. J Biol Chem 279:39240–39250. http://dx.doi.org/10.1074/jbc.M407159200.
   PubMedGoogle Scholar
• Zhang Z, Reese JC. 2004. Ssn6-Tup1 requires the ISW2 complex to position nucleosomes in Saccharomyces cerevisiae. EMBO J 23:2246–2257. http://dx.doi.org/10.1038/sj.emboj.7600227.
   PubMedGoogle Scholar
• Greenall A, Hadcroft AP, Malakasi P, Jones N, Morgan BA, Hoffman CS, Whitehall SK. 2002. Role of fission yeast Tup1-like repressors and Prr1 transcription factor in response to salt stress. Mol Biol Cell 13:2977–2989. http://dx.doi.org/10.1091/mbc.01-12-0568.
   PubMed Web of Science ®Google Scholar
• Hirota K, Hasemi T, Yamada T, Mizuno KI, Hoffman CS, Shibata T, Ohta K. 2004. Fission yeast global repressors regulate the specificity of chromatin alteration in response to distinct environmental stresses. Nucleic Acids Res 32:855–862. http://dx.doi.org/10.1093/nar/gkh251.
   PubMed Web of Science ®Google Scholar
• Hoffman CS, Winston F. 1991. Glucose repression of transcription of the Schizosaccharomyces pombe fbp1 gene occurs by a cAMP signaling pathway. Genes Dev 5:561–571. http://dx.doi.org/10.1101/gad.5.4.561.
   PubMedGoogle Scholar
• Hoffman CS, Winston F. 1989. A transcriptionally regulated expression vector for the fission yeast Schizosaccharomyces pombe. Gene 84:473–479. http://dx.doi.org/10.1016/0378-1119(89)90523-4.
   PubMed Web of Science ®Google Scholar
• Higuchi T, Watanabe Y, Yamamoto M. 2002. Protein kinase A regulates sexual development and gluconeogenesis through phosphorylation of the Zn finger transcriptional activator Rst2p in fission yeast. Mol Cell Biol 22:1–11. http://dx.doi.org/10.1128/MCB.22.1.1-11.2002.
   PubMed Web of Science ®Google Scholar
• Hirota K, Hoffman CS, Ohta K. 2006. Reciprocal nuclear shuttling of two antagonizing Zn finger proteins modulates Tup family corepressor function to repress chromatin remodeling. Eukaryot Cell 5:1980–1989. http://dx.doi.org/10.1128/EC.00272-06.
   PubMed Web of Science ®Google Scholar
• Hirota K, Hoffman CS, Shibata T, Ohta K. 2003. Fission yeast Tup1-like repressors repress chromatin remodeling at the fbp1+ promoter and the ade6-M26 recombination hotspot. Genetics 165:505–515.
   PubMed Web of Science ®Google Scholar
• Janoo RT, Neely LA, Braun BR, Whitehall SK, Hoffman CS. 2001. Transcriptional regulators of the Schizosaccharomyces pombe fbp1 gene include two redundant Tup1p-like corepressors and the CCAAT binding factor activation complex. Genetics 157:1205–1215.
   PubMed Web of Science ®Google Scholar
• Kanoh J, Watanabe Y, Ohsugi M, Iino Y, Yamamoto M. 1996. Schizosaccharomyces pombe gad7+ encodes a phosphoprotein with a bZIP domain, which is required for proper G1 arrest and gene expression under nitrogen starvation. Genes Cells 1:391–408. http://dx.doi.org/10.1046/j.1365-2443.1996.d01-247.x.
   PubMed Web of Science ®Google Scholar
• Shiozaki K, Russell P. 1996. Conjugation, meiosis, and the osmotic stress response are regulated by Spc1 kinase through Atf1 transcription factor in fission yeast. Genes Dev 10:2276–2288. http://dx.doi.org/10.1101/gad.10.18.2276.
   PubMed Web of Science ®Google Scholar
• Wilkinson MG, Samuels M, Takeda T, Toone WM, Shieh JC, Toda T, Millar JB, Jones N. 1996. The Atf1 transcription factor is a target for the StyI stress-activated MAP kinase pathway in fission yeast. Genes Dev 10:2289–2301. http://dx.doi.org/10.1101/gad.10.18.2289.
   PubMed Web of Science ®Google Scholar
• Kunitomo H, Higuchi T, Iino Y, Yamamoto M. 2000. A zinc-finger protein, Rst2p, regulates transcription of the fission yeast ste11(+) gene, which encodes a pivotal transcription factor for sexual development. Mol Biol Cell 11:3205–3217. http://dx.doi.org/10.1091/mbc.11.9.3205.
   PubMed Web of Science ®Google Scholar
• McNabb DS, Tseng KA, Guarente L. 1997. The Saccharomyces cerevisiae Hap5p homolog from fission yeast reveals two conserved domains that are essential for assembly of heterotetrameric CCAAT-binding factor. Mol Cell Biol 17:7008–7018.
   PubMedGoogle Scholar
• McNabb DS, Xing Y, Guarente L. 1995. Cloning of yeast HAP5: a novel subunit of a heterotrimeric complex required for CCAAT binding. Genes Dev 9:47–58. http://dx.doi.org/10.1101/gad.9.1.47.
   PubMed Web of Science ®Google Scholar
• Neely LA, Hoffman CS. 2000. Protein kinase A and mitogen-activated protein kinase pathways antagonistically regulate fission yeast fbp1 transcription by employing different modes of action at two upstream activation sites. Mol Cell Biol 20:6426–6434. http://dx.doi.org/10.1128/MCB.20.17.6426-6434.2000.
   PubMed Web of Science ®Google Scholar
• Watanabe Y, Yamamoto M. 1996. Schizosaccharomyces pombe pcr1+ encodes a CREB/ATF protein involved in regulation of gene expression for sexual development. Mol Cell Biol 16:704–711.
   PubMed Web of Science ®Google Scholar
• Hirota K, Miyoshi T, Kugou K, Hoffman CS, Shibata T, Ohta K. 2008. Stepwise chromatin remodelling by a cascade of transcription initiation of non-coding RNAs. Nature 456:130–134. http://dx.doi.org/10.1038/nature07348.
   PubMed Web of Science ®Google Scholar
• Hirota K, Mizuno K, Shibata T, Ohta K. 2008. Distinct chromatin modulators regulate the formation of accessible and repressive chromatin at the fission yeast recombination hotspot ade6-M26. Mol Biol Cell 19:1162–1173. http://dx.doi.org/10.1091/mbc.E07-04-0377.
   PubMed Web of Science ®Google Scholar
• Hirota K, Ohta K. 2009. Cascade transcription of mRNA-type long non-coding RNAs (mlonRNAs) and local chromatin remodeling. Epigenetics 4:5–7. http://dx.doi.org/10.4161/epi.4.1.7353.
   PubMed Web of Science ®Google Scholar
• Hirota K, Ohta K. 2009. Transcription of mRNA-type long non-coding RNAs (mlonRNAs) disrupts chromatin array. Commun Integr Biol 2:25–26. http://dx.doi.org/10.4161/cib.2.1.7378.
   PubMedGoogle Scholar
• Gutz H, Heslot H, Leupold U, Loprieno N. 1974. Schizosaccharomyces pombe, p 395–446. In King RD (ed), Handbook of genetics, vol 1. Plenum, New York, NY.
   Google Scholar
• Hirota K, Tanaka K, Watanabe Y, Yamamoto M. 2001. Functional analysis of the C-terminal cytoplasmic region of the M-factor receptor in fission yeast. Genes Cells 6:201–214. http://dx.doi.org/10.1046/j.1365-2443.2001.00415.x.
   PubMedGoogle Scholar
• Bahler J, Wu JQ, Longtine MS, Shah NG, McKenzie A, III, Steever AB, Wach A, Philippsen P, Pringle JR. 1998. Heterologous modules for efficient and versatile PCR-based gene targeting in Schizosaccharomyces pombe. Yeast 14:943–951. http://dx.doi.org/10.1002/(SICI)1097-0061(199807)14:10<943::AID-YEA292>3.0.CO;2-Y.
   PubMed Web of Science ®Google Scholar
• Yamada T, Mizuno K, Hirota K, Kon N, Wahls WP, Hartsuiker E, Murofushi H, Shibata T, Ohta K. 2004. Roles of histone acetylation and chromatin remodeling factor in a meiotic recombination hotspot. EMBO J 23:1792–1803. http://dx.doi.org/10.1038/sj.emboj.7600138.
   PubMed Web of Science ®Google Scholar
• Wong KH, Struhl K. 2011. The Cyc8-Tup1 complex inhibits transcription primarily by masking the activation domain of the recruiting protein. Genes Dev 25:2525–2539. http://dx.doi.org/10.1101/gad.179275.111.
   PubMed Web of Science ®Google Scholar
• Papamichos-Chronakis M, Petrakis T, Ktistaki E, Topalidou I, Tzamarias D. 2002. Cti6, a PHD domain protein, bridges the Cyc8-Tup1 corepressor and the SAGA coactivator to overcome repression at GAL1. Mol Cell 9:1297–1305. http://dx.doi.org/10.1016/S1097-2765(02)00545-2.
   PubMedGoogle Scholar
• Nardini M, Gnesutta N, Donati G, Gatta R, Forni C, Fossati A, Vonrhein C, Moras D, Romier C, Bolognesi M, Mantovani R. 2013. Sequence-specific transcription factor NF-Y displays histone-like DNA binding and H2B-like ubiquitination. Cell 152:132–143. http://dx.doi.org/10.1016/j.cell.2012.11.047.
   PubMed Web of Science ®Google Scholar
• Gnesutta N, Nardini M, Mantovani R. 2013. The H2A/H2B-like histone-fold domain proteins at the crossroad between chromatin and different DNA metabolisms. Transcription 4:114–119. http://dx.doi.org/10.4161/trns.25002.
   PubMedGoogle Scholar
• Currie RA. 1998. NF-Y is associated with the histone acetyltransferases GCN5 and P/CAF. J Biol Chem 273:1430–1434. http://dx.doi.org/10.1074/jbc.273.3.1430.
   PubMedGoogle Scholar
• Imbriano C, Gurtner A, Cocchiarella F, Di Agostino S, Basile V, Gostissa M, Dobbelstein M, Del Sal G, Piaggio G, Mantovani R. 2005. Direct p53 transcriptional repression: in vivo analysis of CCAAT-containing G2/M promoters. Mol Cell Biol 25:3737–3751. http://dx.doi.org/10.1128/MCB.25.9.3737-3751.2005.
   PubMed Web of Science ®Google Scholar
• Jin S, Scotto KW. 1998. Transcriptional regulation of the MDR1 gene by histone acetyltransferase and deacetylase is mediated by NF-Y. Mol Cell Biol 18:4377–4384.
   PubMed Web of Science ®Google Scholar
• Li Q, Herrler M, Landsberger N, Kaludov N, Ogryzko VV, Nakatani Y, Wolffe AP. 1998. Xenopus NF-Y pre-sets chromatin to potentiate p300 and acetylation-responsive transcription from the Xenopus hsp70 promoter in vivo. EMBO J 17:6300–6315. http://dx.doi.org/10.1093/emboj/17.21.6300.
   PubMedGoogle Scholar
• Peng Y, Stewart D, Li W, Hawkins M, Kulak S, Ballermann B, Jahroudi N. 2007. Irradiation modulates association of NF-Y with histone-modifying cofactors PCAF and HDAC. Oncogene 26:7576–7583. http://dx.doi.org/10.1038/sj.onc.1210565.
   PubMedGoogle Scholar
• Takeda T, Yamamoto M. 1987. Analysis and in vivo disruption of the gene coding for calmodulin in Schizosaccharomyces pombe. Proc Natl Acad Sci U S A 84:3580–3584. http://dx.doi.org/10.1073/pnas.84.11.3580.
   PubMed Web of Science ®Google Scholar