Home A Genetic Switch An Introduction to Nervous Systems Epigenetics From a to α Genes and Signals Transcriptional Regulation Help

Footnote #2
Moreland R.J., Tirode F., Yan Q., Conaway J.W., Egly J.M., and Conaway R.C. 1999. A role for the TFIIH XPB DNA helicase in promoter escape by RNA polymerase II. J. Biol. Chem. 274: 22127–22130.

Footnote #3
Kim Y.J., Bjorklund S., Li Y., Sayre M.H., and Kornberg R.D. 1994. A multiprotein mediator of transcriptional activation and its interaction with the C-terminal repeat domain of RNA polymerase II. Cell 77: 599–608.
Koleske A.J. and Young R.A. 1994. An RNA polymerase II holoenzyme responsive to activators. Nature 368: 466–469.

Footnote #5
Melcher K. and Xu H.E. 2001. Gal80-Gal80 interaction on adjacent Gal4p binding sites is required for complete GAL gene repression. EMBO J. 20: 841–851.

Footnote #7
DeVit M.J. and Johnston M. 1999. The nuclear exportin Msn5 is required for nuclear export of the Mig1 glucose repressor of Saccharomyces cerevisiae. Curr. Biol. 9: 1231–1241.

Footnote #8
Mapp A.K., Ansari A.Z., Ptashne M., and Dervan P.B. 2000. Activation of gene expression by small molecule transcription factors. Proc. Natl. Acad. Sci. 97: 3930–3935.
Zaman Z., Ansari A.Z., Koh S.S., Young R., and Ptashne M. 2001. Interaction of a transcriptional repressor with the RNA polymerase II holoenzyme plays a crucial role in repression. Proc. Natl. Acad. Sci. 98: 2550–2554.
Kuznetsova S., Ait-Si-Ali S., Nagibneva I., Troalen F., Le Villain J.P., Harel-Bellan A., and Svinarchuk F. 1999. Gene activation by triplex-forming oligonucleotide coupled to the activating domain of protein VP16. Nucleic Acids Res. 27: 3995–4000.

Footnote #9
Uesugi M., Nyanguile O., Lu H., Levine A.J., and Verdine G.L. 1997. Induced alpha helix in the VP16 activation domain upon binding to a human TAF. Science 277: 1310–1313.
Kussie P.H., Gorina S., Marechal V., Elenbaas B., Moreau J., Levine A.J., and Pavletich N.P. 1996. Structure of the MDM2 oncoprotein bound to the p53 tumor suppressor transactivation domain. Science 274: 948–953.
Radhakrishnan I., Perez-Alvarado G.C., Parker D., Dyson H.J., Montminy M.R., and Wright P.E. 1997. Solution structure of the KIX domain of CBP bound to the transactivation domain of CREB: A model for activator:coactivator interactions. Cell 91: 741–752.
Parker D., Rivera M., Zor T., Henrion-Caude A., Radhakrishnan I., Kumar A., Shapiro L.H., Wright P.E., Montminy M., and Brindle P.K. 1999. Role of secondary structure in discrimination between constitutive and inducible activators. Mol. Cell. Biol. 19: 5601–5607.

Footnote #10
Jackson B.M., Drysdale C.M., Natarajan K., and Hinnebusch A.G. 1996. Identification of seven hydrophobic clusters in GCN4 making redundant contributions to transcriptional activation. Mol. Cell. Biol. 16: 5557–5571.

Footnote #11
Ansari A.Z., Reece R.J., and Ptashne M. 1998. A transcriptional activating region with two contrasting modes of protein interaction. Proc. Natl. Acad. Sci. 95: 13543–13548.

Footnote #12
Giniger E. and Ptashne M. 1987. Transcription in yeast activated by a putative amphipathic alpha helix linked to a DNA binding unit. Nature 330: 670–672.
Lu X., Ansari A.Z., and Ptashne M. 2000. An artificial transcriptional activating region with unusual properties. Proc. Natl. Acad. Sci. 97: 1988–1992.

Footnote #13
Gill G. and Ptashne M. 1988. Negative effect of the transcriptional activator GAL4. Nature 334: 721–724.

Footnote #14
Barberis A., Pearlberg J., Simkovich N., Farrell S., Reinagel P., Bamdad C., Sigal G., and Ptashne M. 1995. Contact with a component of the polymerase II holoenzyme suffices for gene activation. Cell 81: 359–368.
Fukasawa T., Fukuma M., Yano K., and Sakurai H. 2001. A genome-wide analysis of transcriptional effect of Gal11 in Saccharomyces cerevisiae: An application of "mini-array hybridization technique". DNA Res. 8: 23–31.

Footnote #15
Farrell S., Simkovich N., Wu Y., Barberis A., and Ptashne M. 1996. Gene activation by recruitment of the RNA polymerase II holoenzyme. Genes Dev. 10: 2359–2367.
Hidalgo P., Ansari A.Z., Schmidt P., Hare B., Simkovich N., Farrell S., Shin E.J., Ptashne M., and Wagner G. 2001. Recruitment of the transcriptional machinery through GAL11P: Structure and interactions of the GAL4 dimerization domain. Genes Dev. 15: 1007–1020.

Footnote #16
Gaudreau L., Keaveney M., Nevado J., Zaman Z., Bryant G.O., Struhl K., and Ptashne M. 1999. Transcriptional activation by artificial recruitment in yeast is influenced by promoter architecture and downstream sequences. Proc. Natl. Acad. Sci. 96: 2668–2673.
Zaman Z., Ansari A.Z., Koh S.S., Young R., and Ptashne M. 2001. Interaction of a transcriptional repressor with the RNA polymerase II holoenzyme plays a crucial role in repression. Proc. Natl. Acad. Sci. 98: 2550–2554.

Footnote #17
Keaveney M. and Struhl K. 1998. Activator-mediated recruitment of the RNA polymerase II machinery is the predominant mechanism for transcriptional activation in yeast. Mol. Cell 1: 917–924.

Footnote #18
Wyrick J.J., Holstege F.C., Jennings E.G., Causton H.C., Shore D., Grunstein M., Lander E.S., and Young R.A. 1999. Chromosomal landscape of nucleosome-dependent gene expression and silencing in yeast. Nature 402: 418–4121.

Footnote #19
Lo W.S., Duggan L., Tolga N.C., Emre, Belotserkovskya R., Lane W.S., Shiekhattar R., and Berger S.L. 2001. Snf1 — A histone kinase that works in concert with the histone acetyltransferase Gcn5 to regulate transcription. Science 293: 1142–1146.

Footnote #20
Luo J., Su F., Chen D., Shiloh A., and Gu W. 2000. Deacetylation of p53 modulates its effect on cell growth and apoptosis. Nature 408: 377–381.
Gu W. and Roeder R.G. 1997. Activation of p53 sequence-specific DNA binding by acetylation of the p53 C-terminal domain. Cell 90: 595–606.

Footnote #21
Steger D.J., Eberharter A., John S., Grant P.A., and Workman J.L. 1998. Purified histone acetyltransferase complexes stimulate HIV-1 transcription from preassembled nucleosomal arrays. Proc. Natl. Acad. Sci. 95: 12924–12929.

Footnote #22
Gaudreau L., Adam M., and Ptashne M. 1998. Activation of transcription in vitro by recruitment of the yeast RNA polymerase II holoenzyme. Mol. Cell 1: 913–916.
Yudkovsky N., Ranish J.A., and Hahn S. 2000. A transcription reinitiation intermediate that is stabilized by activator. Nature 408: 225–229.
Ikeda K., Steger D.J., Eberharter A., and Workman J.L. 1999. Activation domain-specific and general transcription stimulation by native histone acetyltransferase complexes. Mol. Cell. Biol. 19: 855–863.

Footnote #26
Krebs J.E., Fry C.J., Samuels M.L., and Peterson C.L. 2000. Global role for chromatin remodeling enzymes in mitotic gene expression. Cell 102: 587–598.
Deckert J. and Struhl K. 2001. Histone acetylation at promoters is differentially affected by specific activators and repressors. Mol. Cell. Biol. 21: 2726–2735.

Footnote #27
Holstege F.C., Jennings E.G., Wyrick J.J., Lee T.I., Hengartner C.J., Green M.R., Golub T.R., Lander E.S., and Young R.A. 1998. Dissecting the regulatory circuitry of a eukaryotic genome. Cell 95: 717–728.

Footnote #28
Burns L.G. and Peterson C.L. 1997. The yeast SWI-SNF complex facilitates binding of a transcriptional activator to nucleosomal sites in vivo. Mol. Cell. Biol. 17: 4811–4819.

Footnote #30
Cheng X., Zaman Z., Lu Z., Bryant G., Nevado J., and Ptashne M. Modulating roles of TBP-inhibitory and acetyltransferase domains of TAF145 as revealed by activator-by-pass experiments. (in prep.)

Footnote #31
Ansari A., Koh S., Zaman Z., Bongards C., Lehming N., Young R., and Ptashne M. The cyclin-dependent kinase Srb10 is a target of acidic activating regions. Mol. Cell. Biol. (submitted).
Chi Y., Huddleston M.J., Zhang X., Young R.A., Annan R.S., Carr S.A., and Deshaies R.J. 2001. Negative regulation of Gcn4 and Msn2 transcription factors by Srb10 cyclin-dependent kinase. Genes Dev. 15: 1078–1092.
Hirst M., Kobor M.S., Kuriakose N., Greenblatt J., and Sadowski I. 1999. GAL4 is regulated by the RNA polymerase II holoenzyme-associated cyclin-dependent protein kinase SRB10/CDK8. Mol. Cell 3: 673–678.

Footnote #32
Lee D. and Lis J.T. 1998. Transcriptional activation independent of TFIIH kinase and the RNA polymerase II mediator in vivo. Nature 393: 389–392.
Lee D.K., Kim S., and Lis J.T. 1999. Different upstream transcriptional activators have distinct coactivator requirements. Genes Dev. 13: 2934–2939.

Footnote #33
Johnson A.D. 1995. Molecular mechanisms of cell-type determination in budding yeast. Curr. Opin. Genet. Dev. 5: 552–558.

Footnote #35
Cosma M.P., Panizza S., and Nasmyth K. 2001. Cdk1 triggers association of RNA polymerase to cell cycle promoters only after recruitment of the mediator by SBF. Mol. Cell 7: 1213–1220.

Footnote #36
Maxon M.E. and Herskowitz I. 2001. Ash1p is a site-specific DNA-binding protein that actively represses transcription. Proc. Natl. Acad. Sci. 98: 1495–1500.
Sil A. and Herskowitz I. 1996. Identification of asymmetrically localized determinant, Ash1p, required for lineage-specific transcription of the yeast HO gene. Cell 84: 711–722.
Bobola N., Jansen R.P., Shin T.H., and Nasmyth K. 1996. Asymmetric accumulation of Ash1p in postanaphase nuclei depends on a myosin and restricts yeast mating-type switching to mother cells. Cell 84: 699–709.

Footnote #40
Tanner K.G., Landry J., Sternglanz R., and Denu J.M. 2000. Silent information regulator 2 family of NAD- dependent histone/protein deacetylases generates a unique product, 1-O-acetyl-ADP-ribose. Proc. Natl. Acad. Sci. 97: 14178–14182.
Smith J.S., Brachmann C.B., Celic I., Kenna M.A., Muhammad S., Starai V.J., Avalos J.L., Escalante-Semerena J.C., Grubmeyer C., Wolberger C., and Boeke J.D. 2000. A phylogenetically conserved NAD+-dependent protein deacetylase activity in the Sir2 protein family. Proc. Natl. Acad. Sci. 97: 6658–6663.
Imai S., Armstrong C.M., Kaeberlein M., and Guarente L. 2000. Transcriptional silencing and longevity protein Sir2 is an NAD-dependent histone deacetylase. Nature 403: 795–800.
Landry J., Sutton A., Tafrov S.T., Heller R.C., Stebbins J., Pillus L., and Sternglanz R. 2000. The silencing protein SIR2 and its homologs are NAD-dependent protein deacetylases. Proc. Natl. Acad. Sci. 97: 5807–5811.
Tanny J.C. and Moazed D. 2001. Coupling of histone deacetylation to NAD breakdown by the yeast silencing protein Sir2: Evidence for acetyl transfer from substrate to an NAD breakdown product. Proc. Natl. Acad. Sci. 98: 415–420.

Footnote #41
Martin S.G., Laroche T., Suka N., Grunstein M., and Gasser S.M. 1999. Relocalization of telomeric Ku and SIR proteins in response to DNA strand breaks in yeast. Cell 97: 621–633.

Footnote #42
Sekinger E.A. and Gross D.S. 2001. Silenced chromatin is permissive to activator binding and PIC recruitment. Cell 105: 403–414.

Footnote #44
de Bruin D., Zaman Z., Liberatore R.A., and Ptashne M. 2001. Telomere looping permits gene activation by a downstream UAS in yeast. Nature 409: 109–113.

© 2002 by Cold Spring Harbor Laboratory Press. All rights reserved.
No part of these pages, either text or image, may be used for any purpose other than personal use. Therefore, reproduction, modification, storage in a retrieval system, or retransmission, in any form or by any means, electronic, mechanical, or otherwise, for reasons other than personal use, is strictly prohibited without prior written permission.

Home A Genetic Switch An Introduction to Nervous Systems Epigenetics From a to α Genes and Signals Transcriptional Regulation Help