Cold Spring Harbor Teaching Resources

Footnote #2

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Footnote #3

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Footnote #5

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Footnote #7

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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.

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Footnote #9

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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

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Footnote #13

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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.

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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.

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.

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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.

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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).

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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.

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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.

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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.

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