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Multiple Negative Regulators Restrict Recruitment of the SWI/SNF Chromatin Remodeler to the HO Promoter in Saccharomyces cerevisiae.

Parnell EJ, Stillman DJ.

Genetics. 2019 Aug;212(4):1181-1204. doi: 10.1534/genetics.119.302359. Epub 2019 Jun 5.


Establishment and Maintenance of Chromatin Architecture Are Promoted Independently of Transcription by the Histone Chaperone FACT and H3-K56 Acetylation in Saccharomyces cerevisiae.

McCullough LL, Pham TH, Parnell TJ, Connell Z, Chandrasekharan MB, Stillman DJ, Formosa T.

Genetics. 2019 Mar;211(3):877-892. doi: 10.1534/genetics.118.301853. Epub 2019 Jan 24.


A member of the gut mycobiota modulates host purine metabolism exacerbating colitis in mice.

Chiaro TR, Soto R, Zac Stephens W, Kubinak JL, Petersen C, Gogokhia L, Bell R, Delgado JC, Cox J, Voth W, Brown J, Stillman DJ, O'Connell RM, Tebo AE, Round JL.

Sci Transl Med. 2017 Mar 8;9(380). pii: eaaf9044. doi: 10.1126/scitranslmed.aaf9044. Erratum in: Sci Transl Med. 2017 May 3;9(388):.


Disruption of promoter memory by synthesis of a long noncoding RNA.

Yu Y, Yarrington RM, Chuong EB, Elde NC, Stillman DJ.

Proc Natl Acad Sci U S A. 2016 Aug 23;113(34):9575-80. doi: 10.1073/pnas.1601793113. Epub 2016 Aug 9.


Nucleosomes Are Essential for Proper Regulation of a Multigated Promoter in Saccharomyces cerevisiae.

Yarrington RM, Goodrum JM, Stillman DJ.

Genetics. 2016 Feb;202(2):551-63. doi: 10.1534/genetics.115.183715. Epub 2015 Dec 1.


Spatiotemporal cascade of transcription factor binding required for promoter activation.

Yarrington RM, Rudd JS, Stillman DJ.

Mol Cell Biol. 2015 Feb;35(4):688-98. doi: 10.1128/MCB.01285-14. Epub 2014 Dec 15.


The Rts1 regulatory subunit of PP2A phosphatase controls expression of the HO endonuclease via localization of the Ace2 transcription factor.

Parnell EJ, Yu Y, Lucena R, Yoon Y, Bai L, Kellogg DR, Stillman DJ.

J Biol Chem. 2014 Dec 19;289(51):35431-7. doi: 10.1074/jbc.M114.611715. Epub 2014 Oct 28.


PP2ARts1 is a master regulator of pathways that control cell size.

Zapata J, Dephoure N, Macdonough T, Yu Y, Parnell EJ, Mooring M, Gygi SP, Stillman DJ, Kellogg DR.

J Cell Biol. 2014 Feb 3;204(3):359-76. doi: 10.1083/jcb.201309119.


A role for FACT in repopulation of nucleosomes at inducible genes.

Voth WP, Takahata S, Nishikawa JL, Metcalfe BM, Näär AM, Stillman DJ.

PLoS One. 2014 Jan 2;9(1):e84092. doi: 10.1371/journal.pone.0084092. eCollection 2014.


Dancing the cell cycle two-step: regulation of yeast G1-cell-cycle genes by chromatin structure.

Stillman DJ.

Trends Biochem Sci. 2013 Sep;38(9):467-75. doi: 10.1016/j.tibs.2013.06.009. Epub 2013 Jul 16. Review.


Stochastic expression and epigenetic memory at the yeast HO promoter.

Zhang Q, Yoon Y, Yu Y, Parnell EJ, Garay JA, Mwangi MM, Cross FR, Stillman DJ, Bai L.

Proc Natl Acad Sci U S A. 2013 Aug 20;110(34):14012-7. doi: 10.1073/pnas.1306113110. Epub 2013 Jul 8.


Shields up: the Tup1-Cyc8 repressor complex blocks coactivator recruitment.

Parnell EJ, Stillman DJ.

Genes Dev. 2011 Dec 1;25(23):2429-35. doi: 10.1101/gad.181768.111.


Repressive chromatin affects factor binding at yeast HO (homothallic switching) promoter.

Takahata S, Yu Y, Stillman DJ.

J Biol Chem. 2011 Oct 7;286(40):34809-19. doi: 10.1074/jbc.M111.281626. Epub 2011 Aug 12.


Insight into the mechanism of nucleosome reorganization from histone mutants that suppress defects in the FACT histone chaperone.

McCullough L, Rawlins R, Olsen A, Xin H, Stillman DJ, Formosa T.

Genetics. 2011 Aug;188(4):835-46. doi: 10.1534/genetics.111.128769. Epub 2011 May 30.


First time, every time: nucleosomes at a promoter can determine the probability of gene activation.

Voth WP, Stillman DJ.

Dev Cell. 2010 Apr 20;18(4):503-4. doi: 10.1016/j.devcel.2010.04.006.


Nhp6: a small but powerful effector of chromatin structure in Saccharomyces cerevisiae.

Stillman DJ.

Biochim Biophys Acta. 2010 Jan-Feb;1799(1-2):175-80. doi: 10.1016/j.bbagrm.2009.11.010. Review.


The E2F functional analogue SBF recruits the Rpd3(L) HDAC, via Whi5 and Stb1, and the FACT chromatin reorganizer, to yeast G1 cyclin promoters.

Takahata S, Yu Y, Stillman DJ.

EMBO J. 2009 Nov 4;28(21):3378-89. doi: 10.1038/emboj.2009.270. Epub 2009 Sep 10.


yFACT induces global accessibility of nucleosomal DNA without H2A-H2B displacement.

Xin H, Takahata S, Blanksma M, McCullough L, Stillman DJ, Formosa T.

Mol Cell. 2009 Aug 14;35(3):365-76. doi: 10.1016/j.molcel.2009.06.024.


Coupling phosphate homeostasis to cell cycle-specific transcription: mitotic activation of Saccharomyces cerevisiae PHO5 by Mcm1 and Forkhead proteins.

Pondugula S, Neef DW, Voth WP, Darst RP, Dhasarathy A, Reynolds MM, Takahata S, Stillman DJ, Kladde MP.

Mol Cell Biol. 2009 Sep;29(18):4891-905. doi: 10.1128/MCB.00222-09. Epub 2009 Jul 13.


FACT and Asf1 regulate nucleosome dynamics and coactivator binding at the HO promoter.

Takahata S, Yu Y, Stillman DJ.

Mol Cell. 2009 May 14;34(4):405-15. doi: 10.1016/j.molcel.2009.04.010.


Chromosome-scale genetic mapping using a set of 16 conditionally stable Saccharomyces cerevisiae chromosomes.

Reid RJ, Sunjevaric I, Voth WP, Ciccone S, Du W, Olsen AE, Stillman DJ, Rothstein R.

Genetics. 2008 Dec;180(4):1799-808. doi: 10.1534/genetics.108.087999. Epub 2008 Oct 1.


Getting a transcription factor to only one nucleus following mitosis.

Parnell EJ, Stillman DJ.

PLoS Biol. 2008 Sep 16;6(9):e229. doi: 10.1371/journal.pbio.0060229. No abstract available.


Different genetic functions for the Rpd3(L) and Rpd3(S) complexes suggest competition between NuA4 and Rpd3(S).

Biswas D, Takahata S, Stillman DJ.

Mol Cell Biol. 2008 Jul;28(14):4445-58. doi: 10.1128/MCB.00164-08. Epub 2008 May 19.


Regulation of the yeast Ace2 transcription factor during the cell cycle.

Sbia M, Parnell EJ, Yu Y, Olsen AE, Kretschmann KL, Voth WP, Stillman DJ.

J Biol Chem. 2008 Apr 25;283(17):11135-45. doi: 10.1074/jbc.M800196200. Epub 2008 Feb 21.


A role for Chd1 and Set2 in negatively regulating DNA replication in Saccharomyces cerevisiae.

Biswas D, Takahata S, Xin H, Dutta-Biswas R, Yu Y, Formosa T, Stillman DJ.

Genetics. 2008 Feb;178(2):649-59. doi: 10.1534/genetics.107.084202. Epub 2008 Feb 1.


Structural and functional analysis of the Spt16p N-terminal domain reveals overlapping roles of yFACT subunits.

VanDemark AP, Xin H, McCullough L, Rawlins R, Bentley S, Heroux A, Stillman DJ, Hill CP, Formosa T.

J Biol Chem. 2008 Feb 22;283(8):5058-68. Epub 2007 Dec 18.


Forkhead proteins control the outcome of transcription factor binding by antiactivation.

Voth WP, Yu Y, Takahata S, Kretschmann KL, Lieb JD, Parker RL, Milash B, Stillman DJ.

EMBO J. 2007 Oct 17;26(20):4324-34. Epub 2007 Sep 27.


Chd1 and yFACT act in opposition in regulating transcription.

Biswas D, Dutta-Biswas R, Stillman DJ.

Mol Cell Biol. 2007 Sep;27(18):6279-87. Epub 2007 Jul 9.


Systematic hybrid LOH: a new method to reduce false positives and negatives during screening of yeast gene deletion libraries.

Alvaro D, Sunjevaric I, Reid RJ, Lisby M, Stillman DJ, Rothstein R.

Yeast. 2006 Oct-Nov;23(14-15):1097-106.


Opposing roles for Set2 and yFACT in regulating TBP binding at promoters.

Biswas D, Dutta-Biswas R, Mitra D, Shibata Y, Strahl BD, Formosa T, Stillman DJ.

EMBO J. 2006 Oct 4;25(19):4479-89. Epub 2006 Sep 14.


SWI/SNF binding to the HO promoter requires histone acetylation and stimulates TATA-binding protein recruitment.

Mitra D, Parnell EJ, Landon JW, Yu Y, Stillman DJ.

Mol Cell Biol. 2006 Jun;26(11):4095-110.


The yeast FACT complex has a role in transcriptional initiation.

Biswas D, Yu Y, Prall M, Formosa T, Stillman DJ.

Mol Cell Biol. 2005 Jul;25(14):5812-22.


ACE2, CBK1, and BUD4 in budding and cell separation.

Voth WP, Olsen AE, Sbia M, Freedman KH, Stillman DJ.

Eukaryot Cell. 2005 Jun;4(6):1018-28.


Role for Nhp6, Gcn5, and the Swi/Snf complex in stimulating formation of the TATA-binding protein-TFIIA-DNA complex.

Biswas D, Imbalzano AN, Eriksson P, Yu Y, Stillman DJ.

Mol Cell Biol. 2004 Sep;24(18):8312-21.


TATA-binding protein mutants that are lethal in the absence of the Nhp6 high-mobility-group protein.

Eriksson P, Biswas D, Yu Y, Stewart JM, Stillman DJ.

Mol Cell Biol. 2004 Jul;24(14):6419-29.


A unified nomenclature for protein subunits of mediator complexes linking transcriptional regulators to RNA polymerase II.

Bourbon HM, Aguilera A, Ansari AZ, Asturias FJ, Berk AJ, Bjorklund S, Blackwell TK, Borggrefe T, Carey M, Carlson M, Conaway JW, Conaway RC, Emmons SW, Fondell JD, Freedman LP, Fukasawa T, Gustafsson CM, Han M, He X, Herman PK, Hinnebusch AG, Holmberg S, Holstege FC, Jaehning JA, Kim YJ, Kuras L, Leutz A, Lis JT, Meisterernest M, Naar AM, Nasmyth K, Parvin JD, Ptashne M, Reinberg D, Ronne H, Sadowski I, Sakurai H, Sipiczki M, Sternberg PW, Stillman DJ, Strich R, Struhl K, Svejstrup JQ, Tuck S, Winston F, Roeder RG, Kornberg RD.

Mol Cell. 2004 Jun 4;14(5):553-7. No abstract available.


pRS yeast vectors with a LYS2 marker.

Eriksson P, Thomas LR, Thorburn A, Stillman DJ.

Biotechniques. 2004 Feb;36(2):212-3. No abstract available.


The Zap1 transcriptional activator also acts as a repressor by binding downstream of the TATA box in ZRT2.

Bird AJ, Blankman E, Stillman DJ, Eide DJ, Winge DR.

EMBO J. 2004 Mar 10;23(5):1123-32. Epub 2004 Feb 19.


Changes in developmental state: demolish the old to construct the new.

Voth WP, Stillman DJ.

Genes Dev. 2003 Sep 15;17(18):2201-4. No abstract available.


ACE2 is required for daughter cell-specific G1 delay in Saccharomyces cerevisiae.

Laabs TL, Markwardt DD, Slattery MG, Newcomb LL, Stillman DJ, Heideman W.

Proc Natl Acad Sci U S A. 2003 Sep 2;100(18):10275-80. Epub 2003 Aug 22.


Regulation of TATA-binding protein binding by the SAGA complex and the Nhp6 high-mobility group protein.

Yu Y, Eriksson P, Bhoite LT, Stillman DJ.

Mol Cell Biol. 2003 Mar;23(6):1910-21.


Defects in SPT16 or POB3 (yFACT) in Saccharomyces cerevisiae cause dependence on the Hir/Hpc pathway: polymerase passage may degrade chromatin structure.

Formosa T, Ruone S, Adams MD, Olsen AE, Eriksson P, Yu Y, Rhoades AR, Kaufman PD, Stillman DJ.

Genetics. 2002 Dec;162(4):1557-71.


Mutations in the pho2 (bas2) transcription factor that differentially affect activation with its partner proteins bas1, pho4, and swi5.

Bhoite LT, Allen JM, Garcia E, Thomas LR, Gregory ID, Voth WP, Whelihan K, Rolfes RJ, Stillman DJ.

J Biol Chem. 2002 Oct 4;277(40):37612-8. Epub 2002 Jul 26.


Functional mapping of Bas2. Identification of activation and Bas1-interaction domains.

Hannum C, Kulaeva OI, Sun H, Urbanowski JL, Wendus A, Stillman DJ, Rolfes RJ.

J Biol Chem. 2002 Sep 13;277(37):34003-9. Epub 2002 Jul 10.


Regulation of Fas-associated death domain interactions by the death effector domain identified by a modified reverse two-hybrid screen.

Thomas LR, Stillman DJ, Thorburn A.

J Biol Chem. 2002 Sep 13;277(37):34343-8. Epub 2002 Jul 9.


Correlation between chromatin association and transcriptional regulation for the Act3p/Arp4 nuclear actin-related protein of Saccharomyces cerevisiae.

Harata M, Zhang Y, Stillman DJ, Matsui D, Oma Y, Nishimori K, Mochizuki R.

Nucleic Acids Res. 2002 Apr 15;30(8):1743-50.


The protein kinase Pho85 is required for asymmetric accumulation of the Ash1 protein in Saccharomyces cerevisiae.

McBride HJ, Sil A, Measday V, Yu Y, Moffat J, Maxon ME, Herskowitz I, Andrews B, Stillman DJ.

Mol Microbiol. 2001 Oct;42(2):345-53.


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