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Molecular and Cellular Biology Volume 21, 2001 - Issue 2
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Transcriptional Regulation

Remodeling of Yeast CUP1 Chromatin Involves Activator-Dependent Repositioning of Nucleosomes over the Entire Gene and Flanking Sequences

Chang-Hui ShenLaboratory of Cellular and Developmental Biology (NIDDK), National Institutes of Health, Bethesda, Maryland20892-2715
,
Benoit P. LeblancLaboratory of Cellular and Developmental Biology (NIDDK), National Institutes of Health, Bethesda, Maryland20892-2715
,
Jennifer A. AlfieriLaboratory of Cellular and Developmental Biology (NIDDK), National Institutes of Health, Bethesda, Maryland20892-2715
&
David J. ClarkLaboratory of Cellular and Developmental Biology (NIDDK), National Institutes of Health, Bethesda, Maryland20892-2715Correspondence[email protected]
Pages 534-547 | Received 03 Oct 2000, Accepted 01 Nov 2000, Published online: 28 Mar 2023

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Sakshi Singh, Rakesh Kumar Sahu & Raghuvir Singh Tomar. (2021) The N-Terminal Tail of Histone H3 Regulates Copper Homeostasis in . Molecular and Cellular Biology 41:2.
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DavidJ. Clark. (2010) Nucleosome Positioning, Nucleosome Spacing and the Nucleosome Code. Journal of Biomolecular Structure and Dynamics 27:6, pages 781-793.
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Silvia Jimeno-González, Fernando Gómez-Herreros, Paula M. Alepuz & Sebastián Chávez. (2006) A Gene-Specific Requirement for FACT during Transcription Is Related to the Chromatin Organization of the Transcribed Region. Molecular and Cellular Biology 26:23, pages 8710-8721.
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Yeonjung Kim, Neil McLaughlin, Kim Lindstrom, Toshio Tsukiyama & David J. Clark. (2006) Activation of Saccharomyces cerevisiae HIS3 Results in Gcn4p-Dependent, SWI/SNF-Dependent Mobilization of Nucleosomes over the Entire Gene. Molecular and Cellular Biology 26:22, pages 8607-8622.
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Peter R. Eriksson, Geetu Mendiratta, Neil B. McLaughlin, Tyra G. Wolfsberg, Leonardo Mariño-Ramírez, Tiffany A. Pompa, Mohendra Jainerin, David Landsman, Chang-Hui Shen & David J. Clark. (2005) Global Regulation by the Yeast Spt10 Protein Is Mediated through Chromatin Structure and the Histone Upstream Activating Sequence Elements. Molecular and Cellular Biology 25:20, pages 9127-9137.
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Sevinc Ercan, Joseph C. Reese, Jerry L. Workman & Robert T. Simpson. (2005) Yeast Recombination Enhancer Is Stimulated by Transcription Activation. Molecular and Cellular Biology 25:18, pages 7976-7987.
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Chang-Hui Shen, Benoit P. Leblanc, Carolyn Neal, Ramin Akhavan & David J. Clark. (2002) Targeted Histone Acetylation at the Yeast CUP1 Promoter Requires the Transcriptional Activator, the TATA Boxes, and the Putative Histone Acetylase Encoded by SPT10. Molecular and Cellular Biology 22:18, pages 6406-6416.
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Articles from other publishers (35)

Bojan Žunar, Christine Mosrin, Héléne Bénédetti & Béatrice Vallée. (2022) Re-engineering of CUP1 promoter and Cup2/Ace1 transactivator to convert Saccharomyces cerevisiae into a whole-cell eukaryotic biosensor capable of detecting 10 nM of bioavailable copper. Biosensors and Bioelectronics 214, pages 114502.
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Ashish Kumar Singh, Tamás Schauer, Lena Pfaller, Tobias Straub & Felix Mueller-Planitz. (2021) The biogenesis and function of nucleosome arrays. Nature Communications 12:1.
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Chang-Hui Shen & James Allan. (2021) MNase Digestion Protection Patterns of the Linker DNA in Chromatosomes. Cells 10:9, pages 2239.
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Amparo Pascual-Ahuir, Josep Fita-Torró & Markus Proft. (2020) Capturing and Understanding the Dynamics and Heterogeneity of Gene Expression in the Living Cell. International Journal of Molecular Sciences 21:21, pages 8278.
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Hemant K. Prajapati, Josefina Ocampo & David J. Clark. (2020) Interplay among ATP-Dependent Chromatin Remodelers Determines Chromatin Organisation in Yeast. Biology 9:8, pages 190.
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Răzvan V. Chereji, Peter R. Eriksson, Josefina Ocampo, Hemant K. Prajapati & David J. Clark. (2019) Accessibility of promoter DNA is not the primary determinant of chromatin-mediated gene regulation. Genome Research 29:12, pages 1985-1995.
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Tomohiro Fuse, Akio Yanagida & Mitsuhiro Shimizu. (2019) The Yeast Minichromosome System Consisting of Highly Positioned Nucleosomes <i>in Vivo</i>. Biological and Pharmaceutical Bulletin 42:2, pages 289-294.
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Răzvan V. Chereji, Srinivas Ramachandran, Terri D. Bryson & Steven Henikoff. (2018) Precise genome-wide mapping of single nucleosomes and linkers in vivo. Genome Biology 19:1.
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Gunjan D. Mehta, David A. Ball, Peter R. Eriksson, Razvan V. Chereji, David J. Clark, James G. McNally & Tatiana S. Karpova. (2018) Single-Molecule Analysis Reveals Linked Cycles of RSC Chromatin Remodeling and Ace1p Transcription Factor Binding in Yeast. Molecular Cell 72:5, pages 875-887.e9.
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Tomohiro Fuse, Koji Katsumata, Koya Morohoshi, Yukio Mukai, Yuichi Ichikawa, Hitoshi Kurumizaka, Akio Yanagida, Takeshi Urano, Hiroaki Kato & Mitsuhiro Shimizu. (2017) Parallel mapping with site-directed hydroxyl radicals and micrococcal nuclease reveals structural features of positioned nucleosomes in vivo. PLOS ONE 12:10, pages e0186974.
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Arvind Panday & Anne Grove. (2016) The high mobility group protein HMO1 functions as a linker histone in yeast. Epigenetics & Chromatin 9:1.
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Hope A. Cole, Feng Cui, Josefina Ocampo, Tara L. Burke, Tatiana Nikitina, V. Nagarajavel, Naoe Kotomura, Victor B. Zhurkin & David J. Clark. (2016) Novel nucleosomal particles containing core histones and linker DNA but no histone H1. Nucleic Acids Research 44:2, pages 573-581.
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Corinna Lieleg, Nils Krietenstein, Maria Walker & Philipp Korber. (2014) Nucleosome positioning in yeasts: methods, maps, and mechanisms. Chromosoma 124:2, pages 131-151.
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Jian Liu, Hélène Martin-Yken, Frédéric Bigey, Sylvie Dequin, Jean-Marie François & Jean-Pascal Capp. (2015) Natural Yeast Promoter Variants Reveal Epistasis in the Generation of Transcriptional-Mediated Noise and Its Potential Benefit in Stressful Conditions. Genome Biology and Evolution 7:4, pages 969-984.
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Roshini N. WimalarathnaPo Yun PanChang-Hui Shen. (2014) Co-dependent recruitment of Ino80p and Snf2p is required for yeast CUP1 activation . Biochemistry and Cell Biology 92:1, pages 69-75.
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Hope A. Cole, V. Nagarajavel & David J. Clark. (2012) Perfect and imperfect nucleosome positioning in yeast. Biochimica et Biophysica Acta (BBA) - Gene Regulatory Mechanisms 1819:7, pages 639-643.
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Roshini N. Wimalarathna, Po Yun Pan & Chang-Hui Shen. (2012) Chromatin repositioning activity and transcription machinery are both recruited by Ace1p in yeast CUP1 activation. Biochemical and Biophysical Research Communications 422:4, pages 658-663.
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Hope A. Cole, Bruce H. Howard & David J. Clark. 2012. Nucleosomes, Histones & Chromatin Part B. Nucleosomes, Histones & Chromatin Part B 145 168 .
Hope A. Cole, Bruce H. Howard & David J. Clark. (2011) Activation-induced disruption of nucleosome position clusters on the coding regions of Gcn4-dependent genes extends into neighbouring genes. Nucleic Acids Research 39:22, pages 9521-9535.
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An Jansen & Kevin J. Verstrepen. (2011) Nucleosome Positioning in Saccharomyces cerevisiae. Microbiology and Molecular Biology Reviews 75:2, pages 301-320.
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Michelle Esposito, Paulina Konarzewska, Oluwafemi Odeyale & Chang-Hui Shen. (2010) Gene-wide histone acetylation at the yeast INO1 requires the transcriptional activator Ino2p. Biochemical and Biophysical Research Communications 391:2, pages 1285-1290.
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Karl A. Zawadzki, Alexandre V. Morozov & James R. Broach. (2009) Chromatin-dependent Transcription Factor Accessibility Rather than Nucleosome Remodeling Predominates during Global Transcriptional Restructuring in Saccharomyces cerevisiae . Molecular Biology of the Cell 20:15, pages 3503-3513.
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Jason Ford, Oluwafemi Odeyale, Antonious Eskandar, Nafila Kouba & Chang-Hui Shen. (2007) A SWI/SNF- and INO80-dependent nucleosome movement at the INO1 promoter. Biochemical and Biophysical Research Communications 361:4, pages 974-979.
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Wilbur Tong, Olga I. Kulaeva, David J. Clark & Leonard C. Lutter. (2006) Topological Analysis of Plasmid Chromatin from Yeast and Mammalian Cells. Journal of Molecular Biology 361:5, pages 813-822.
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David J. Clark & Chang‐Hui Shen. 2006. DNA Microarrays, Part A: Array Platforms and Wet-Bench Protocols. DNA Microarrays, Part A: Array Platforms and Wet-Bench Protocols 416 430 .
Hui-Ching Kuo, John D. Moore & Jocelyn E. Krebs. (2005) Histone H2A and Spt10 Cooperate to Regulate Induction and Autoregulation of the CUP1 Metallothionein. Journal of Biological Chemistry 280:1, pages 104-111.
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Yeonjung Kim, Chang-Hui Shen & David J Clark. (2004) Purification and nucleosome mapping analysis of native yeast plasmid chromatin. Methods 33:1, pages 59-67.
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Irene García, Ramón Gonzalez, Dennis Gómez & Claudio Scazzocchio. (2004) Chromatin Rearrangements in the prnD-prnB Bidirectional Promoter: Dependence on Transcription Factors . Eukaryotic Cell 3:1, pages 144-156.
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S. Zeilinger, M. Schmoll, M. Pail, R. L. Mach & C. P. Kubicek. (2003) Nucleosome transactions on the Hypocrea jecorina ( Trichoderma reesei) cellulase promoter cbh2 associated with cellulase induction. Molecular Genetics and Genomics 270:1, pages 46-55.
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Robert T Simpson, Charles E Ducker, John D Diller & Chun Ruan. 2003. Chromatin and Chromatin Remodeling Enzymes, Part A. Chromatin and Chromatin Remodeling Enzymes, Part A 158 170 .
Yeonjung Kim & David J. Clark. (2002) SWI/SNF-dependent long-range remodeling of yeast HIS3 chromatin . Proceedings of the National Academy of Sciences 99:24, pages 15381-15386.
Crossref
Chang-Hui Shen & David J. Clark. (2001) DNA Sequence Plays a Major Role in Determining Nucleosome Positions in Yeast CUP1 Chromatin. Journal of Biological Chemistry 276:37, pages 35209-35216.
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Stavros Lomvardas & Dimitris Thanos. (2001) Nucleosome Sliding via TBP DNA Binding In Vivo. Cell 106:6, pages 685-696.
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Keith A. Koch, Stephane Allard, Nicholas Santoro, Jacques Cote & Dennis J. Thiele. (2001) The Candida glabrata Amt1 copper-sensing transcription factor requires Swi/Snf and Gcn5 at a critical step in copper detoxification. Molecular Microbiology 40:5, pages 1165-1174.
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. (2001) Current Awareness. Yeast 18:6, pages 577-584.
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