My NCBISign In
Global nucleosome occupancy in yeast
Bradley E Bernstein, Chih Long Liu, Emily L Humphrey, Ethan O Perlstein, Stuart L Schreiber
Genome Biol. 2004; 5(9): R62. Published online 2004 August 20. doi: 10.1186/gb-2004-5-9-r62
PMCID:
PMC522869
Abstract Full Text PDF–1.6M

Is Cited by the Following 110 Articles in this Archive:

Cell-type-specific nuclei purification from whole animals for genome-wide expression and chromatin profiling
Florian A. Steiner, Paul B. Talbert, Sivakanthan Kasinathan, Roger B. Deal, Steven Henikoff
Genome Res. 2012 April; 22(4): 766–777. doi: 10.1101/gr.131748.111
PMCID:
PMC3317158
Abstract Full Text PDF–1.3M
Chromatin and Transcription in Yeast
Oliver J. Rando, Fred Winston
Genetics. 2012 February; 190(2): 351–387. doi: 10.1534/genetics.111.132266
PMCID:
PMC3276623
Free in PMC on 2013/02/01
A genomic model of condition-specific nucleosome behavior explains transcriptional activity in yeast
Judith B. Zaugg, Nicholas M. Luscombe
Genome Res. 2012 January; 22(1): 84–94. doi: 10.1101/gr.124099.111
PMCID:
PMC3246209
Abstract Full Text PDF–1.3M
Analysis of Biological Features Associated with Meiotic Recombination Hot and Cold Spots in Saccharomyces cerevisiae
Loren Hansen, Nak-Kyeong Kim, Leonardo Mariño-Ramírez, David Landsman
PLoS One. 2011; 6(12): e29711. Published online 2011 December 29. doi: 10.1371/journal.pone.0029711
PMCID:
PMC3248464
Abstract Full Text PDF–746K Supplementary Material
A pre-initiation complex at the 3′-end of genes drives antisense transcription independent of divergent sense transcription
Struan C. Murray, Ana Serra Barros, David A. Brown, Peter Dudek, Jonathan Ayling, Jane Mellor
Nucleic Acids Res. 2012 March; 40(6): 2432–2444. Published online 2011 November 28. doi: 10.1093/nar/gkr1121
PMCID:
PMC3315312
Abstract Full Text PDF–1.0M Supplementary Material
Nonspecific Transcription-Factor-DNA Binding Influences Nucleosome Occupancy in Yeast
Ariel Afek, Itamar Sela, Noa Musa-Lempel, David B. Lukatsky
Biophys J. 2011 November 16; 101(10): 2465–2475. doi: 10.1016/j.bpj.2011.10.012
PMCID:
PMC3218343
Free in PMC on 2012/11/16
Epigenetic Regulation of Polymerase II Transcription Initiation in Trypanosoma cruzi: Modulation of Nucleosome Abundance, Histone Modification, and Polymerase Occupancy by O-Linked Thymine DNA Glucosylation
Dilrukshi Ekanayake, Robert Sabatini
Eukaryot Cell. 2011 November; 10(11): 1465–1472. doi: 10.1128/EC.05185-11
PMCID:
PMC3209055
Abstract Full Text PDF–585K Supplementary Material
Transcriptional Regulation in Saccharomyces cerevisiae: Transcription Factor Regulation and Function, Mechanisms of Initiation, and Roles of Activators and Coactivators
Steven Hahn, Elton T. Young
Genetics. 2011 November; 189(3): 705–736. doi: 10.1534/genetics.111.127019
PMCID:
PMC3213380
Free in PMC on 2012/11/01
Nucleosome-coupled expression differences in closely-related species
Yuanfang Guan, Victoria Yao, Kyle Tsui, Marinella Gebbia, Maitreya J Dunham, Corey Nislow, Olga G Troyanskaya
BMC Genomics. 2011; 12: 466. Published online 2011 September 26. doi: 10.1186/1471-2164-12-466
PMCID:
PMC3209474
Abstract Full Text PDF–1.7M Supplementary Material
The Disequilibrium of Nucleosomes Distribution along Chromosomes Plays a Functional and Evolutionarily Role in Regulating Gene Expression
Peng Cui, Qiang Lin, Lingfang Zhang, Feng Ding, Chengqi Xin, Daoyong Zhang, Fanglin Sun, Songnian Hu, Jun Yu
PLoS One. 2011; 6(8): e23219. Published online 2011 August 19. doi: 10.1371/journal.pone.0023219
PMCID:
PMC3158759
Abstract Full Text PDF–999K Supplementary Material
Genome-Wide Integration on Transcription Factors, Histone Acetylation and Gene Expression Reveals Genes Co-Regulated by Histone Modification Patterns
Yayoi Natsume-Kitatani, Motoki Shiga, Hiroshi Mamitsuka
PLoS One. 2011; 6(7): e22281. Published online 2011 July 29. doi: 10.1371/journal.pone.0022281
PMCID:
PMC3146477
Abstract Full Text PDF–831K Supplementary Material
Selective Removal of Promoter Nucleosomes by the RSC Chromatin Remodeling Complex
Yahli Lorch, Joachim Griesenbeck, Hinrich Boeger, Barbara Maier-Davis, Roger D. Kornberg
Nat Struct Mol Biol. Author manuscript; available in PMC 2012 February 1.
Published in final edited form as: Nat Struct Mol Biol. 2011 July 3; 18(8): 881–885. doi: 10.1038/nsmb.2072
PMCID:
PMC3150231
Abstract Full Text PDF–1.4M Supplementary Material
Transcription Factor–Dependent Chromatin Remodeling at Heat Shock and Copper-Responsive Promoters in Chlamydomonas reinhardtii
Daniela Strenkert, Stefan Schmollinger, Frederik Sommer, Miriam Schulz-Raffelt, Michael Schroda
Plant Cell. 2011 June; 23(6): 2285–2301. Published online 2011 June 24. doi: 10.1105/tpc.111.085266
PMCID:
PMC3160021
Abstract Full Text PDF–1.5M Supplementary Material
Dynamics of Nucleosome Invasion by DNA Binding Proteins
Hannah S. Tims, Kaushik Gurunathan, Marcia Levitus, Jonathan Widom
J Mol Biol. Author manuscript; available in PMC 2012 August 12.
Published in final edited form as: J Mol Biol. 2011 August 12; 411(2): 430–448. Published online 2011 June 6. doi: 10.1016/j.jmb.2011.05.044
PMCID:
PMC3164294
Free in PMC on 2012/08/12
Nucleosome Positioning in Saccharomyces cerevisiae
An Jansen, Kevin J. Verstrepen
Microbiol Mol Biol Rev. 2011 June; 75(2): 301–320. doi: 10.1128/MMBR.00046-10
PMCID:
PMC3122627
Free in PMC on 2012/06/01
An effect of DNA sequence on nucleosome occupancy and removal
Xin Wang, Gene O. Bryant, Monique Floer, Dan Spagna, Mark Ptashne
Nat Struct Mol Biol. Author manuscript; available in PMC 2011 October 1.
Published in final edited form as: Nat Struct Mol Biol. 2011 April; 18(4): 507–509. Published online 2011 March 6. doi: 10.1038/nsmb.2017
PMCID:
PMC3071895
Abstract Full Text PDF–894K Supplementary Material
The RSC chromatin remodelling enzyme has a unique role in directing the accurate positioning of nucleosomes
Christian J Wippo, Lars Israel, Shinya Watanabe, Andreas Hochheimer, Craig L Peterson, Philipp Korber
EMBO J. 2011 April 6; 30(7): 1277–1288. Published online 2011 February 22. doi: 10.1038/emboj.2011.43
PMCID:
PMC3094113
Abstract Full Text PDF–1.3M Supplementary Material
Hmo1 directs pre-initiation complex assembly to an appropriate site on its target gene promoters by masking a nucleosome-free region
Koji Kasahara, Yoshifumi Ohyama, Tetsuro Kokubo
Nucleic Acids Res. 2011 May; 39(10): 4136–4150. Published online 2011 February 2. doi: 10.1093/nar/gkq1334
PMCID:
PMC3105432
Abstract Full Text PDF–8.9M Supplementary Material
Yeast H2A.Z, FACT complex and RSC regulate transcription of tRNA gene through differential dynamics of flanking nucleosomes
Sahasransu Mahapatra, Pooran S. Dewari, Anubhav Bhardwaj, Purnima Bhargava
Nucleic Acids Res. 2011 May; 39(10): 4023–4034. Published online 2011 January 25. doi: 10.1093/nar/gkq1286
PMCID:
PMC3105386
Abstract Full Text PDF–5.5M Supplementary Material
Integrative model of genomic factors for determining binding site selection by estrogen receptor-α
Roy Joseph, Yuriy L Orlov, Mikael Huss, Wenjie Sun, Say Li Kong, Leena Ukil, You Fu Pan, Guoliang Li, Michael Lim, Jane S Thomsen, Yijun Ruan, Neil D Clarke, Shyam Prabhakar, Edwin Cheung, Edison T Liu
Mol Syst Biol. 2010; 6: 456. Published online 2010 December 21. doi: 10.1038/msb.2010.109
PMCID:
PMC3018168
Abstract Full Text PDF–2.0M Supplementary Material
Extensive role of the general regulatory factors, Abf1 and Rap1, in determining genome-wide chromatin structure in budding yeast
Mythily Ganapathi, Michael J. Palumbo, Suraiya A. Ansari, Qiye He, Kyle Tsui, Corey Nislow, Randall H. Morse
Nucleic Acids Res. 2011 March; 39(6): 2032–2044. Published online 2010 November 16. doi: 10.1093/nar/gkq1161
PMCID:
PMC3064788
Abstract Full Text PDF–12M Supplementary Material
Identifying the Combinatorial Effects of Histone Modifications by Association Rule Mining in Yeast
Jiang Wang, Xianhua Dai, Qian Xiang, Yangyang Deng, Jihua Feng, Zhiming Dai, Caisheng He
Evol Bioinform Online. 2010; 6: 113–131. Published online 2010 September 20.
PMCID:
PMC2964047
Abstract Full Text PDF–1.4M Supplementary Material
Prediction of Nucleosome Positioning Based on Transcription Factor Binding Sites
Xianfu Yi, Yu-Dong Cai, Zhisong He, WeiRen Cui, Xiangyin Kong
PLoS One. 2010; 5(9): e12495. Published online 2010 September 1. doi: 10.1371/journal.pone.0012495
PMCID:
PMC2931695
Abstract Full Text PDF–218K Supplementary Material
Chromatin Remodeling around Nucleosome-Free Regions Leads to Repression of Noncoding RNA Transcription
Adam N. Yadon, Daniel Van de Mark, Ryan Basom, Jeffrey Delrow, Iestyn Whitehouse, Toshio Tsukiyama
Mol Cell Biol. 2010 November; 30(21): 5110–5122. Published online 2010 August 30. doi: 10.1128/MCB.00602-10
PMCID:
PMC2953044
Abstract Full Text PDF–4.2M
In Vitro Reconstitution of PHO5 Promoter Chromatin Remodeling Points to a Role for Activator-Nucleosome Competition In Vivo
Franziska Ertel, A. Barbara Dirac-Svejstrup, Christina Bech Hertel, Dorothea Blaschke, Jesper Q. Svejstrup, Philipp Korber
Mol Cell Biol. 2010 August; 30(16): 4060–4076. Published online 2010 June 21. doi: 10.1128/MCB.01399-09
PMCID:
PMC2916437
Abstract Full Text PDF–2.5M
Genomic Approaches Uncover Increasing Complexities in the Regulatory Landscape at the Human SCL (TAL1) Locus
Pawandeep Dhami, Alexander W. Bruce, Johanna H. Jim, Shane C. Dillon, Amanda Hall, Jonathan L. Cooper, Nicolas Bonhoure, Kelly Chiang, Peter D. Ellis, Cordelia Langford, Robert M. Andrews, David Vetrie
PLoS One. 2010; 5(2): e9059. Published online 2010 February 5. doi: 10.1371/journal.pone.0009059
PMCID:
PMC2816701
Abstract Full Text PDF–1.8M Supplementary Material
Nucleosome landscape and control of transcription in the human malaria parasite
Nadia Ponts, Elena Y. Harris, Jacques Prudhomme, Ivan Wick, Colleen Eckhardt-Ludka, Glenn R. Hicks, Gary Hardiman, Stefano Lonardi, Karine G. Le Roch
Genome Res. 2010 February; 20(2): 228–238. doi: 10.1101/gr.101063.109
PMCID:
PMC2813478
Abstract Full Text PDF–1.0M
The organization of nucleosomes around splice sites
Wei Chen, Liaofu Luo, Lirong Zhang
Nucleic Acids Res. 2010 May; 38(9): 2788–2798. Published online 2010 January 21. doi: 10.1093/nar/gkq007
PMCID:
PMC2875036
Abstract Full Text PDF–2.1M Supplementary Material
New insights into two distinct nucleosome distributions: comparison of cross-platform positioning datasets in the yeast genome
Jihua Feng, Xianhua Dai, Qian Xiang, Zhiming Dai, Jiang Wang, Yangyang Deng, Caisheng He
BMC Genomics. 2010; 11: 33. Published online 2010 January 15. doi: 10.1186/1471-2164-11-33
PMCID:
PMC2824721
Abstract Full Text PDF–3.4M Supplementary Material
A novel strategy of transcription regulation by intragenic nucleosome ordering
Cédric Vaillant, Leonor Palmeira, Guillaume Chevereau, Benjamin Audit, Yves d'Aubenton-Carafa, Claude Thermes, Alain Arneodo
Genome Res. 2010 January; 20(1): 59–67. doi: 10.1101/gr.096644.109
PMCID:
PMC2798831
Abstract Full Text PDF–1.1M
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