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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
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 Is Cited by the Following 100 Articles in this Archive:
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
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
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
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
G+C content dominates intrinsic nucleosome occupancy
Desiree Tillo, Timothy R Hughes
BMC Bioinformatics. 2009; 10: 442. Published online 2009 December 22. doi: 10.1186/1471-2105-10-442
PMCID:
PMC2808325
Abstract Full Text PDF–720K Supplementary Material
Genome-wide nucleosome mapping of Plasmodium falciparum reveals histone-rich coding and histone-poor intergenic regions and chromatin remodeling of core and subtelomeric genes
Scott J Westenberger, Long Cui, Neekesh Dharia, Elizabeth Winzeler, Liwang Cui
BMC Genomics. 2009; 10: 610. Published online 2009 December 16. doi: 10.1186/1471-2164-10-610
PMCID:
PMC2801526
Abstract Full Text PDF–2.9M Supplementary Material
Insights into distinct regulatory modes of nucleosome positioning
Zhiming Dai, Xianhua Dai, Qian Xiang, Jihua Feng, Yangyang Deng, Jiang Wang
BMC Genomics. 2009; 10: 602. Published online 2009 December 14. doi: 10.1186/1471-2164-10-602
PMCID:
PMC2799443
Abstract Full Text PDF–897K Supplementary Material
Active VSG Expression Sites in Trypanosoma brucei Are Depleted of Nucleosomes
Tara M. Stanne, Gloria Rudenko
Eukaryot Cell. 2010 January; 9(1): 136–147. Published online 2009 November 13. doi: 10.1128/EC.00281-09
PMCID:
PMC2805301
Abstract Full Text PDF–1.3M Supplementary Material
Formaldehyde-Assisted Isolation of Regulatory Elements
Peter L. Nagy, David H. Price
Wiley Interdiscip Rev Syst Biol Med. Author manuscript; available in PMC 2010 November 1.
Published in final edited form as: Wiley Interdiscip Rev Syst Biol Med. 2009 November 1; 1(3): 400–406. doi: 10.1002/wsbm.36
PMCID:
PMC2800794
Abstract Full Text PDF–96K
BayesPI - a new model to study protein-DNA interactions: a case study of condition-specific protein binding parameters for Yeast transcription factors
Junbai Wang, Morigen
BMC Bioinformatics. 2009; 10: 345. Published online 2009 October 20. doi: 10.1186/1471-2105-10-345
PMCID:
PMC2771022
Abstract Full Text PDF–486K Supplementary Material
Epigenetic inheritance of an inducibly nucleosome-depleted promoter and its associated transcriptional state in the apparent absence of transcriptional activators
Ryosuke Ohsawa, Melissa Adkins, Jessica K Tyler
Epigenetics Chromatin. 2009; 2: 11. Published online 2009 September 11. doi: 10.1186/1756-8935-2-11
PMCID:
PMC2749832
Abstract Full Text PDF–2.5M
DYNAMICS AND FUNCTION OF COMPACT NUCLEOSOME ARRAYS
Michael G. Poirier, Eugene Oh, Hannah S. Tims, Jonathan Widom
Nat Struct Mol Biol. Author manuscript; available in PMC 2010 March 1.
Published in final edited form as: Nat Struct Mol Biol. 2009 September; 16(9): 938–944. Published online 2009 August 23. doi: 10.1038/nsmb.1650
PMCID:
PMC2748796
Abstract Full Text PDF–2.4M Supplementary Material
Epigenetics of human T cells during the G0→G1 transition
Alexander E. Smith, Constantinos Chronis, Manolis Christodoulakis, Stephen J. Orr, Nicholas C. Lea, Natalie A. Twine, Akshay Bhinge, Ghulam J. Mufti, N. Shaun B. Thomas
Genome Res. 2009 August; 19(8): 1325–1337. doi: 10.1101/gr.085530.108
PMCID:
PMC2720178
Abstract Full Text PDF–1.4M
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