MolecularCell, Volume 35, Issue 1, 10 July 2009, Pages 82-92
Alexander A. Shishkin1, Irina Voineagu1, Robert Matera1, Nicole Cherng1, Brook T. Chernet1, Maria M. Krasilnikova2, Vidhya Narayanan3, Kirill S. Lobachev3 and Sergei M. Mirkin1, ,
1Department of Biology, Tufts University, Medford, MA 02155, USA
2Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA 16802, USA
3School of Biology and Institute for Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, GA 30332
Received 22 August 2008; revised 7 January 2009; accepted 18 June 2009. Published: July 9, 2009. Available online 9 July 2009.
Keywords: DNA repeats , GAA repeats, Friedreich's ataxia, chimeric URA3 gene, rates of expansions of GAA repeats.
Thursday, July 9, 2009
Of yeast and men: Unraveling the molecular mechanisms of Friedreich's ataxia
Public release date: 9-Jul-2009
EurekAlert¡
This news is in reference to this work: Large-Scale Expansions of Friedreich's Ataxia GAA Repeats in Yeast
EurekAlert¡
This news is in reference to this work: Large-Scale Expansions of Friedreich's Ataxia GAA Repeats in Yeast
Genome-wide analysis of interactions between ATP-dependent chromatin remodeling and histone modifications
OPEN ACCES
Zhiming Dai , Xianhua Dai , Qian Xiang , Jihua Feng , Jiang Wang , Yangyang Deng and Caisheng He
BMC Genomics 2009, 10:304doi:10.1186/1471-2164-10-304
Published: 8 July 2009
Background
ATP-dependent chromatin remodeling and the covalent modification of histones play central roles in determining chromatin structure and function. Although several specific interactions between these two activities have been elaborated, the global landscape remains to be elucidated.
Results
In this paper, we have developed a computational method to generate the first genome-wide landscape of interactions between ATP-dependent chromatin remodeling and the covalent modification of histones in Saccharomyces cerevisiae. Our method succeeds in identifying known interactions and uncovers many previously unknown interactions between these two activities. Analysis of the genome-wide picture revealed that transcription-related modifications tend to interact with more chromatin remodelers. Our results also demonstrate that most chromatin remodeling-modification interactions act via interactions of remodelers with both histone-modifying enzymes and histone residues. We also found that the co-occurrence of both modification and remodeling has significantly different influences on multiple gene features (e.g. nucleosome occupancy) compared with the presence of either one.
Conclusions
We gave the first genome-wide picture of ATP-dependent chromatin remodeling-histone modification interactions. We also revealed how these two activities work together to regulate chromatin structure and function. Our results suggest that distinct strategies for regulating chromatin activity are selectively employed by genes with different properties.
Full text: http://www.biomedcentral.com/content/pdf/1471-2164-10-304.pdf
Zhiming Dai , Xianhua Dai , Qian Xiang , Jihua Feng , Jiang Wang , Yangyang Deng and Caisheng He
BMC Genomics 2009, 10:304doi:10.1186/1471-2164-10-304
Published: 8 July 2009
Background
ATP-dependent chromatin remodeling and the covalent modification of histones play central roles in determining chromatin structure and function. Although several specific interactions between these two activities have been elaborated, the global landscape remains to be elucidated.
Results
In this paper, we have developed a computational method to generate the first genome-wide landscape of interactions between ATP-dependent chromatin remodeling and the covalent modification of histones in Saccharomyces cerevisiae. Our method succeeds in identifying known interactions and uncovers many previously unknown interactions between these two activities. Analysis of the genome-wide picture revealed that transcription-related modifications tend to interact with more chromatin remodelers. Our results also demonstrate that most chromatin remodeling-modification interactions act via interactions of remodelers with both histone-modifying enzymes and histone residues. We also found that the co-occurrence of both modification and remodeling has significantly different influences on multiple gene features (e.g. nucleosome occupancy) compared with the presence of either one.
Conclusions
We gave the first genome-wide picture of ATP-dependent chromatin remodeling-histone modification interactions. We also revealed how these two activities work together to regulate chromatin structure and function. Our results suggest that distinct strategies for regulating chromatin activity are selectively employed by genes with different properties.
Full text: http://www.biomedcentral.com/content/pdf/1471-2164-10-304.pdf
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