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Logo of bmcgenoBioMed Centralsearchsubmit a manuscriptregisterthis articleBMC Genomics
BMC Genomics. 2009; 10: 304.
Published online Jul 8, 2009. doi:  10.1186/1471-2164-10-304
PMCID: PMC2713269
Genome-wide analysis of interactions between ATP-dependent chromatin remodeling and histone modifications
Zhiming Dai,1 Xianhua Dai,corresponding author1 Qian Xiang,1 Jihua Feng,1 Jiang Wang,1 Yangyang Deng,1 and Caisheng He1
1Electronic Department, Sun Yat-Sen University, Guangzhou, PR China
corresponding authorCorresponding author.
Zhiming Dai: zhimdai/at/; Xianhua Dai: issdxh/at/; Qian Xiang: xiangq/at/; Jihua Feng: fengjihua/at/; Jiang Wang: wrdzsu2003/at/; Yangyang Deng: vijor/at/; Caisheng He: hecaisheng/at/
Received March 27, 2009; Accepted July 8, 2009.
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.
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.
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.
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