Genome-wide analysis of the effect of histone modifications on the coexpression of neighboring genes in <it>Saccharomyces cerevisiae</it>
<p>Abstract</p> <p>Background</p> <p>Neighboring gene pairs in the genome of <it>Saccharomyces cerevisiae </it>have a tendency to be expressed at the same time. The distribution of histone modifications along chromatin fibers is suggested to be an important...
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BMC
2010-10-01
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| Series: | BMC Genomics |
| Online Access: | http://www.biomedcentral.com/1471-2164/11/550 |
| _version_ | 1818664442195345408 |
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| author | Wang Jiang He Caisheng Dai Zhiming Xiang Qian Dai Xianhua Deng Yangyang Feng Jihua |
| author_facet | Wang Jiang He Caisheng Dai Zhiming Xiang Qian Dai Xianhua Deng Yangyang Feng Jihua |
| author_sort | Wang Jiang |
| collection | DOAJ |
| description | <p>Abstract</p> <p>Background</p> <p>Neighboring gene pairs in the genome of <it>Saccharomyces cerevisiae </it>have a tendency to be expressed at the same time. The distribution of histone modifications along chromatin fibers is suggested to be an important mechanism responsible for such coexpression. However, the extent of the contribution of histone modifications to the coexpression of neighboring genes is unclear.</p> <p>Results</p> <p>We investigated the similarity of histone modification between neighboring genes using autocorrelation analysis and composite profiles. Our analysis showed that neighboring genes had similar levels or changes of histone modifications, especially those transcribed in the same direction. The similarities, however, were restricted to 1 or 2 neighboring genes. Moreover, the expression of a gene was significantly correlated with histone modification of its neighboring gene(s), but this was limited to only 1 or 2 neighbors. Using a hidden Markov model (HMM), we found more than 2000 chromatin domains with similar acetylation changes as the cultures changed and a considerable number of these domains covered 2-4 genes. Gene pairs within domains exhibited a higher level of coexpression than random pairs and shared similar functions.</p> <p>Conclusions</p> <p>The results of this study suggest that similar histone modifications occur within only a small local chromatin region in yeast. The modifications generally have an effect on coexpression with only 1 or 2 neighboring genes. Some blocking mechanism(s) might strictly restrain the distribution of histone modifications in yeast.</p> |
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| institution | Directory Open Access Journal |
| issn | 1471-2164 |
| language | English |
| last_indexed | 2024-12-17T05:32:48Z |
| publishDate | 2010-10-01 |
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| spelling | doaj.art-cc016fa990084d439c2abcf2d767b9542022-12-21T22:01:41ZengBMCBMC Genomics1471-21642010-10-0111155010.1186/1471-2164-11-550Genome-wide analysis of the effect of histone modifications on the coexpression of neighboring genes in <it>Saccharomyces cerevisiae</it>Wang JiangHe CaishengDai ZhimingXiang QianDai XianhuaDeng YangyangFeng Jihua<p>Abstract</p> <p>Background</p> <p>Neighboring gene pairs in the genome of <it>Saccharomyces cerevisiae </it>have a tendency to be expressed at the same time. The distribution of histone modifications along chromatin fibers is suggested to be an important mechanism responsible for such coexpression. However, the extent of the contribution of histone modifications to the coexpression of neighboring genes is unclear.</p> <p>Results</p> <p>We investigated the similarity of histone modification between neighboring genes using autocorrelation analysis and composite profiles. Our analysis showed that neighboring genes had similar levels or changes of histone modifications, especially those transcribed in the same direction. The similarities, however, were restricted to 1 or 2 neighboring genes. Moreover, the expression of a gene was significantly correlated with histone modification of its neighboring gene(s), but this was limited to only 1 or 2 neighbors. Using a hidden Markov model (HMM), we found more than 2000 chromatin domains with similar acetylation changes as the cultures changed and a considerable number of these domains covered 2-4 genes. Gene pairs within domains exhibited a higher level of coexpression than random pairs and shared similar functions.</p> <p>Conclusions</p> <p>The results of this study suggest that similar histone modifications occur within only a small local chromatin region in yeast. The modifications generally have an effect on coexpression with only 1 or 2 neighboring genes. Some blocking mechanism(s) might strictly restrain the distribution of histone modifications in yeast.</p>http://www.biomedcentral.com/1471-2164/11/550 |
| spellingShingle | Wang Jiang He Caisheng Dai Zhiming Xiang Qian Dai Xianhua Deng Yangyang Feng Jihua Genome-wide analysis of the effect of histone modifications on the coexpression of neighboring genes in <it>Saccharomyces cerevisiae</it> BMC Genomics |
| title | Genome-wide analysis of the effect of histone modifications on the coexpression of neighboring genes in <it>Saccharomyces cerevisiae</it> |
| title_full | Genome-wide analysis of the effect of histone modifications on the coexpression of neighboring genes in <it>Saccharomyces cerevisiae</it> |
| title_fullStr | Genome-wide analysis of the effect of histone modifications on the coexpression of neighboring genes in <it>Saccharomyces cerevisiae</it> |
| title_full_unstemmed | Genome-wide analysis of the effect of histone modifications on the coexpression of neighboring genes in <it>Saccharomyces cerevisiae</it> |
| title_short | Genome-wide analysis of the effect of histone modifications on the coexpression of neighboring genes in <it>Saccharomyces cerevisiae</it> |
| title_sort | genome wide analysis of the effect of histone modifications on the coexpression of neighboring genes in it saccharomyces cerevisiae it |
| url | http://www.biomedcentral.com/1471-2164/11/550 |
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