Dynamic DNA cytosine methylation in the <it>Populus trichocarpa </it>genome: tissue-level variation and relationship to gene expression
<p>Abstract</p> <p>Background</p> <p>DNA cytosine methylation is an epigenetic modification that has been implicated in many biological processes. However, large-scale epigenomic studies have been applied to very few plant species, and variability in methylation among s...
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| Format: | Article |
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BMC
2012-01-01
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| Series: | BMC Genomics |
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| Online Access: | http://www.biomedcentral.com/1471-2164/13/27 |
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| author | Vining Kelly J Pomraning Kyle R Wilhelm Larry J Priest Henry D Pellegrini Matteo Mockler Todd C Freitag Michael Strauss Steven H |
| author_facet | Vining Kelly J Pomraning Kyle R Wilhelm Larry J Priest Henry D Pellegrini Matteo Mockler Todd C Freitag Michael Strauss Steven H |
| author_sort | Vining Kelly J |
| collection | DOAJ |
| description | <p>Abstract</p> <p>Background</p> <p>DNA cytosine methylation is an epigenetic modification that has been implicated in many biological processes. However, large-scale epigenomic studies have been applied to very few plant species, and variability in methylation among specialized tissues and its relationship to gene expression is poorly understood.</p> <p>Results</p> <p>We surveyed DNA methylation from seven distinct tissue types (vegetative bud, male inflorescence [catkin], female catkin, leaf, root, xylem, phloem) in the reference tree species black cottonwood (<it>Populus trichocarpa)</it>. Using 5-methyl-cytosine DNA immunoprecipitation followed by Illumina sequencing (MeDIP-seq), we mapped a total of 129,360,151 36- or 32-mer reads to the <it>P. trichocarpa </it>reference genome. We validated MeDIP-seq results by bisulfite sequencing, and compared methylation and gene expression using published microarray data. Qualitative DNA methylation differences among tissues were obvious on a chromosome scale. Methylated genes had lower expression than unmethylated genes, but genes with methylation in transcribed regions ("gene body methylation") had even lower expression than genes with promoter methylation. Promoter methylation was more frequent than gene body methylation in all tissues except male catkins. Male catkins differed in demethylation of particular transposable element categories, in level of gene body methylation, and in expression range of genes with methylated transcribed regions. Tissue-specific gene expression patterns were correlated with both gene body and promoter methylation.</p> <p>Conclusions</p> <p>We found striking differences among tissues in methylation, which were apparent at the chromosomal scale and when genes and transposable elements were examined. In contrast to other studies in plants, gene body methylation had a more repressive effect on transcription than promoter methylation.</p> |
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| institution | Directory Open Access Journal |
| issn | 1471-2164 |
| language | English |
| last_indexed | 2024-04-13T12:55:30Z |
| publishDate | 2012-01-01 |
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| series | BMC Genomics |
| spelling | doaj.art-1c95b9d783e342358137d1f5cdde88782022-12-22T02:46:05ZengBMCBMC Genomics1471-21642012-01-011312710.1186/1471-2164-13-27Dynamic DNA cytosine methylation in the <it>Populus trichocarpa </it>genome: tissue-level variation and relationship to gene expressionVining Kelly JPomraning Kyle RWilhelm Larry JPriest Henry DPellegrini MatteoMockler Todd CFreitag MichaelStrauss Steven H<p>Abstract</p> <p>Background</p> <p>DNA cytosine methylation is an epigenetic modification that has been implicated in many biological processes. However, large-scale epigenomic studies have been applied to very few plant species, and variability in methylation among specialized tissues and its relationship to gene expression is poorly understood.</p> <p>Results</p> <p>We surveyed DNA methylation from seven distinct tissue types (vegetative bud, male inflorescence [catkin], female catkin, leaf, root, xylem, phloem) in the reference tree species black cottonwood (<it>Populus trichocarpa)</it>. Using 5-methyl-cytosine DNA immunoprecipitation followed by Illumina sequencing (MeDIP-seq), we mapped a total of 129,360,151 36- or 32-mer reads to the <it>P. trichocarpa </it>reference genome. We validated MeDIP-seq results by bisulfite sequencing, and compared methylation and gene expression using published microarray data. Qualitative DNA methylation differences among tissues were obvious on a chromosome scale. Methylated genes had lower expression than unmethylated genes, but genes with methylation in transcribed regions ("gene body methylation") had even lower expression than genes with promoter methylation. Promoter methylation was more frequent than gene body methylation in all tissues except male catkins. Male catkins differed in demethylation of particular transposable element categories, in level of gene body methylation, and in expression range of genes with methylated transcribed regions. Tissue-specific gene expression patterns were correlated with both gene body and promoter methylation.</p> <p>Conclusions</p> <p>We found striking differences among tissues in methylation, which were apparent at the chromosomal scale and when genes and transposable elements were examined. In contrast to other studies in plants, gene body methylation had a more repressive effect on transcription than promoter methylation.</p>http://www.biomedcentral.com/1471-2164/13/27EpigeneticsepigenomicsDNA methylation5-methylcytosine<it>Populus</it> |
| spellingShingle | Vining Kelly J Pomraning Kyle R Wilhelm Larry J Priest Henry D Pellegrini Matteo Mockler Todd C Freitag Michael Strauss Steven H Dynamic DNA cytosine methylation in the <it>Populus trichocarpa </it>genome: tissue-level variation and relationship to gene expression BMC Genomics Epigenetics epigenomics DNA methylation 5-methylcytosine <it>Populus</it> |
| title | Dynamic DNA cytosine methylation in the <it>Populus trichocarpa </it>genome: tissue-level variation and relationship to gene expression |
| title_full | Dynamic DNA cytosine methylation in the <it>Populus trichocarpa </it>genome: tissue-level variation and relationship to gene expression |
| title_fullStr | Dynamic DNA cytosine methylation in the <it>Populus trichocarpa </it>genome: tissue-level variation and relationship to gene expression |
| title_full_unstemmed | Dynamic DNA cytosine methylation in the <it>Populus trichocarpa </it>genome: tissue-level variation and relationship to gene expression |
| title_short | Dynamic DNA cytosine methylation in the <it>Populus trichocarpa </it>genome: tissue-level variation and relationship to gene expression |
| title_sort | dynamic dna cytosine methylation in the it populus trichocarpa it genome tissue level variation and relationship to gene expression |
| topic | Epigenetics epigenomics DNA methylation 5-methylcytosine <it>Populus</it> |
| url | http://www.biomedcentral.com/1471-2164/13/27 |
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