Dynamic DNA cytosine methylation in the Populus trichocarpa genome: tissue-level variation and relationship to gene expression

BMC Genomics

Research Article

Henry D Priest¹  Todd C Mockler²  Steven H Strauss³  Kelly J Vining³  Matteo Pellegrini⁴  Michael Freitag⁵  Kyle R Pomraning⁶  Larry J Wilhelm⁷ 

[1] Department of Botany and Plant Pathology, Oregon State University, 97331, Corvallis, OR, USA;Center for Genome Research and Biocomputing, Oregon State University, 97331, Corvallis, OR, USA;Department of Botany and Plant Pathology, Oregon State University, 97331, Corvallis, OR, USA;Center for Genome Research and Biocomputing, Oregon State University, 97331, Corvallis, OR, USA;The Donald Danforth Plant Science Center, 63132, St. Louis, MO, USA;Department of Forest Ecosystems and Society, Oregon State University, 97331, Corvallis, OR, USA;Department of Molecular, Cell and Developmental Biology, University of California, Los Angeles, 90024, Los Angeles, CA, USA;Dept. of Biochemistry and Biophysics, Oregon State University, 97331, Corvallis, OR, USA;Center for Genome Research and Biocomputing, Oregon State University, 97331, Corvallis, OR, USA;Molecular and Cellular Biology Program, Oregon State University, 97331, Corvallis, OR, USA;Dept. of Biochemistry and Biophysics, Oregon State University, 97331, Corvallis, OR, USA;Oregon Health Sciences University, 97002, Portland, OR, USA;

关键词: Epigenetics;    epigenomics;    DNA methylation;    5-methylcytosine;    Populus;   

DOI  :  10.1186/1471-2164-13-27

 received in 2011-09-05, accepted in 2012-01-17,  发布年份 2012

来源: Springer

【 摘 要 】

BackgroundDNA 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.ResultsWe 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 (Populus trichocarpa). 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 P. trichocarpa 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.ConclusionsWe 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.

【 授权许可】

Unknown   
© Vining et al; licensee BioMed Central Ltd. 2012. This article is published under license to BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.