title: Dynamic DNA cytosine methylation in the Populus trichocarpa genome: tissue-level variation and relationship to gene expression.
abstract: BACKGROUND
  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.
  
  
  RESULTS
  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 (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.
  
  
  CONCLUSIONS
  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.
authors.affiliation: Department of Forest Ecosystems and Society, Oregon State University, Corvallis, 97331, USA.
authors.forename: Kelly J
authors.initials: KJ
authors.lastname: Vining
authors.forename: Kyle R
authors.initials: KR
authors.lastname: Pomraning
authors.forename: Larry J
authors.initials: LJ
authors.lastname: Wilhelm
authors.forename: Henry D
authors.initials: HD
authors.lastname: Priest
authors.forename: Matteo
authors.initials: M
authors.lastname: Pellegrini
authors.forename: Todd C
authors.initials: TC
authors.lastname: Mockler
authors.forename: Michael
authors.initials: M
authors.lastname: Freitag
authors.forename: Steven H
authors.initials: SH
authors.lastname: Strauss
mesh_terms: D032461:Chromosomes, Plant / Q000235:genetics*; D003596:Cytosine / Q000378:metabolism*; D019175:DNA Methylation; D044127:Epigenesis, Genetic; D018506:Gene Expression Regulation, Plant; D032107:Populus / Q000235:genetics* / Q000378:metabolism; D011401:Promoter Regions, Genetic; D017421:Sequence Analysis
chemical_list: D003596:Cytosine