MeDIP main paper
Dynamic DNA Cytosine Methylation in the Populus trichocarpa Genome
The biological functions and variability of DNA cytosine methylation during plant life spans are poorly understood, especially in long-lived perennial plants such as trees. Our goal is to describe genome-level epigenetic variation at during development in the forest tree reference species Populus trichocarpa. We have surveyed DNA methylation in seven poplar tissue types  from different developmental stages (vegetative bud, male flower (catkin), female catkin, leaf, root, xylem, phloem) using 5-methyl-cytosine DNA immunoprecipitation followed by Illumina sequencing (MeDIP-seq) and mapping of sequencing reads to the P. trichocarpa reference genome. We validated MeDIP-seq  results using bisulfite sequencing of a number of targets representing a range of MeDIP-seq signal. In addition, we compared methylation patterns to gene expression levels using microarray data. Gross differences in DNA methylation among tissues were obvious on a chromosome scale, and likely centromeres apparent on some chromosomes. While overall patterns of methylation over genes and transposable elements were consistent with those seen in Arabidopsis, we found substantial differences among tissues in methylation of particular genes. Methylated genes had lower expression than unmethylated genes, but genes with body methylation had lower expression than genes with promoter methylation. Promoter methylation was more frequent that gene body methylation in all tissues except male catkins. Male catkins also differed from the other tissues in demethylation of particular transposable element categories, in level of methylation over gene bodies, and in expression range of body-methylated genes. This is the first comprehensive study of tissue-level DNA methylation variation in a tree species.