Methylome of DNase I sensitive chromatin in Populus trichocarpa shoot apical meristematic cells: a simplified approach revealing characteristics of gene‐body DNA methylation in open chromatin state

Abstract

SummaryDNA methylation is involved in the control of plant development and adaptation to the environment through modifications of chromatin compaction and gene expression. In poplar (Populus trichocarpa), a perennial plant, variations in DNA methylation have been reported between genotypes and tissues or in response to drought. Nevertheless, the relationships between gene-body DNA methylation, gene expression and chromatin compaction still need clarification.Here, DNA methylation was mapped in the noncondensed chromatin fraction from P. trichocarpa shoot apical meristematic cells, the center of plant morphogenesis, where DNA methylation variations could influence the developmental trajectory. DNase I was used to isolate the noncondensed chromatin fraction. Methylated sequences were immunoprecipitated, sequenced using Illumina/Solexa technology and mapped on the v2.0 poplar genome. Bisulfite sequencing of candidate sequences was used to confirm mapping data and to assess cytosine contexts and methylation levels.While the methylated DNase I hypersensitive site fraction covered 1.9% of the poplar genome, it contained sequences corresponding to 74% of poplar gene models, mostly exons. The level and cytosine context of gene-body DNA methylation varied with the structural characteristics of the genes.Taken together, our data show that DNA methylation is widespread and variable among genes in open chromatin of meristematic cells, in agreement with a role in their developmental trajectory.

Epigenetic Variability in the Genetically Uniform Forest Tree Species Pinus pinea L

“…Although the number of studies about epigenetic variation associated with biotic and abiotic stresses in plants is increasing, few studies are focused on forest tree species, with perhaps the exception of poplar [10], [11], [30], [31]. Trees, and especially conifers, are key models for the study of stress adaptation due to their longevity and long-life cycles [9], [32].…”

Forest tree genomics: 10 achievements from the past 10 years and future prospects

“…Indeed, determination of the poplar methylome revealed features particular to this tree, such as a higher CHG methylation level than reported for other plants (Feng et al 2010) and low levels of methylation at DNA recombination hotspots (Slavov et al 2012). Furthermore, gene-body DNA methylation is extensive in the open chromatin state, linked to structural gene characteristics (gene size and copy number) and correlated with tissue-specific gene expression Lafon-Placette et al 2013;Vining et al 2013). DNA methylation is also involved in regulating stress response genes (Liang et al 2014;Maury and Lafon-Placette, unpublished data).…”

Application of Genomic Technologies to the Breeding of Trees

“…Recently, genome wide studies of methylated DNA immunoprecipitation followed by high-throughput sequencing (MeDIP-seq) were used to characterize the DNA methylome of Populus trichocarpa during in vitro culture and plant transformation methods, in micropropagated explants, calli, and regenerated plants (Vining et al, 2013). MeDIP-seq was also employed to find tissue-specific features in Populus (Vining et al, 2012; Lafon-Placette et al, 2013) and developmentally regulated regions in leaves of Eucalyptus globulus (Hasbún et al, 2016). On the other hand, numerous chromatin modifications involving histone acetylation, methylation, phosphorylation, and ubiquitination among others can be assayed by genome wide sequencing of immunoprecipitated chromatin (ChIP-seq).…”