Developmental variation in DNA methylation in poplar (Populus trichocarpa)
© Vining et al; licensee BioMed Central Ltd. 2011
Published: 13 September 2011
Using methylated DNA immunoprecipitation followed by high-throughput sequencing (MeDIP-seq), we analyzed DNA methylation patterns in the P. trichocarpa genome in relation to four biological processes: bud dormancy and release, mature organ maintenance, in vitro organogenesis, and methylation suppression. Here, we report results from Illumina sequencing of nine sampled tissues, each representing 1 to 2 biological replicates. We sequenced 26M – 97M reads per tissue type, and validated our MeDIP-seq results using bisulfite sequencing of selected targets.
Unique MeDIP-seq reads covered ~30-60% of genome space at an average depth of 4 to 12 reads/nucleotide. Transposons and other repeat elements were enriched within the methylated fraction of the genome. The pattern of gene model methylation showed higher methylation at promoters, in the middle of coding regions, and 3’ to ends of genes, similar to that observed in other plant and animal species. Numbers of methylated genes identified varied widely by tissue type.
We have developed a customized genome browser (Gbrowse version 1.69), compatible with the most recent (v2.2) P. trichocarpa genome assembly, at which our data can be explored: http://poplar.cgrb.oregonstate.edu.
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