The Interplay of DNA Methylation, Histone Modification and Gene Activity in Soybean Seed Development

In seed development, the correlations between epigenetic mechanisms and gene activity are still largely unknown. We used soybean (Glycine max) seed embryo to study the effects of DNA methylation and histone modification on gene activity during seed development. We used BS-Seq (Bisulfite Sequencing) to study genome-wide DNA methylation patterns at single-base resolution and ChIP-Seq (Chromatin Immunoprecipitation Sequencing) to study genomic regions associated with active and repressive histone modification markers, H3K4m3 and H3K27m3, respectively. Genes in seed development were categorized into four groups: genes associated with (1) H3K4m3 marker, (2) H3K27m3 marker, (3) both H3K4m3 and H3K27m3 markers, and (4) no H3K4m3 and no H3K27m3 markers. We explored the interrelationship of gene activity, DNA methylation in CG-, CHG- and CHH-context, and histone modificaitons during seed development.