Figure 4

Biological processes enriched among the SDG8 direct targets and functional validation. (A) A network view of enriched biological processes among the 728 direct targets of SDG8 (bound by SDG8 and hypomethylated in sdg8-5). To generate this graph, gene regulatory network was first generated for the 728 SDG8 direct targets using Gene Network tool in VirtualPlant [50] with the Arabidopsis multinetwork interaction database. The regulatory edges were required to have one transcription factor binding site and gene expression correlation >0.7 calculated from the transcriptome in this study. The resulting gene network was then analyzed to generate the enriched biological process network shown in (A) (see Materials and methods). (B) Chlorophyll content in sdg8-5 is significantly lower than that in WT, supporting the ‘photosynthesis’ pathway being regulated by SDG8. The error bars represent standard error of the mean.