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BackgroundHistone methylation modifies the epigenetic state of target genes to regulate gene expression in the context of developmental and environmental changes. Previously, we used a positive genetic screen to identify an Arabidopsis mutant, cli186, which was impaired in carbon and light signaling. Here, we report a deletion of the Arabidopsis histone methyltransferase SDG8 in this mutant (renamed sdg8-5), which provides a unique opportunity to study the global function of a specific histone methyltransferase within a multicellular organism.ResultsTo assess the specific role of SDG8, we examine how the global histone methylation patterns and transcriptome were altered in the sdg8-5 deletion mutant compared to wild type, within the context of transient light and carbon treatments. Our results reveal that the sdg8 deletion is associated with a significant reduction of H3K36me3, preferentially towards the 3′ end of the gene body, accompanied by a reduction in gene expression. We uncover 728 direct targets of SDG8 that have altered methylation in the sdg8-5 mutant and are also bound by SDG8. As a group, this set of SDG8 targets is enriched in specific biological processes including defense, photosynthesis, nutrient metabolism and energy metabolism. Importantly, 64% of these SDG8 targets are responsive to light and/or carbon signals.ConclusionsThe histone methyltransferase SDG8 functions to regulate the H3K36 methylation of histones associated with gene bodies in Arabidopsis. The H3K36me3 mark in turn is associated with high-level expression of a specific set of light and/or carbon responsive genes involved in photosynthesis, metabolism and energy production.Electronic supplementary materialThe online version of this article (doi:10.1186/s13059-015-0640-2) contains supplementary material, which is available to authorized users.

BackgroundNitrogen and light are two major regulators of plant metabolism and development. While genes involved in the control of each of these signals have begun to be identified, regulators that integrate gene responses to nitrogen and light signals have yet to be determined. Here, we evaluate the role of bZIP1, a transcription factor involved in light and nitrogen sensing, by exposing wild-type (WT) and bZIP1 T-DNA null mutant plants to a combinatorial space of nitrogen (N) and light (L) treatment conditions and performing transcriptome analysis. We use ANOVA analysis combined with clustering and Boolean modeling, to evaluate the role of bZIP1 in mediating L and N signaling genome-wide.ResultsThis transcriptome analysis demonstrates that a mutation in the bZIP1 gene can alter the L and/or N-regulation of several gene clusters. More surprisingly, the bZIP1 mutation can also trigger N and/or L regulation of genes that are not normally controlled by these signals in WT plants. This analysis also reveals that bZIP1 can, to a large extent, invert gene regulation (e.g., several genes induced by N in WT plants are repressed by N in the bZIP1 mutant).ConclusionThese findings demonstrate that the bZIP1 mutation triggers a genome-wide de-regulation in response to L and/or N signals that range from i) a reduction of the L signal effect, to ii) unlocking gene regulation in response to L and N combinations. This systems biology approach demonstrates that bZIP1 tunes L and N signaling relationships genome-wide, and can suppress regulatory mechanisms hypothesized to be needed at different developmental stages and/or environmental conditions.