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Background  Histone 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.    Results  To 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.    Conclusions  The 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 material  The online version of this article (doi:10.1186/s13059-015-0640-2) contains supplementary material, which is available to authorized users.

The histone methyltransferase SDG8 mediates the epigenetic modification of light and carbon responsive genes in plants