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

• DOI: 10.1186/s13059-015-0640-2
• Publication Date: 2015-04-13T12:59:09Z
• Authors: Ying Li; Indrani Mukherjee; Karen E Thum; Milos Tanurdzic; Manpreet S Katari; Mariana Obertello; Molly B Edwards; W Richard McCombie; Robert A Martienssen; Gloria M Coruzzi
• Keywords: 0301 basic medicine; Evolution; Arabidopsis; Genes, Plant; 1105 Ecology; Epigenesis, Genetic; 1307 Cell Biology; Arabidopsis-thaliana; 03 medical and health sciences; Behavior and Systematics; 1311 Genetics; Gene Expression Regulation, Plant; https://purl.org/becyt/ford/1.6; Genome-wide; https://purl.org/becyt/ford/1; 580; 2. Zero hunger; Arabidopsis Proteins; Research; Gene Expression Profiling; Chromosome Mapping; Reproducibility of Results; Functional genomics; Histone-Lysine N-Methyltransferase; DNA Methylation; Carbon; HISTONE METHYLTRANSFERASE; Multigene Family; 8. Economic growth; Transcription factor; Gene Deletion

Abstract 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.