Dynamic Landscapes of Four Histone Modifications during Deetiolation in Arabidopsis

Abstract

Abstract Although landscapes of several histone marks are now available for Arabidopsis thaliana and Oryza sativa, such profiles remain static and do not provide information about dynamic changes of plant epigenomes in response to developmental or environmental cues. Here, we analyzed the effects of light on four histone modifications (acetylation and trimethylation of lysines 9 and 27 on histone H3: H3K9ac, H3K9me3, H3K27ac, and H3K27me3, respectively). Our genome-wide profiling of H3K9ac and H3K27ac revealed that these modifications are nontransposable element gene-specific. By contrast, we found that H3K9me3 and H3K27me3 target nontransposable element genes, but also intergenic regions and transposable elements. Specific light conditions affected the number of modified regions as well as the overall correlation strength between the presence of specific modifications and transcription. Furthermore, we observed that acetylation marks not only ELONGATED HYPOCOTYL5 and HY5-HOMOLOG upon deetiolation, but also their downstream targets. We found that the activation of photosynthetic genes correlates with dynamic acetylation changes in response to light, while H3K27ac and H3K27me3 potentially contribute to light regulation of the gibberellin metabolism. Thus, this work provides a dynamic portrait of the variations in histone modifications in response to the plant's changing light environment and strengthens the concept that histone modifications represent an additional layer of control for light-regulated genes involved in photomorphogenesis.