Editors' ChoicePlant biology

Lighting Up the Epigenome

Sci. Signal.  22 Dec 2009:
Vol. 2, Issue 102, pp. ec405
DOI: 10.1126/scisignal.2102ec405

One of the most important environmental signals for plants is light. Studies of individual genes have shown that light influences gene expression by regulating the activity of light-dependent transcription factors as well as by triggering chromatin remodeling at specific genes. Charron et al. performed a genome-scale analysis of the changes in four histone posttranslational modifications (acetylation and trimethylation of lysines 9 and 27 of histone 3, H3K9ac, H3K27ac, H3K9me3, and H3K27me3) in Arabidopsis seedlings grown in the dark (D seedlings) and seedlings grown in the dark and then transferred to the light for 6 hours (D to L seedlings). They found that D seedlings had more regions containing H3K9me3 and H3K27ac, whereas D to L seedlings had more regions with H3K9ac and H3K27me3. There was a positive correlation between gene expression and the abundance of H3K9ac and H3K27ac modifications, consistent with acetylation promoting active gene transcription, and there was a negative correlation between gene expression and the abundance of H3K27me3 modifications. HY5 and HYH are two light-regulated transcription factors that are important for photomorphogenesis. Charron et al. found that in D to L seedlings there was a substantial increase in H3K9ac in the transcribed (HY5) or promoter (HYH) regions of these genes compared with the genes in the D seedlings. Unexpectedly, this same modification also occurred on a large fraction of the HY5 target genes, and its abundance at these targets was greater in the D to L seedlings than in the D seedlings. Not only do plants exhibit developmental and morphogenic changes in response to light, they also exhibit changes in metabolism. Genes encoding components of photosynthetic pathways were generally acetylated, but not methylated, in either the light or the dark condition, yet most of these genes were stimulated in the D to L seedlings. Thus, the authors suggest that acetylation may be a prerequisite to light-stimulated transcription of these genes. Analysis of several specific metabolic genes showed that H3K9ac increased in some genes in the D to L seedlings. Gibberellin is a plant hormone that is also regulated by light, and Charron et al. found that histone modifications differed depending on where the gene product acted within the cell. Cytoplasmic components of the gibberellin synthesis pathway tended to be encoded by genes modified by H3K27me3 in the dark, and those encoding products active in the plastid or endomembranes tended to show increased H3K27ac in the light. This study reveals that global epigenetic regulation of plant gene expression contributes to photomorphogenesis and light-stimulated changes in metabolism.

J.-B. F. Charron, H. He, A. A. Elling, X. W. Deng, Dynamic landscapes of four histone modifications during deetoliation in Arabidopsis. Plant Cell preview, published 11 December 2009 as 10.1105/tpc.109.066845. [Online Journal]