Dynamic Histone Modifications in Light-Regulated Gene Expression

Chromatin can be modified via DNA methylation and/or histone marks, and these chemical modifications can affect transcription levels. However, evidence is mounting that specific modifications act not as simple positive or negative regulators, but rather in complex combinations whose effects depend upon context (reviewed in Berger, 2007). New work from Charron et al. (pages nnn) examines dynamic changes in histone modification at the genome level to ask whether it could play a role in light-regulated gene expression. Seedlings undergo photomorphogenesis upon exposure to light, and the authors postulate that the concomitant change in the transcriptome (reviewed in Jiao et al., 2007) is a good candidate for involving chromatin regulation of global transcription patterns. Charron et al. compared Arabidopsis thaliana seedlings that had been grown entirely in the dark (etiolated) to those that had been exposed to the light for 6 h (deetiolated). In agreement with previous reports, they found that 15% of the genes that were expressed in seedlings were either induced or repressed by exposure to light. They then mapped global patterns of four histone marks by immunoprecipitating regions of the genome associated with those modifications and hybridizing the resulting DNA to microarrays. This analysis showed that all four modifications were enriched in regions of the genome where genes are found. In addition, there were differences between etiolated and deetiolated plants in modification levels, providing evidence that histone modification could play a role in regulating the large-scale changes in gene expression seen in these plants. Charron et al. found that although there was a fair amount of overlap between the two growth conditions in the specific genes that were targeted by each modification, there were also many genes that were targeted differentially. These data point to the complexity of the histone modification code; the same modifications appear to be light regulated on some genes and not on others. The authors then examined their expression data for correlations with histone modification. In this analysis too, there were differences between etiolated and deetiolated plants. Intriguingly, light exposure changed the degree to which a specific acetylation mark was correlated with gene expression, suggesting that in the two treatments there are different factors reading the histone modification code. The authors went on to examine modifications in genes encoding two transcription factors involved in photomorphogenesis. Both had high levels of a particular acetylatation mark in the light but not in the dark (see figure). Furthermore, the same mark also affected putative downstream targets of at least one of these transcription factors. This ability to mark multiple levels of a transcription cascade is consistent with chromatin modification playing a role in changing global gene expression patterns. Overall, Charron et al. provide a dynamic view of histone modification patterns throughout the genome. Although the field is at the early stages of understanding these patterns, these data emphasize the complexity of the system as well as its potential to regulate gene expression at the genome level.