Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, Conecticut 06520, USA.
Plant Cell. 2009 Dec;21(12):3732-48. doi: 10.1105/tpc.109.066845. Epub 2009 Dec 11.
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.
虽然现在已经有几种组蛋白标记物的图谱可用于拟南芥和水稻，但这些图谱是静态的，无法提供关于植物表观基因组对发育或环境线索的动态变化的信息。在这里，我们分析了光对四种组蛋白修饰（组蛋白 H3 上赖氨酸 9 和 27 的乙酰化和三甲基化：H3K9ac、H3K9me3、H3K27ac 和 H3K27me3）的影响。我们对 H3K9ac 和 H3K27ac 的全基因组分析表明，这些修饰是非转座元件基因特异性的。相比之下，我们发现 H3K9me3 和 H3K27me3 靶向非转座元件基因，但也靶向基因间区和转座元件。特定的光照条件不仅影响修饰区域的数量，还影响特定修饰的存在与转录之间的整体相关性强度。此外，我们观察到，乙酰化标记不仅在去黄化时影响 ELONGATED HYPOCOTYL5 和 HY5-HOMOLOG，还影响它们的下游靶标。我们发现，光合作用基因的激活与光响应中动态乙酰化变化相关，而 H3K27ac 和 H3K27me3 可能有助于光调控赤霉素代谢。因此，这项工作提供了组蛋白修饰在植物不断变化的光照环境中变化的动态图景，并加强了这样一种概念，即组蛋白修饰代表了参与光形态建成的光调控基因的额外控制层。
