Diurnal changes in the histone H3 signature H3K9ac|H3K27ac|H3S28p are associated with diurnal gene expression in Arabidopsis
Diurnal changes in the histone H3 signature H3K9ac|H3K27ac|H3S28p are associated with diurnal gene expression in Arabidopsis
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DOI：
10.1111/pce.12811
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发表时间：
2016-11-01
影响因子：
7.3
通讯作者：
Gruissem, Wilhelm
中科院分区：
文献类型：
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作者：
Baerenfaller, Katja;Shu, Huan;Gruissem, Wilhelm
翻译后染色质修饰是光信号传导和生物钟功能的重要调节机制。昼夜转录水平变化的调节需要根据当时的环境条件对通常活跃的基因的表达进行微调。我们在短日照最佳和缺水条件下生长的拟南芥完全展开的第 6 片叶子中，使用染色质免疫沉淀和测序 (ChIP-Seq)，研究了组蛋白修饰 H3K4me3、H3K9ac、H3K9me2、H3S10p、H3K27ac、H3K27me3 和 H3S28p 与转录物表达的昼夜变化之间的关联。我们发现了一天结束时和晚上结束时的 H3K9ac、H3K27ac 和 H3S28p 特征差异，该特征与昼夜转录水平的变化相关。具有这种特征的基因具有特定的过度表达的启动子元件，并编码显着富集转录因子、生物钟和淀粉分解代谢过程的蛋白质。在最佳浇水（H3S10p）和缺水（H3K4me3）植物中普遍存在额外的激活修饰。这些数据表明了一种昼夜转录水平调节机制，其中抑制转录因子的结合减少有助于激活 H3K9ac、H3K27ac 和 H3S28p 染色质修饰。仅在一天中需要表达时，基因上存在激活染色质修饰模式，这可以解释为什么某些基因在昼夜周期中可被差异诱导。调节昼夜转录水平变化需要对一般活跃基因的表达进行微调。我们发现了在一天结束和晚上结束时激活 H3K9ac、H3K27ac 和 H3S28p 组蛋白修饰的特征的变化，这些变化与昼夜转录水平波动相关。具有这种特征的基因具有特定的过度表达的启动子元件，并且它们富含转录因子、生物钟和淀粉分解代谢过程。这表明了涉及 H3K9ac|H3K27ac|H3S28p 特征的昼夜转录水平调节机制，并解释了为什么某些基因在昼夜周期中具有差异诱导性。
Post-translational chromatin modifications are an important regulatory mechanism in light signalling and circadian clock function. The regulation of diurnal transcript level changes requires fine-tuning of the expression of generally active genes depending on the prevailing environmental conditions. We investigated the association of histone modifications H3K4me3, H3K9ac, H3K9me2, H3S10p, H3K27ac, H3K27me3 and H3S28p with diurnal changes in transcript expression using chromatin immunoprecipitations followed by sequencing (ChIP-Seq) in fully expanded leaves 6 of Arabidopsis thaliana grown in short-day optimal and water-deficit conditions. We identified a differential H3K9ac, H3K27ac and H3S28p signature between end-of-day and end-of-night that is correlated with changes in diurnal transcript levels. Genes with this signature have particular over-represented promoter elements and encode proteins that are significantly enriched for transcription factors, circadian clock and starch catabolic process. Additional activating modifications were prevalent in optimally watered (H3S10p) and in water-deficit (H3K4me3) plants. The data suggest a mechanism for diurnal transcript level regulation in which reduced binding of repressive transcription factors facilitates activating H3K9ac, H3K27ac and H3S28p chromatin modifications. The presence of activating chromatin modification patterns on genes only at times of the day when their expression is required can explain why some genes are differentially inducible during the diurnal cycle.Regulation of diurnal transcript level changes requires fine-tuning of the expression of generally active genes. We identified changes in a signature of activating H3K9ac, H3K27ac and H3S28p histone modifications between the end-of-day and end-of-night that correlate with diurnal transcript level fluctuations. Genes with this signature have particular over-represented promoter elements, and they are enriched for transcription factors, circadian clock and starch catabolic process. This suggests a mechanism for diurnal transcript level regulation involving the H3K9ac|H3K27ac|H3S28p signature and explains why some genes are differentially inducible during the diurnal cycle.