Baerenfaller Katja, Shu Huan, Hirsch-Hoffmann Matthias, Fütterer Johannes, Opitz Lennart, Rehrauer Hubert, Hennig Lars, Gruissem Wilhelm
Department of Biology, ETH Zurich, Zurich, 8092, Switzerland.
Program of Molecular Medicine, University of Massachusetts Medical School, Worcester, MA, USA.
Plant Cell Environ. 2016 Nov;39(11):2557-2569. doi: 10.1111/pce.12811. Epub 2016 Sep 30.
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.
翻译后染色质修饰是光信号传导和生物钟功能中的一种重要调控机制。昼夜转录水平变化的调控需要根据当前环境条件对一般活跃基因的表达进行微调。我们使用染色质免疫沉淀测序（ChIP-Seq）研究了组蛋白修饰H3K4me3、H3K9ac、H3K9me2、H3S10p、H3K27ac、H3K27me3和H3S28p与拟南芥完全展开叶片6在短日最佳和水分亏缺条件下生长时转录表达的昼夜变化之间的关联。我们在昼末和夜末之间鉴定出了一种差异H3K9ac、H3K27ac和H3S28p特征，其与昼夜转录水平的变化相关。具有这种特征的基因具有特别富集的启动子元件，并编码在转录因子、生物钟和淀粉分解代谢过程中显著富集的蛋白质。额外的激活修饰在水分充足（H3S10p）和水分亏缺（H3K4me3）的植物中普遍存在。数据表明了一种昼夜转录水平调控机制，其中抑制性转录因子结合的减少促进了激活H3K9ac、H3K27ac和H3S28p染色质修饰。仅在一天中需要表达的时间点基因上存在激活染色质修饰模式，可以解释为什么一些基因在昼夜周期中差异可诱导。
