Coordination of nuclear and plastid transcription for chloroplast biogenesis requires H4 acetylation by the NuA4 complex

Chloroplast biogenesis represents a crucial step in seedling development, and is essential for the transition to autotrophic growth in plants. This light-controlled process relies on the transcription of nuclear and plastid genomes that drives the effective assembly and regulation of the photosynthetic machinery. Here we reveal a novel regulation level for this process by showing the involvement of chromatin remodelling in the coordination of nuclear and plastid gene expression for proper chloroplast biogenesis and function. The two Arabidopsis homologs of the yeast EPL1 proteins, core components of the NuA4 histone acetyl-transferase complex, are essential for the correct assembly and performance of chloroplasts. EPL1 proteins are necessary for the coordinated expression of nuclear genes encoding most of the components of chloroplast transcriptional machinery, specifically promoting H4K5Ac deposition in these loci. These data unveil a key participation of epigenetic regulatory mechanisms in the coordinated expression of the nuclear and plastid genomes. Overall design: Transcriptomic profiling through RNAseq of Arabidopsis plants grown on 1/2x Murashige & Skoog medium supplemented with 1% sucrose under long day photoperiod (16h light / 8h dark). Plants were grown at 22°C for 14 days, taking samples at Zeitgeber time (ZT) ZT8. Three libraries were generated using RNA from three independent experiments.

叶绿体生物发生（Chloroplast biogenesis）是幼苗发育过程中的关键环节，对植物完成向自养生长（autotrophic growth）的转变不可或缺。这一受光调控的过程依赖于细胞核与质体基因组的转录，以驱动光合装置的有效组装与功能调控。本研究揭示了该过程的全新调控层级：研究证实染色质重塑（chromatin remodelling）参与协调细胞核与质体基因的表达，进而保障叶绿体的正常生物发生与功能行使。酵母NuA4组蛋白乙酰转移酶复合物（NuA4 histone acetyl-transferase complex）的核心组分EPL1蛋白（EPL1 proteins）的两个拟南芥（Arabidopsis）同源蛋白，对于叶绿体的正确组装与功能发挥至关重要。EPL1蛋白可促进编码叶绿体大部分转录装置组分的核基因的协同表达，并特异性地在这些基因位点介导组蛋白H4赖氨酸5乙酰化（H4K5Ac）修饰。上述数据揭示了表观遗传调控机制（epigenetic regulatory mechanisms）在细胞核与质体基因组的协同表达中发挥关键作用。

实验整体设计：将拟南芥植株种植于添加1%蔗糖的1/2浓度Murashige & Skoog培养基（1/2x Murashige & Skoog medium）上，于长日照光周期（16小时光照/8小时黑暗）、22℃条件下培养14天，在节律时间（Zeitgeber time，ZT）ZT8时采集样本。采用三次独立实验提取的RNA构建了三个测序文库，通过RNA测序（RNAseq）完成转录组分析。