Fujian Provincial Key Laboratory of Plant Functional Biology, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, China.
Basic Forestry and Proteomics Research Center, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Fujian Agriculture and Forestry University, Fuzhou, China.
J Exp Bot. 2022 Aug 11;73(14):4696-4715. doi: 10.1093/jxb/erac155.
Flag leaf senescence is an important biological process that drives the remobilization of nutrients to the growing organs of rice. Leaf senescence is controlled by genetic information via gene expression and histone modification, but the precise mechanism is as yet unclear. Here, we analysed genome-wide acetylated lysine residue 9 of histone H3 (H3K9ac) enrichment by chromatin immunoprecipitation-sequencing (ChIP-seq), and examined its association with transcriptomes by RNA-seq during flag leaf aging in rice (Oryza sativa). We found that genome-wide H3K9 acetylation levels increased with age-dependent senescence in rice flag leaf, and there was a positive correlation between the density and breadth of H3K9ac with gene expression and transcript elongation. During flag leaf aging, we observed 1249 up-regulated differentially expressed genes (DEGs) and 996 down-regulated DEGs, showing a strong relationship between temporal changes in gene expression and gain/loss of H3K9ac. We produced a landscape of H3K9 acetylation-modified gene expression targets that include known senescence-associated genes, metabolism-related genes, as well as miRNA biosynthesis-related genes. Our findings reveal a complex regulatory network of metabolism- and senescence-related pathways mediated by H3K9ac, and elucidate patterns of H3K9ac-mediated regulation of gene expression during flag leaf aging in rice.
旗叶衰老是一个重要的生物学过程，它驱动着营养物质向水稻生长器官的再转移。叶片衰老受基因表达和组蛋白修饰等遗传信息控制，但确切的机制尚不清楚。在这里，我们通过染色质免疫沉淀测序（ChIP-seq）分析了全基因组乙酰化赖氨酸残基 9 的组蛋白 H3（H3K9ac）富集，并通过 RNA-seq 研究了其在水稻旗叶衰老过程中的转录组的相关性。我们发现，全基因组 H3K9 乙酰化水平随水稻旗叶的年龄相关性衰老而增加，H3K9ac 的密度和广度与基因表达和转录延伸呈正相关。在旗叶衰老过程中，我们观察到 1249 个上调的差异表达基因（DEGs）和 996 个下调的 DEGs，表明基因表达的时间变化与 H3K9ac 的获得/丧失之间存在很强的关系。我们生成了一个 H3K9 乙酰化修饰基因表达靶标的图谱，其中包括已知的与衰老相关的基因、代谢相关基因以及 miRNA 生物合成相关基因。我们的研究结果揭示了一个由 H3K9ac 介导的代谢和衰老相关途径的复杂调控网络，并阐明了 H3K9ac 介导的基因表达调控在水稻旗叶衰老过程中的模式。
