Genome-wide H3K9 acetylation level increases with age-dependent senescence of flag leaf in rice
Genome-wide H3K9 acetylation level increases with age-dependent senescence of flag leaf in rice
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DOI：
10.1093/jxb/erac155
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发表时间：
2022-06-08
影响因子：
6.9
通讯作者：
Miao, Ying
中科院分区：
文献类型：
--
作者：
Zhang, Yu;Li, Yanyun;Miao, Ying
旗叶衰老是一个重要的生物过程，可驱动水稻生长器官重新调动养分。叶片衰老是通过基因表达和组蛋白修饰由遗传信息控制的，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) 分析了组蛋白 H3 (H3K9ac) 富集的全基因组乙酰化赖氨酸残基 9，并通过 RNA-seq 检查了其在水稻 (Oryza sativa) 旗叶衰老过程中与转录组的关联。我们发现，水稻旗叶中全基因组 H3K9 乙酰化水平随着年龄依赖性衰老而增加，并且 H3K9ac 的密度和宽度与基因表达和转录物延伸呈正相关。在旗叶衰老过程中，我们观察到 1249 个上调的差异表达基因 (DEG) 和 996 个下调的 DEG，显示基因表达的时间变化与 H3K9ac 的获得/损失之间存在密切关系。我们制作了一系列 H3K9 乙酰化修饰的基因表达靶标，其中包括已知的衰老相关基因、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 H3K9ac 介导的代谢和衰老相关途径的复杂调控网络，并阐明了水稻旗叶衰老过程中 H3K9ac 介导的基因表达调控模式。全基因组 H3K9 乙酰化水平随着水稻旗叶年龄依赖性衰老而增加，H3K9ac 的密度和宽度与转录物伸长和表达呈正相关 涉及复杂的代谢介导的衰老网络的许多基因。
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.Genome-wide H3K9 acetylation level increases with age-dependent senescence in rice flag leaf, and the density and breadth of H3K9ac positively correlate with transcript elongation and expression of many genes involved in a complex metabolism-mediated senescence network.