Wang Likai, Zhang Fan, Rode Siddharth, Chin Kevin K, Ko Eun Esther, Kim Jonghwan, Iyer Vishwanath R, Qiao Hong
Institute for Cellular and Molecular Biology, The University of Texas at Austin, Austin, 78712, Texas, USA.
The Center for Systems and Synthetic Biology, The University of Texas at Austin, Austin, 78712, Texas, USA.
BMC Genomics. 2017 Jul 17;18(1):538. doi: 10.1186/s12864-017-3929-6.
Histone acetylation and deacetylation are essential for gene regulation and have been implicated in the regulation of plant hormone responses. Many studies have indicated the role of histone acetylation in ethylene signaling; however, few studies have investigated how ethylene signaling regulates the genomic landscape of chromatin states. Recently, we found that ethylene can specifically elevate histone H3K14 acetylation and the non-canonical histone H3K23 acetylation in etiolated seedlings and the gene activation is positively associated with the elevation of H3K14Ac and H3K23Ac in response to ethylene. To assess the role of H3K9, H3K14, and H3K23 histone modifications in the ethylene response, we examined how ethylene regulates histone acetylation and the transcriptome at global level and in ethylene regulated genes both in wild type (Col-0) and ein2-5 seedlings.
Our results revealed that H3K9Ac, H3K14Ac, and H3K23Ac are preferentially enriched around the transcription start sites and are positively correlated with gene expression levels in Col-0 and ein2-5 seedlings both with and without ethylene treatment. In the absence of ethylene, no combinatorial effect of H3K9Ac, H3K14Ac, and H3K23Ac on gene expression was detected. In the presence of ethylene, however, combined enrichment of the three histone acetylation marks was associated with high gene expression levels, and this ethylene-induced change was EIN2 dependent. In addition, we found that ethylene-regulated genes are expressed at medium or high levels, and a group of ethylene regulated genes are marked by either one of H3K9Ac, H3K14Ac or H3K23Ac. In this group of genes, the levels of H3K9Ac were altered by ethylene, but in the absence of ethylene the levels of H3K9Ac and peak breadths are distinguished in up- and down- regulated genes. In the presence of ethylene, the changes in the peak breadths and levels of H3K14Ac and H3K23Ac are required for the alteration of gene expressions.
Our study reveals that the plant hormone ethylene induces combinatorial effects of H3K9Ac, K14Ac and K23Ac histone acetylation in gene expression genome widely. Further, for a group of ethylene regulated genes, in the absence of ethylene the levels and the covered breadths of H3K9Ac are the preexist markers for distinguishing up- and down- regulated genes, the change in the peak breadths and levels of H3K14Ac and H3K23Ac are required for the alteration of gene expression in the presence of ethylene.
组蛋白乙酰化和去乙酰化对于基因调控至关重要，并参与植物激素反应的调节。许多研究表明组蛋白乙酰化在乙烯信号传导中的作用；然而，很少有研究调查乙烯信号如何调节染色质状态的基因组格局。最近，我们发现乙烯可以特异性地提高黄化幼苗中组蛋白H3K14乙酰化和非经典组蛋白H3K23乙酰化水平，并且基因激活与响应乙烯时H3K14Ac和H3K23Ac的升高呈正相关。为了评估H3K9、H3K14和H3K23组蛋白修饰在乙烯反应中的作用，我们研究了乙烯如何在整体水平以及野生型（Col-0）和ein2-5幼苗中乙烯调控基因中调节组蛋白乙酰化和转录组。
我们的结果表明，无论有无乙烯处理，H3K9Ac、H3K14Ac和H3K23Ac在Col-0和ein2-5幼苗的转录起始位点周围优先富集，并且与基因表达水平呈正相关。在没有乙烯的情况下，未检测到H3K9Ac、H3K14Ac和H3K23Ac对基因表达的组合效应。然而，在有乙烯的情况下，三种组蛋白乙酰化标记的联合富集与高基因表达水平相关，并且这种乙烯诱导的变化是EIN2依赖性的。此外，我们发现乙烯调控的基因以中等或高水平表达，并且一组乙烯调控的基因以H3K9Ac、H3K14Ac或H3K23Ac中的一种为标记。在这组基因中，乙烯改变了H3K9Ac的水平，但在没有乙烯的情况下，上调和下调基因中H3K9Ac的水平和峰宽是有区别的。在有乙烯的情况下，基因表达的改变需要H3K14Ac和H3K23Ac的峰宽和水平的变化。
我们的研究表明，植物激素乙烯在全基因组范围内诱导基因表达中H3K9Ac、K14Ac和K23Ac组蛋白乙酰化的组合效应。此外，对于一组乙烯调控的基因，在没有乙烯的情况下，H3K9Ac的水平和覆盖宽度是区分上调和下调基因的预先存在的标记，在有乙烯的情况下，基因表达的改变需要H3K14Ac和H3K23Ac的峰宽和水平的变化。
