Chromatin State-Based Analysis of Epigenetic H3K4me3 Marks of Arabidopsis in Response to Dark Stress
Chromatin State-Based Analysis of Epigenetic H3K4me3 Marks of Arabidopsis in Response to Dark Stress
复制标题
基于染色质状态的拟南芥响应暗胁迫的表观遗传 H3K4me3 标记分析
DOI：
10.3389/fgene.2019.00306
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发表时间：
2019-04
影响因子：
3.7
通讯作者：
Su Zhen
中科院分区：
文献类型：
--
作者：
Yan Hengyu;Liu Yue;Zhang Kang;Song James;Xu Wenying;Su Zhen
光对于植物的生长和发育至关重要。长时间的黑暗会导致基因表达发生巨大变化，导致叶片衰老、下胚轴生长、叶柄伸长、叶面积减少和提前开花等。然而，表观遗传水平上对黑暗反应的潜在机制仍然很大程度上未知。在本研究中，我们进行了 ChIP-seq，以在拟南芥中在 3 天的持续黑暗和正常光照条件下生成 H3K4me3 的全局表观基因组图谱。我们应用染色质状态分析和自组织作图（SOM）来研究暗应激下表观遗传调控的组合。 SOM图谱根据多种不同的表观基因组数据集对基因组上的片段进行聚类，打破了表观遗传标记在基因组上分散分布的限制。通过SOM分析，我们还发现H3K4me3的信号主要在黑暗后增强。对H3K4me3改变的基因和差异表达基因的分析表明，显示黑暗增加的H3K4me3的基因主要参与衰老和自噬，并且黑暗诱导的衰老和自然衰老之间存在串扰。总之，我们利用染色质状态和 SOM 分析研究了拟南芥表观遗传 H3K4me3 标记响应暗胁迫的调控。我们的研究揭示了表观基因组响应暗应激的调控机制，并且我们研究中使用的基于染色质状态的SOM分析也将有助于其他多种表观遗传标记动态变化的研究。
Light is essential to plant growth and development. Extended darkness causes dramatic gene expression changes, leading to leaf senescence, hypocotyl growth, petiole elongation, reduced leaf area, and early flowering, etc. However, the underlying mechanism of response to darkness at epigenetic levels remains largely unknown. In this study, we conducted ChIP-seq to generate global epigenomic profiles of H3K4me3 under 3-day extended darkness and normal light conditions in Arabidopsis. We applied chromatin state analysis together with self-organization mapping (SOM) to study the combination of epigenetic regulation under dark stress. The SOM map clusters the segments on the genome according to multiple diverse epigenomic datasets, which breaks the limit of dispersed distribution of epigenetic marks on the genome. Through SOM analysis, we also found that the signals of H3K4me3 were mainly increased after darkness. Analysis of H3K4me3-changed genes together with differentially expressed genes indicated that the genes showing dark-increased H3K4me3 were most involved in senescence and autophagy, and cross-talk existed between dark-induced and natural senescence. In summary, we studied the regulation of the epigenetic H3K4me3 marks of Arabidopsis in response to dark stress using chromatin state and SOM analyses. Our study revealed the regulatory mechanisms of the epigenome in response to dark stress, and SOM analysis based on chromatin states used in our study will also be helpful for other studies on dynamic changes of multiple epigenetic marks.
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影响因子：
7.4
作者：
Casal, JJ
通讯作者：
Casal, JJ
影响因子：
3
作者：
Wendl MC
通讯作者：
Wendl MC
DOI：
10.1111/pce.13357
发表时间：
2018-10
期刊：
Plant, cell & environment
影响因子：
--
作者：
Proietti S;Caarls L;Coolen S;Van Pelt JA;Van Wees SCM;Pieterse CMJ
通讯作者：
Pieterse CMJ
影响因子：
11.4
作者：
Roudier, Francois;Ahmed, Ikhlak;Berard, Caroline;Sarazin, Alexis;Mary-Huard, Tristan;Cortijo, Sandra;Bouyer, Daniel;Caillieux, Erwann;Duvernois-Berthet, Evelyne;Al-Shikhley, Liza;Giraut, Laurene;Despres, Barbara;Drevensek, Stephanie;Barneche, Fredy;Derozier, Sandra;Brunaud, Veronique;Aubourg, Sebastien;Schnittger, Arp;Bowler, Chris;Martin-Magniette, Marie-Laure;Robin, Stephane;Caboche, Michel;Colot, Vincent
通讯作者：
Colot, Vincent
影响因子：
48
作者：
Langmead, Ben;Salzberg, Steven L.
通讯作者：
Salzberg, Steven L.