Systematic Analysis of Differential H3K27me3 and H3K4me3 Deposition in Callus and Seedling Reveals the Epigenetic Regulatory Mechanisms Involved in Callus Formation in Rice
Systematic Analysis of Differential H3K27me3 and H3K4me3 Deposition in Callus and Seedling Reveals the Epigenetic Regulatory Mechanisms Involved in Callus Formation in Rice
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愈伤组织和幼苗中 H3K27me3 和 H3K4me3 差异沉积的系统分析揭示了水稻愈伤组织形成中涉及的表观遗传调控机制
DOI：
10.3389/fgene.2020.00766
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发表时间：
2020-07
影响因子：
3.7
通讯作者：
Su Zhen
中科院分区：
文献类型：
--
作者：
Zhao Nannan;Zhang Kang;Wang Chunchao;Yan Hengyu;Liu Yue;Xu Wenying;Su Zhen
植物的生长和发育是通过分生组织细胞活动进行的，细胞命运的转变伴随着表观遗传修饰。具有细胞多能性的愈伤组织表现出持续细胞分裂的能力，是研究植物分生组织分化的理想材料。通过比较愈伤组织和幼苗的表观遗传修饰差异，可以揭示染色质状态的变化以及各种表观遗传修饰对植物生长发育的影响，并可以确定与植物生长发育相关的关键基因，为植物生长发育调控提供新的见解。在这项研究中，我们使用各种抗体在水稻种子诱导的愈伤组织和生长约15天的幼苗中进行ChIP测定，以检查H3 K27 me 3和H3 K4 me 3的差异沉积。此外，从国家生物技术信息中心下载了相应组织中DNase I超敏感位点的数据。我们分析了4，562个愈伤组织H3 K27 me 3减少的基因，特别是愈伤组织中编码转录因子的基因，发现大多数转录因子，包括AP 2-ERREBP、NAC和HB基因家族，与生长发育相关。与分生作用相关的基因如OsWOX 9、OsWOX 11、OsPLT 4、OsPLT 5和OsSHR也包括在内。相反，H3 K4 me 3正调控愈伤组织的特性，通过其较高的沉积在愈伤组织比在幼苗。我们进一步对45组Affyssin基因芯片阵列进行了转录组学分析，并确定了1，565个在愈伤组织中优先表达的基因。水稻愈伤组织的发育和根的发育具有共同的调控机制。我们发现，这些基因，这是与分生组织，需要去除H3 K27 me 3和沉积H3 K4 me 3，和DNA酶I-超敏感位点，以保持一个相对活跃的状态在愈伤组织比在幼苗。本研究为愈伤组织形成的表观遗传机制提供了新的数据，并为植物细胞分裂和分化的研究提供了新的资源。
Plant growth and development occurs through meristematic cell activity, and cell fate transition is accompanied by epigenetic modifications. Callus with cell pluripotency exhibits the ability to undergo continued cell division, and is ideal for studying plant meristematic differentiation. By comparing the differential epigenetic modifications between callus and seedling, the changes in chromatin state and effects of various epigenetic modifications on the growth and development of plants can be revealed, and the key genes related to plant growth and development can be identified, providing novel insights into the regulation of plant growth and development. In this study, we performed ChIP assays using various antibodies in rice seed-induced callus and seedlings grown for about 15 days to examine the differential deposition of H3K27me3 and H3K4me3. Furthermore, data for DNase I-hypersensitive sites in the corresponding tissues were downloaded from National Center for Biotechnology Information. We analyzed 4,562 callus H3K27me3-decreased genes especially those encoding transcription factors in callus, and found that most of the transcription factors, including AP2-ERREBP, NAC, and HB gene families, were related to growth and development. Genes related to meristemization, such as OsWOX9, OsWOX11, OsPLT4, OsPLT5, and OsSHR, were also included. In contrast, H3K4me3 positively regulated callus characteristics through its higher deposition in the callus than in the seedling. We further performed transcriptomic analysis on 45 sets of Affymetrix GeneChip arrays and identified 1,565 genes preferentially expressed in the callus. Callus development and root development in rice were found to share a common regulatory mechanism. We found that these genes, which are associated with meristems, require the removal of H3K27me3 and the deposition of H3K4me3, and DNase I-hypersensitive sites to maintain a relatively active state in the callus than in the seedling. The present study provides novel data about the epigenetic mechanisms involved in callus formation and additional resources for the study of cell division and differentiation in plants.
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影响因子：
46.9
作者：
Trapnell C;Williams BA;Pertea G;Mortazavi A;Kwan G;van Baren MJ;Salzberg SL;Wold BJ;Pachter L
通讯作者：
Pachter L
OSRAP2.6转录因子通过与激活的激酶-C 1（RACK1）的受体相互作用来促进水稻先天免疫。
DOI：
10.1186/1939-8433-5-35
发表时间：
2012-12-11
期刊：
Rice (New York, N.Y.)
影响因子：
--
作者：
Wamaitha MJ;Yamamoto R;Wong HL;Kawasaki T;Kawano Y;Shimamoto K
通讯作者：
Shimamoto K
影响因子：
48
作者：
Langmead, Ben;Salzberg, Steven L.
通讯作者：
Salzberg, Steven L.
影响因子：
11.6
作者：
Zhao, Yu;Hu, Yongfeng;Zhou, Dao-Xiu
通讯作者：
Zhou, Dao-Xiu
agriGO v2.0：农业社区的 GO 分析工具包，2017 年更新
影响因子：
14.9
作者：
Tian T;Liu Y;Yan H;You Q;Yi X;Du Z;Xu W;Su Z
通讯作者：
Su Z