The pattern of DNA methylation alteration, and its association with the changes of gene expression and alternative splicing during phosphate starvation in tomato.
The pattern of DNA methylation alteration, and its association with the changes of gene expression and alternative splicing during phosphate starvation in tomato.
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番茄磷酸盐饥饿过程中 DNA 甲基化改变的模式及其与基因表达和选择性剪接变化的关系。
DOI：
10.1111/tpj.15486
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发表时间：
2021-09
期刊：
影响因子：
--
通讯作者：
Tengbo Huang
中科院分区：
文献类型：
--
作者：
Peng Tian;Zeteng Lin;Dongbo Lin;Shuangyu Dong;Jianzi Huang;Tengbo Huang
DNA甲基化的改变与植物对磷饥饿（Pi-）的反应中的基因表达改变有关，磷饥饿是一种影响植物生长和生产力的常见胁迫。然而，在园艺模式种番茄中，Pi-胁迫下DNA甲基化的动态及其与基因转录和选择性剪接（AS）变化的关系尚不清楚。在这里，我们进行了综合甲基化组和转录组分析的番茄幼苗磷缺乏和充足的条件下。我们发现Pi-引起总体甲基化水平的轻微增加，具有数百万个差异甲基化胞嘧啶（DmCs）和几百个差异甲基化区域（DMR）。我们还鉴定了数千个Pi-诱导的差异表达（DE）和差异AS（DAS）基因，发现DmCs更多地分布在非表达基因中，而不是DE或DAS基因中。此外，DNA甲基化改变与转录变化弱相关，但与DAS事件无关，与转座因子（TE）重叠的hyper-CHH-DMR在PSR基因的一个子集中富集。我们认为DNA甲基化改变可能与某些PSR基因的差异表达有关，但这些改变大多数可能控制附近TE的表达，而不是直接影响PSR基因的转录或AS。此外，Pi-后甲基化变化的模式可能在很大程度上取决于TE分布。总之，我们的研究提供了全面的见解DNA甲基化与基因转录和AS下的Pi-在番茄，并可能有助于揭示植物胁迫反应的表观遗传机制的新作用。
DNA methylation is changed and associates with gene expression alterations in plant response to phosphate starvation (Pi-), a common stress that impacts plant growth and productivity. However, in the horticultural model species tomato, the dynamics of DNA methylation and its relation with the changes of gene transcription and alternative splicing (AS) under Pi- are unknown. Here, we performed integrative methylome and transcriptome analyses of tomato seedlings under Pi deficient and sufficient conditions. We found Pi- caused a slight increase in overall methylation level, with millions of differentially methylated cytosines (DmCs) and a few hundred differentially methylated regions (DMRs). We also identified thousands of differentially expressed (DE) and differential AS (DAS) genes induced by Pi-, and found DmCs were more distributed in non-expressed genes than in DE or DAS genes. Moreover, DNA methylation alterations weakly correlated with transcription changes but not DAS events, and hyper-CHH-DMRs overlapping with transposable elements (TEs) were enriched in a subset of PSR genes. We propose that DNA methylation changes may associate with differential expression of some PSR genes, but most of these changes probably control the expression of nearby TEs, rather than directly affecting transcription or AS of PSR genes. Besides, the pattern of methylation changes upon Pi- may largely be shaped by TE distributions. Together, our study provides comprehensive insights into the association of DNA methylation with gene transcription and AS under Pi- in tomato, and may contribute to unveiling novel roles of epigenetic mechanisms in plant stress response.
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DOI：
10.1016/b978-0-12-809633-8.20106-4
发表时间：
2020-02
期刊：
--
影响因子：
--
作者：
A. Prjibelski;Anton I. Korobeynikov;Alla L. Lapidus
通讯作者：
A. Prjibelski;Anton I. Korobeynikov;Alla L. Lapidus
影响因子：
16.6
作者：
Maeda Y;Konishi M;Kiba T;Sakuraba Y;Sawaki N;Kurai T;Ueda Y;Sakakibara H;Yanagisawa S
通讯作者：
Yanagisawa S
影响因子：
6.9
作者：
Di Zhang;Moxian Chen;F. Zhu;Jianhua Zhang;Ying-Gao Liu
通讯作者：
Di Zhang;Moxian Chen;F. Zhu;Jianhua Zhang;Ying-Gao Liu
DOI：
--
发表时间：
2017
期刊：
--
影响因子：
--
作者：
S. Nishida;Yusuke Kakei;Y. Shimada;T. Fujiwara
通讯作者：
S. Nishida;Yusuke Kakei;Y. Shimada;T. Fujiwara
影响因子：
11.6
作者：
Chen, Yi-Fang;Li, Li-Qin;Wu, Wei-Hua
通讯作者：
Wu, Wei-Hua