ATAC-seq and RNA-seq reveal the role of AGL18 in regulating fruit ripening via ethylene-auxin crosstalk in papaya
ATAC-seq and RNA-seq reveal the role of AGL18 in regulating fruit ripening via ethylene-auxin crosstalk in papaya
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DOI：
10.1016/j.postharvbio.2022.111984
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发表时间：
2022-05-26
影响因子：
7
通讯作者：
Zhu, Xiaoyang
中科院分区：
文献类型：
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作者：
Cai, Jiahui;Wu, Ziling;Zhu, Xiaoyang
木瓜(番木瓜)是产量第三大的热带水果。它是一种跃变型水果，由于生理上的迅速腐烂，极易腐烂。化合物1-甲基环丙烯(1-MCP)是一种有效的乙烯受体抑制剂，能与乙烯受体相互作用，避免其生理激活。本研究利用ATAC-SEQ技术对果实经不同1-MCP处理后的开放染色质进行检测。结果表明，可接近的开放染色质的差异峰在基因间隔区和启动子区域得到了丰富。在已鉴定的各种差异调控转录因子中，MADS和AP2/ERF-ERF占很大比例。KEGG分析表明，在1-MCP处理下，植物激素信号转导在番木瓜成熟过程中起关键作用。对ATAC-seq和RNA-seq数据进行综合分析，以建立短期和长期1-MCP处理下成熟相关基因的表达谱。包括MADS(CpAGL18)在内的多种转录因子和8个与乙烯和生长素信号通路相关的差异表达基因(DEG)与果实软化和成熟有关。有趣的是，在对照条件下，CpAGL18的表达在成熟过程中显著增加，但在长期1-MCP处理下，CpAGL18的表达强烈抑制。启动子分析预测了CpACS1和CpSAUR32中MADS的顺式作用元件。此外，通过EMSA(凝胶迁移率改变分析)、Y1H(酵母单杂交)和CHIP-qPCR(染色质免疫沉淀和定量聚合酶链式反应)检测，证实了CpAGL18与CpACS1和CpSAUR32启动子在体内外的结合。最后，双荧光素酶报告实验显示CpAGL18激活了CpACS1和CpSAUR32的启动子。这些发现表明，CpAGL18通过整合乙烯和生长素信号，在番木瓜果实软化和成熟过程中发挥关键作用。
Papaya (Carica papaya) is the third most-produced tropical fruit. It is a climacteric fruit, which is extremely perishable due to rapid physiological disintegration. The compound 1-methylcyclopropene (1-MCP) is an efficient ethylene receptor inhibitor that can interact with ethylene receptors and avoid its physiological activation. In this study, ATAC-seq was exploited to detect the accessible open chromatin of fruit after different 1-MCP treatments. The results revealed that the differential peaks of accessible open chromatin were enriched in the intergenic and promoter regions. MADS and AP2/ERF-ERF accounted for a large proportion among the various differential regulated transcription factors identified. KEGG enrichment analysis showed that plant hormone signaling is critical in papaya ripening under 1-MCP treatment. Integrated analysis of the ATAC-seq and RNA-seq data was performed to establish the expression profiles of ripening related genes under short-term and long-term 1-MCP treatments. Multiple transcriptional factors, including MADS (CpAGL18), and eight ethylene and auxin signal pathway-related differentially expressed genes (DEGs) were found associated with fruit softening and ripening. Interestingly, CpAGL18 expression significantly increased during ripening under control condition but was strongly suppressed under long-term 1-MCP treatment. The promoter analysis predicted cis-acting elements of MADS in CpACS1 and CpSAUR32. In addition, EMSA (Electrophoretic mobility shift assay), Y1H (Yeast one hybrid) and ChIP-qPCR (Chromatin immunoprecipitation and quantitative PCR) assays verified CpAGL18 binding to the promoters of CpACS1 and CpSAUR32 in vivo and in vitro. Finally, the dual-luciferase reporter assay revealed that CpAGL18 activated the promoters of CpACS1 and CpSAUR32. These findings suggest that CpAGL18 plays a key role in fruit softening and ripening in papaya by integrating ethylene and auxin signaling.