利用 RNA-seq 和 ATAC-seq 鉴定和表征猕猴桃中与 m6A 修饰相关的基因

IF 5.7 1区 农林科学 Q1 HORTICULTURE Horticultural Plant Journal Pub Date : 2024-03-05 DOI:10.1016/j.hpj.2024.02.001
Xiaoli Hu, Tong Li, Changbin Xu, Yanna Xu, Congjun You, Xinyi Li, Jinli Gong, Xiaolong Li, Xuepeng Sun
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引用次数: 0

摘要

N-甲基腺苷(mA)RNA修饰是一种调节真核生物中RNA命运的保守机制。尽管其意义重大,但目前还缺乏对猕猴桃等非模式植物中 mA 相关基因的全面分析。在此,我们根据同源性和系统发育推断在猕猴桃基因组中鉴定了 36 个 mA 相关基因。我们对mA修饰的书写器、橡皮擦和阅读器家族进行了生物信息学和进化分析。对从各种生物和非生物胁迫下的样本中收集的公开 RNA-seq 数据进行的再分析表明,大多数 mA 相关基因在不同条件下都有显著表达。通过构建基因共表达网络,我们发现在猕猴桃的发育和成熟过程中,多个 mA 相关基因与转录因子(TFs)以及受体类基因之间存在显著的相关性。此外,我们还对不同的猕猴桃组织进行了 ATAC-seq 分析,以研究 mA 相关基因的调控机制。我们发现了 10 个共同的开放染色质区域,它们至少存在于两个组织中,这些区域可能是 MADS 蛋白、C2H2 蛋白和其他预测的 TFs 的潜在结合位点。我们的研究全面揭示了猕猴桃中 mA 相关成分的基因家族,这将为探索猕猴桃发育和适应过程中的转录后调控机制奠定基础。
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Identification and characterization of genes related to m6A modification in kiwifruit using RNA-seq and ATAC-seq
N-methyladenosine (mA) RNA modification is a conserved mechanism that regulates the fate of RNA across eukaryotic organisms. Despite its significance, a comprehensive analysis of mA-related genes in non-model plants, such as kiwifruit, is lacking. Here, we identified 36 mA-related genes in the kiwifruit genome according to homology and phylogenetic inference. We performed bioinformatics and evolutionary analyses of the writer, eraser, and reader families of mA modification. Reanalysis of public RNA-seq data collected from samples under various biotic and abiotic stresses indicated that most mA-related genes were remarkably expressed under different conditions. Through construction of gene co-expression networks, we found significant correlations between several mA-related genes and transcription factors (TFs) as well as receptor-like genes during the development and ripening of kiwifruit. Furthermore, we performed ATAC-seq assays on diverse kiwifruit tissues to investigate the regulatory mechanisms of mA-related genes. We identified 10 common open chromatin regions that were present in at least two tissues, and these regions might serve as potential binding sites for MADS protein, C2H2 protein, and other predicted TFs. Our study offers comprehensive insights into the gene family of mA-related components in kiwifruit, which will lay foundation for exploring mechanisms of post-transcriptional regulation involved in development and adaptation of kiwifruit.
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来源期刊
Horticultural Plant Journal
Horticultural Plant Journal Environmental Science-Ecology
CiteScore
9.60
自引率
14.00%
发文量
293
审稿时长
33 weeks
期刊介绍: Horticultural Plant Journal (HPJ) is an OPEN ACCESS international journal. HPJ publishes research related to all horticultural plants, including fruits, vegetables, ornamental plants, tea plants, and medicinal plants, etc. The journal covers all aspects of horticultural crop sciences, including germplasm resources, genetics and breeding, tillage and cultivation, physiology and biochemistry, ecology, genomics, biotechnology, plant protection, postharvest processing, etc. Article types include Original research papers, Reviews, and Short communications.
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