拟南芥花发育早期转录组和蛋白质组表达的年代学研究。

IF 5.6 2区 生物学 Q1 PLANT SCIENCES Journal of Experimental Botany Pub Date : 2025-01-08 DOI:10.1093/jxb/eraf005
Raquel Álvarez-Urdiola, José Tomás Matus, Víctor Manuel González-Miguel, Martí Bernardo-Faura, José Luis Riechmann
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引用次数: 0

摘要

通过转录组分析,人们对拟南芥早期花发育的复杂基因调控格局进行了广泛的研究,通过对关键转录因子的全基因组结合分析,人们获得了控制花器官发育的基因网络。相比之下,蛋白质组在花发育过程中的动态特性却鲜为人知。在这项研究中,我们描述了花早期发育不同阶段的花蛋白质组,并将其与无偏倚的转录表达数据进行了关联。利用基于apetala1的花诱导系统进行了Shotgun蛋白质组学和转录本分析。开发了一个特定的分析管道来处理时间过程蛋白质组学数据。总共鉴定出8,924个蛋白和23,069个转录本。共表达分析显示rna -蛋白对聚集在不同的表达模式模块中。我们观察到RNA和蛋白质水平变化之间的总体正相关,但也发现了RNA/蛋白质对中与反相关基因表达变化的亚群,并发现它们在激素应答通路中富集。此外,本文报道的RNA-seq数据集进一步扩展了对在花早期发育过程中表达变化的基因的鉴定,并且将其与先前发表的AP1 ChIP-seq数据集相结合,可以鉴定更多的AP1直接和高可信度靶点。
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Chronology of transcriptome and proteome expression during early Arabidopsis flower development.

The complex gene regulatory landscape underlying early flower development in Arabidopsis has been extensively studied through transcriptome profiling, and gene networks controlling floral organ development have been derived from the analyses of genome wide binding of key transcription factors. In contrast, the dynamic nature of the proteome during the flower development process is much less understood. In this study, we characterized the floral proteome at different stages during early flower development and correlated it with unbiased transcript expression data. Shotgun proteomics and transcript profiling were conducted using an APETALA1-based floral induction system. A specific analysis pipeline to process the time-course proteomics data was developed. In total, 8,924 proteins and 23,069 transcripts were identified. Co-expression analysis revealed that RNA-protein pairs clustered in various expression pattern modules. An overall positive correlation between RNA and protein level changes was observed, but subgroups of RNA/protein pairs with anticorrelated gene expression changes were also identified and found to be enriched in hormone responsive pathways. In addition, the RNA-seq dataset reported here further expanded the identification of genes whose expression changes during early flower development, and its combination with previously published AP1 ChIP-seq datasets allowed the identification of additional AP1 direct and high-confidence targets.

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来源期刊
Journal of Experimental Botany
Journal of Experimental Botany 生物-植物科学
CiteScore
12.30
自引率
4.30%
发文量
450
审稿时长
1.9 months
期刊介绍: The Journal of Experimental Botany publishes high-quality primary research and review papers in the plant sciences. These papers cover a range of disciplines from molecular and cellular physiology and biochemistry through whole plant physiology to community physiology. Full-length primary papers should contribute to our understanding of how plants develop and function, and should provide new insights into biological processes. The journal will not publish purely descriptive papers or papers that report a well-known process in a species in which the process has not been identified previously. Articles should be concise and generally limited to 10 printed pages.
期刊最新文献
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