The RNA degradome: a precious resource for deciphering RNA processing and regulation codes in plants
The RNA degradome: a precious resource for deciphering RNA processing and regulation codes in plants
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DOI：
10.1080/15476286.2020.1757898
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发表时间：
2020-04
期刊：
影响因子：
4.1
通讯作者：
Xiaoxia Ma;Xiaopu Yin;Zhonghai Tang;Hidetaka Ito;C. Shao;Y. Meng;Tian Xie
中科院分区：
文献类型：
--
作者：
Xiaoxia Ma;Xiaopu Yin;Zhonghai Tang;Hidetaka Ito;C. Shao;Y. Meng;Tian Xie
摘要植物RNA降解组是由RNA周转、成熟和质量监测等生物化学途径降解的RNA片段的集合体。近年来，降解组测序（degradome-seq）文库成为研究RNA加工和调控的丰富宝库。在这里，我们简要概述了degradome-seq数据在植物RNA生物学中的应用，特别是在非编码RNA加工和小RNA引导的靶切割方面。同时也介绍了它在RNA研究领域的一些新应用，如核糖核酸内切酶切割位点的体内定位、去帽RNA片段5 ′端保守基序的鉴定以及转录本蛋白质结合区域的寻找等。更重要的是，我们提出了一个模型，生物学家推断的基础上degradome-seq数据的转录和/或转录后调控基因差异表达的贡献。最后，我们希望基于降解组的分析方法能够广泛应用于真核生物RNA生物学的研究。
ABSTRACT The plant RNA degradome was defined as an aggregate of the RNA fragments degraded from various biochemical pathways, such as RNA turnover, maturation and quality surveillance. In recent years, the degradome sequencing (degradome-seq) libraries became a rich storehouse for researchers to study on RNA processing and regulation. Here, we provided a brief overview of the uses of degradome-seq data in plant RNA biology, especially on non-coding RNA processing and small RNA-guided target cleavages. Some novel applications in RNA research area, such as in vivo mapping of the endoribonucleolytic cleavage sites, identification of conserved motifs at the 5ʹ ends of the uncapped RNA fragments, and searching for the protein-binding regions on the transcripts, were also mentioned. More importantly, we proposed a model for the biologists to deduce the contributions of transcriptional and/or post-transcriptional regulation to gene differential expression based on degradome-seq data. Finally, we hope that the degradome-based analytical methods could be widely applied for the studies on RNA biology in eukaryotes.