植物体内RNA二级结构探测方法的研究进展

Research Progress in the Approaches to in vivo RNA Secondary Structure Profiling in Plants

生物体内的RNA因氢键等作用配对折叠形成复杂的二级结构及三级结构,并根据环境产生动态变化,由此行使功能。植物中的基因表达调控及配体感应都与RNA的结构相关,RNA结构也被认为是转录后调控的一项影响因素,RNA的结构对与之互作的蛋白的结构和功能产生影响,因此研究RNA功能过程中解析RNA结构尤为关键。目前,RNA二级结构的探测实验方法从X-射线经过酶切及化学探针标记,发展至结合高通量测序即可建构模型。此外,机器学习等方法也为RNA结构的探测提供了新的思路。本文综述了影响体内RNA结构的因素及近年来用于植物体内RNA结构预测的方法,讨论了现有方法的应用限制下对RNA二级结构预测新方法开发的意义及存在的问题,展望计算机预测方法与实验方法未来的发展趋势,旨为后续RNA结构相关研究提供方法参考。

RNAs fold into complex secondary and tertiary structures via hydrogen bond pairing to enable their diverse functions in cells after dynamic changes according to environment.RNA structure is considered to be related to the regulation of gene expression and ligand sensing in plants,and is also considered to be an important factor in post-transcriptional regulation.Structured RNA can also affect the dimensional structure of RNA binding proteins and their functions.Thus,the analysis of RNA structure is particularly critical in the study of RNA function.At present,various detection methods for RNA secondary structure(RSS)has been developed from X-ray to enzyme digestion and chemical probe labeling,which can be combined with high-throughput sequencing to construct models.In addition,machine learning and other methods also provide new ideas for the detection of RNA structure.In this review,we summarize the factors affecting the RNA structure in vivo and recent reported methods for probing RNA structure in vivo,discuss the significances of developing novel prediction methods for RSS under the limitations of current methods as well as the issues,and prospect the future development trend of computer prediction methods and experimental methods,aiming to provide a methodological reference for subsequent research on RNA structure.