长链非编码RNA稳定性相关RNA结构元件与RNA降解关系研究

The present studies show that long noncoding RNAs (lncRNAs) are associated with many biological processes. However, there is few studies on lncRNA degradation, one pivotal step in cell metabolism. In comparison with mRNAs, long noncoding RNAs (lncRNAs) not only have a significant difference in structure and function, but also have special features in stability and degradation mechanism. Therefore, it is an emergent problem to elucidate how cell accurately detect those lncRNAs to be degraded. To this end, here we hypothesize that there exists a class of dynamic RNA secondary structure elements, i.e., the labels to guild RNA degradation. These labels are recognized by particular proteins in the cell, which will initiate lncRNA degradation by RNase. This kind of lncRNA degradation system, composed of RNA secondary structure elements-binding proteins-RNase, is very similar to protein degradation system, consisted of ubiquitin-Ubiquitin ligase-proteasome. To confirm the hypothesis, here we intend to apply newly developed high-throughput sequencing methods such as CLIP and CLASH, biomass spectrometry, and bioinformatics to obtain and validate RNA secondary structure elements and binding proteins associated with lncRNA degradation, and to comprehensively explore the relationship between lncRNA degradation and RNA secondary structure elements, binding proteins and RNase in the cells. Finally, through systematically elucidating the complex mechanism of lncRNA degradation, and the characteristics of degradation for different classes of lncRNAs, we hope a new breakthrough will be realized in lncRNA degradation study.

长链非编码RNA不仅与mRNA在结构和功能上存在显著差异，在稳定性和降解机制上也具有特殊性。阐明细胞是如何实现对降解lncRNA精确识别是该领域重要科学问题。我们提出假说：在lncRNA分子中存在一类动态RNA二级结构“元件”—指导RNA降解“标签”。该标签被细胞中特定蛋白分子识别，进而启动RNase对lncRNA降解。“RNA二级结构元件—结合蛋白分子—RNase” 构成的指导的lncRNA降解系统，相当于“泛素—泛素连接酶—蛋白酶体”构成的蛋白质降解系统。为证实该假说，本研究利用分析RNA结构的高通量测序、生物质谱和生物信息学方法获取并验证lncRNA降解相关的RNA二级结构“元件”及其结合蛋白分子，探讨lncRNA降解与RNA二级结构“元件”、结合蛋白因子和核酸酶在细胞内的关联关系，阐明lncRNA降解的复杂机制，发现不同类型lncRNA降解调控规律，实现lncRNA代谢研究新突破。

长链非编码RNA不仅与mRNA在结构和功能上存在显著差异，在稳定性和降解机制上也具有特殊性。阐明细胞是如何实现对降解lncRNA精确识别是该领域重要科学问题。本研究获得全面的人肺癌细胞(A549)lncRNA半衰期数据集，研究分析了影响lncRNA和mRNA稳定性的因素，包括表达水平、GC含量、转录本长度、外显子个数、转录本的核质分布、RNA结合蛋白质、miRNA的结合、二级结构元件和kmer组成等，分别计算了各因素与lncRNA稳定性的相关性，并利用深度学习综合分析多个影响因素与RNA稳定性之间的关系。研究发现RNA二级结构元件和多种序列特征对单外显子lncRNA和多外显子mRNA的稳定性具有影响。基于kmer组成分析，发现多种kmer影响单外显子lncRNA和多外显子mRNA的稳定性，细胞核和细胞质的不同分布对lncRNA和mRNA的稳定性影响不同。针对mRNA同样进行了多种因素的研究，发现密码子、cDNA、CDS、5’(3’)UTR 不同区域的RNA二级结构元件影响mRNA稳定性。同时开展了RNA相关的RNA酶和蛋白质分子的功能研究。本研究对lncRNA的稳定性进行了较为系统的多因素分析，揭示了不同因素在影响lncRNA稳定性上的作用，为全面阐明影响lncRNA稳定性的分子机制奠定了基础。