Department of Physics, Zhejiang University of Science and Technology, Hangzhou, Zhejiang 310008, China.
Institute of Bioinformatics and Medical Engineering, Jiangsu University of Technology, Changzhou, Jiangsu 213001, China.
Int J Biol Macromol. 2022 Nov 30;221:1345-1355. doi: 10.1016/j.ijbiomac.2022.09.115. Epub 2022 Sep 15.
The pausing event in RNA molecule folding that occurs during the cotranscription process plays a critical role in cellular RNA function. Based on Conformational Resampling through Kinetic Relaxation (CRKR), this paper investigates a method to reveal the specifics of pausing for RNA cotranscriptional folding of 117-nucleotide E. coli SRP RNA and 73-nucleotide HIV-1 TAR RNA. It can be inferred from the results that pausing events generate valid cotranscriptional conformational rearrangement to protect the function structures and influence the folding pathway, which is remarkably consistent with the experimental results. Additionally, different transcription speeds result in different levels of protection capability. The folding pathway or conformational rearrangement can also be affected by a change in transcription speed after pausing site. These findings illuminate that RNAs with functional structures undergo complex rearrangement folding in pausing events, and different RNAs prefer different speeds for specific folding pathways. Moreover, pausing in particular circumstances can be employed to regulate the population of final functional structures. In conclusion, this paper offers fresh perspectives on the pausing event in the cotranscriptional folding of RNAs.
RNA 分子折叠过程中的暂停事件在细胞 RNA 功能中起着关键作用。基于构象重采样通过动力学松弛（CRKR），本文研究了一种揭示 117 核苷酸大肠杆菌 SRP RNA 和 73 核苷酸 HIV-1 TAR RNA 共转录折叠中暂停的方法。结果表明，暂停事件产生有效的共转录构象重排，以保护功能结构并影响折叠途径，这与实验结果非常一致。此外，不同的转录速度导致不同水平的保护能力。折叠途径或构象重排也可能受到暂停后转录速度变化的影响。这些发现表明，具有功能结构的 RNA 在暂停事件中经历复杂的重排折叠，不同的 RNA 为特定的折叠途径偏好不同的速度。此外，在特定情况下暂停可以用来调节最终功能结构的种群。总之，本文为 RNA 共转录折叠中的暂停事件提供了新的视角。
