Institute of Bioorganic Chemistry Polish Academy of Sciences, Noskowskiego 12/14, 61-704, Poznan, Poland.
Department of Biochemistry and Biophysics and Center for RNA Biology, School of Medicine and Dentistry, University of Rochester, 601 Elmwood Avenue, Box 712, Rochester, NY, 14642, USA.
Nat Commun. 2022 Mar 11;13(1):1271. doi: 10.1038/s41467-022-28817-4.
There is increasing interest in the roles of covalently modified nucleotides in RNA. There has been, however, an inability to account for modifications in secondary structure prediction because of a lack of software and thermodynamic parameters. We report the solution for these issues for N-methyladenosine (mA), allowing secondary structure prediction for an alphabet of A, C, G, U, and mA. The RNAstructure software now works with user-defined nucleotide alphabets of any size. We also report a set of nearest neighbor parameters for helices and loops containing mA, using experiments. Interestingly, N-methylation decreases folding stability for adenosines in the middle of a helix, has little effect on folding stability for adenosines at the ends of helices, and increases folding stability for unpaired adenosines stacked on a helix. We demonstrate predictions for an N-methylation-activated protein recognition site from MALAT1 and human transcriptome-wide effects of N-methylation on the probability of adenosine being buried in a helix.
人们对共价修饰核苷酸在 RNA 中的作用越来越感兴趣。然而，由于缺乏软件和热力学参数，无法解释二级结构预测中的修饰。我们报告了针对 N-甲基腺苷 (mA) 的这些问题的解决方案，允许对包含 A、C、G、U 和 mA 的字母表进行二级结构预测。RNAstructure 软件现在可以与任何大小的用户定义核苷酸字母表一起使用。我们还报告了一组使用实验确定的包含 mA 的螺旋和环的最近邻参数。有趣的是，N-甲基化会降低螺旋中间腺苷的折叠稳定性，对螺旋末端腺苷的折叠稳定性影响很小，并且会增加螺旋上未配对腺苷的堆积折叠稳定性。我们展示了来自 MALAT1 的 N-甲基化激活蛋白识别位点的预测，以及人类转录组中 N-甲基化对腺苷被埋藏在螺旋中的概率的影响。
