RNA abasic sites and the mechanisms involved in their regulation are mostly unknown; in contrast, DNA abasic sites are well-studied. We found surprisingly that, in yeast and human cells, RNA abasic sites are prevalent. When a base is lost from RNA, the remaining ribose is found as a closed-ring or an open-ring sugar with a reactive C1′ aldehyde group. Using primary amine-based reagents that react with the aldehyde group, we uncovered evidence for abasic sites in nascent RNA, messenger RNA, and ribosomal RNA from yeast and human cells. Mass spectroscopic analysis confirmed the presence of RNA abasic sites. The RNA abasic sites were found to be coupled to R-loops. We show that human methylpurine DNA glycosylase cleaves N-glycosidic bonds on RNA and that human apurinic/apyrimidinic endonuclease 1 incises RNA abasic sites in RNA–DNA hybrids. Our results reveal that, in yeast and human cells, there are RNA abasic sites, and we identify a glycosylase that generates these sites and an AP endonuclease that processes them.

RNA 脱碱基位点及其调控机制大多是未知的；相比之下，DNA 脱碱基位点得到了很好的研究。我们惊奇地发现，在酵母和人类细胞中，RNA 脱碱基位点普遍存在。当 RNA 中的一个碱基丢失时，剩余的核糖被发现为带有反应性 C1' 醛基的闭环或开环糖。使用与醛基反应的基于伯胺的试剂，我们发现了来自酵母和人类细胞的新生 RNA、信使 RNA 和核糖体 RNA 中无碱基位点的证据。质谱分析证实了 RNA 脱碱基位点的存在。发现 RNA 脱碱基位点与 R 环偶联。我们表明，人类甲基嘌呤 DNA 糖基化酶切割 RNA 上的 N-糖苷键，人类脱嘌呤/脱嘧啶核酸内切酶 1 切割 RNA-DNA 杂交体中的 RNA 脱碱基位点。