RNA abasic sites in yeast and human cells

Author:

Liu Yaojuan,Rodriguez Yesenia,Ross Robert L.,Zhao Ruoxia,Watts Jason A.,Grunseich Christopher,Bruzel Alan,Li Dongjun,Burdick Joshua T.,Prasad RajendraORCID,Crouch Robert J.ORCID,Limbach Patrick A.,Wilson Samuel H.,Cheung Vivian G.ORCID

Abstract

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.

Funder

Howard Hughes Medical Institute

HHS | National Institutes of Health

DOD | Defense Threat Reduction Agency

Publisher

Proceedings of the National Academy of Sciences

Subject

Multidisciplinary

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