Directing RNA-modifying machineries towards endogenous RNAs: opportunities and challenges.

Over 170 chemical modifications naturally occur on RNA and alter diverse aspects of RNA life. Recently developed tools based on the RNA-modifying machinery have enabled the exogenous introduction of RNA modifications into cells. RNA recorders are tools that utilize RNA-binding proteins (RBPs) to guide the RNA-modifying machinery to target sites with the aim of recording the RNA–RBP interactome or RNA modification maps. RNA modulators are tools that redirect the RNA-modifying machinery towards endogenous RNAs to edit RNA bases, thus correcting genetic disease-associated mutations. RNA sensors direct the RNA-modifying machinery together with a reporter to an RNA molecule of interest to enable cell type- and tissue-specific RNA sensing. Engineering both the RNA-binding and -modifying modules of the RNA-modifying machinery is necessary to reach sufficient on-target activity while minimizing off-target activity. Over 170 chemical modifications can be naturally installed on RNA, all of which are catalyzed by dedicated machineries. These modifications can alter RNA sequence structure, stability, and translation as well as serving as quality control marks that record aspects of RNA processing. The diverse roles played by RNAs within cells has motivated endeavors to exogenously introduce RNA modifications at target sites for diverse purposes ranging from recording RNA:protein interactions to therapeutic applications. Here, we discuss these applications and the approaches that have been employed to engineer RNA-modifying machineries, and highlight persisting challenges and perspectives. Over 170 chemical modifications can be naturally installed on RNA, all of which are catalyzed by dedicated machineries. These modifications can alter RNA sequence structure, stability, and translation as well as serving as quality control marks that record aspects of RNA processing. The diverse roles played by RNAs within cells has motivated endeavors to exogenously introduce RNA modifications at target sites for diverse purposes ranging from recording RNA:protein interactions to therapeutic applications. Here, we discuss these applications and the approaches that have been employed to engineer RNA modification machineries, and highlight persisting challenges and perspectives. [ABSTRACT FROM AUTHOR]