The cell line A-to-I RNA editing catalogue

• Published in: Nucleic acids research 2020-06, Vol.48 (11), p.5849-5858
• Main Authors: Schaffer, Amos A, Kopel, Eli, Hendel, Ayal, Picardi, Ernesto, Levanon, Erez Y, Eisenberg, Eli
• Format: Article
• Language: English
• Subjects: Data Resources and Analyses
• ISSN: 0305-1048; 1362-4962
• DOI: 10.1093/nar/gkaa305

Abstract Adenosine-to-inosine (A-to-I) RNA editing is a common post transcriptional modification. It has a critical role in protecting against false activation of innate immunity by endogenous double stranded RNAs and has been associated with various regulatory processes and diseases such as autoimmune and cardiovascular diseases as well as cancer. In addition, the endogenous A-to-I editing machinery has been recently harnessed for RNA engineering. The study of RNA editing in humans relies heavily on the usage of cell lines as an important and commonly-used research tool. In particular, manipulations of the editing enzymes and their targets are often developed using cell line platforms. However, RNA editing in cell lines behaves very differently than in normal and diseased tissues, and most cell lines exhibit low editing levels, requiring over-expression of the enzymes. Here, we explore the A-to-I RNA editing landscape across over 1000 human cell lines types and show that for almost every editing target of interest a suitable cell line that mimics normal tissue condition may be found. We provide CLAIRE, a searchable catalogue of RNA editing levels across cell lines available at http://srv00.recas.ba.infn.it/atlas/claire.html, to facilitate rational choice of appropriate cell lines for future work on A-to-I RNA editing.