Genome-wide quantification of base-editing activity

Endogenously, DNA and RNA base-editing play key roles in adaptive and innate immunity and have been implicated in various diseases, including cancer. In addition, the prospects of using base-editing for precision genetic-engineering have attracted much interest recently. We present a computational approach to quantify systematically the global activity of base-editors, endogenous or engineered.

The most common endogenous RNA modification is Adenosine-to-inosine RNA editing, catalyzed by the ADAR enzymes. Loss of ADAR1 function in tumors promotes sensing of IFN-inducible dsRNAs, leading to enhanced tumor inflammation and heightened IFN sensitivity. Methods for quantification of ADAR activity are sought after, due to an increasing interest in the role of ADARs in cancer and auto-immune disorders, as well as attempts to harness the ADAR enzymes for RNA engineering. We present the Alu Editing Index (AEI), a robust and simple-to-use computational tool devised for quantification of ADAR activity. We map global editing across a large dataset of healthy human samples and identify putative regulators of ADAR, as well as previously unknown factors affecting the observed Alu editing levels. The AEI tool is available at https://github.com/a2iEditing/RNAEditingIndexer

These results have been accepted for publication in Nature Methods (in press).

Extension of this approach can be used to quantify off-target activity of engineered editing enzymes, a major concern for genome/RNA engineering applications. Indeed, we find that many recently-proposed state-of-the-art base-editors have an appreciable, previously unnoticed, level of off-target editing, both in DNA and RNA. The editing index tool is therefore a useful tool for developing next-generation base editors.