Adenosine-to-inosine (A-to-I) RNA editing is a conserved post-transcriptional mechanism mediated by ADAR enzymes that diversifies the transcriptome by altering selected nucleotides in RNA molecules. Although many editing sites have recently been discovered, the extent to which most sites are edited and how the editing is regulated in different biological contexts are not fully understood. Here we report dynamic spatiotemporal patterns and new regulators of RNA editing, discovered through an extensive profiling of A-to-I RNA editing in 8,551 human samples (representing 53 body sites from 552 individuals) from the Genotype-Tissue Expression (GTEx) project and in hundreds of other primate and mouse samples. We show that editing levels in non-repetitive coding regions vary more between tissues than editing levels in repetitive regions. Globally, ADAR1 is the primary editor of repetitive sites and ADAR2 is the primary editor of non-repetitive coding sites, whereas the catalytically inactive ADAR3 predominantly acts as an inhibitor of editing. Cross-species analysis of RNA editing in several tissues revealed that species, rather than tissue type, is the primary determinant of editing levels, suggesting stronger cis-directed regulation of RNA editing for most sites, although the small set of conserved coding sites is under stronger trans-regulation. In addition, we curated an extensive set of ADAR1 and ADAR2 targets and showed that many editing sites display distinct tissue-specific regulation by the ADAR enzymes in vivo. Further analysis of the GTEx data revealed several potential regulators of editing, such as AIMP2, which reduces editing in muscles by enhancing the degradation of the ADAR proteins. Collectively, our work provides insights into the complex cis- and trans-regulation of A-to-I editing.

Cardiovascular Research Institute University of California San Francisco San Francisco California 94158 USA

Central European Institute of Technology Masaryk University Kamenice Brno 625 00 Czech Republic

Department of Anesthesia Stanford University School of Medicine Stanford California 94305 USA

Department of Genetics Stanford University School of Medicine Stanford California 94305 USA

Department of Genetics Washington University School of Medicine St Louis Missouri 63108 USA

Department of Life Sciences University of Trieste 34127 Trieste Italy and National Laboratory CIB Area Science Park 34149 Trieste Italy

Department of Medicine St Vincent's Hospital University of Melbourne Fitzroy Victoria 3065 Australia

Department of Molecular Cellular and Developmental Biology University of California Santa Barbara Santa Barbara California 93106 USA

Department of Pathology and Immunology Washington University School of Medicine St Louis Missouri 63108 USA

Genome Institute of Singapore Agency for Science Technology and Research Singapore 138672 Singapore

MRC Human Genetics Unit Institute of Genetics and Molecular Medicine University of Edinburgh Edinburgh EH4 2XU UK

School of Chemical and Biomedical Engineering Nanyang Technological University Singapore 637459 Singapore

St Vincent's Institute of Medical Research Fitzroy Victoria 3065 Australia

The Wistar Institute Philadelphia Pennsylvania 19104 USA

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