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Dynamic landscape and regulation of RNA editing in mammals

Author(s): Tan, Meng H; Li, Qin; Shanmugam, Raghuvaran; Piskol, Robert; Kohler, Jennefer; et al

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Abstract: 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 molecules1. Although many editing sites have recently been discovered2,3,4,5,6,7, the extent to which most sites are edited and how the editing is regulated in different biological contexts are not fully understood8,9,10. 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.
Publication Date: 2017
Citation: Tan, Meng How, Qin Li, Raghuvaran Shanmugam, Robert Piskol, Jennefer Kohler, Amy N. Young, Kaiwen Ivy Liu, Rui Zhang, Gokul Ramaswami, Kentaro Ariyoshi, Ankita Gupte, Liam P. Keegan, Cyril X. George, Avinash Ramu, Ni Huang, Elizabeth A. Pollina, Dena S. Leeman, Alessandra Rustighi, Y. P. Sharon Goh, GTEx Consortium, Ajay Chawla, Giannino Del Sal, Gary Peltz, Anne Brunet, Donald F. Conrad, Charles E. Samuel, Mary A. O’Connell, Carl R. Walkley, Kazuko Nishikura, and Jin Billy Li. "Dynamic landscape and regulation of RNA editing in mammals." Nature 550, no. 7675 (2017): 249-254. doi:10.1038/nature24041
DOI: 10.1038/nature24041
ISSN: 0028-0836
EISSN: 1476-4687
Pages: 249 - 254
Type of Material: Journal Article
Journal/Proceeding Title: Nature
Version: Author's manuscript



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