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Dynamic landscape and regulation of RNA editing in mammals
Tan, Meng How Li, Qin Shanmugam, Raghuvaran Piskol, Robert Kohler, Jennefer Young, Amy N. Liu, Kaiwen Ivy Zhang, Rui Ramaswami, Gokul Ariyoshi, Kentaro
Tan, Meng How
Li, Qin
Shanmugam, Raghuvaran
Piskol, Robert
Kohler, Jennefer
Young, Amy N.
Liu, Kaiwen Ivy
Zhang, Rui
Ramaswami, Gokul
Ariyoshi, Kentaro
Author
Tan, Meng How
Li, Qin
Shanmugam, Raghuvaran
Piskol, Robert
Kohler, Jennefer
Young, Amy N.
Liu, Kaiwen Ivy
Zhang, Rui
Ramaswami, Gokul
Ariyoshi, Kentaro
Gupte, Ankita
Keegan, Liam P.
George, Cyril X.
Ramu, Avinash
Huang, Ni
Pollina, Elizabeth A.
Leeman, Dena S.
Rustighi, Alessandra
Sharon Goh, Y. P.
GTEx Consortium,
Chawla, Ajay
Del Sal, Giannino
Peltz, Gary
Brunet, Anne
Conrad, Donald F.
Samuel, Charles E.
O'Connell, Mary A.
Walkley, Carl R.
Nishikura, Kazuko
GTEx Consortium
Li, Qin
Shanmugam, Raghuvaran
Piskol, Robert
Kohler, Jennefer
Young, Amy N.
Liu, Kaiwen Ivy
Zhang, Rui
Ramaswami, Gokul
Ariyoshi, Kentaro
Gupte, Ankita
Keegan, Liam P.
George, Cyril X.
Ramu, Avinash
Huang, Ni
Pollina, Elizabeth A.
Leeman, Dena S.
Rustighi, Alessandra
Sharon Goh, Y. P.
GTEx Consortium,
Chawla, Ajay
Del Sal, Giannino
Peltz, Gary
Brunet, Anne
Conrad, Donald F.
Samuel, Charles E.
O'Connell, Mary A.
Walkley, Carl R.
Nishikura, Kazuko
GTEx Consortium
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.
Keywords
Date
2017
Type
Journal article
Journal
Nature
Book
Volume
550
Issue
Page Range
249-254
Article Number
ACU Department
Mary MacKillop Institute for Health Research
Faculty of Health Sciences
Faculty of Health Sciences
Collections
Relation URI
Source URL
Event URL
Open Access Status
License
File Access
Controlled