Genomic analysis of ADAR1 binding and its involvement in multiple RNA processing pathways.

Jae Hoon Bahn,Jaegyoon Ahn,Xianzhi Lin,Xinshu Xiao,Qing Zhang,Mete Civelek,Jae-Hyung Lee

doi:10.1038/ncomms7355

Jae Hoon Bahn, Jaegyoon Ahn + Show 5 more

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https://doi.org/10.1038/ncomms7355

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Abstract

Adenosine deaminases acting on RNA (ADARs) are the primary factors underlying adenosine to inosine (A-to-I) editing in metazoans. Here we report the first global study of ADAR1-RNA interaction in human cells using CLIP-Seq. A large number of CLIP sites are observed in Alu repeats, consistent with ADAR1's function in RNA editing. Surprisingly, thousands of other CLIP sites are located in non-Alu regions, revealing functional and biophysical targets of ADAR1 in the regulation of alternative 3' UTR usage and miRNA biogenesis. We observe that binding of ADAR1 to 3' UTRs precludes binding by other factors, causing 3' UTR lengthening. Similarly, ADAR1 interacts with DROSHA and DGCR8 in the nucleus and possibly out-competes DGCR8 in primary miRNA binding, which enhances mature miRNA expression. These functions are dependent on ADAR1's editing activity, at least for a subset of targets. Our study unfolds a broad landscape of the functional roles of ADAR1.

Highlights

Adenosine deaminases acting on RNA (ADARs) are the primary factors underlying adenosine to inosine (A-to-I) editing in metazoans
While ADAR1 binding to Alu regions enables the discovery of new insights regarding A-to-I editing, its binding to non-Alu sites reveals a number of functional roles related to regulation of alternative 30 untranslated region (UTR) usage and primary miRNA processing in the nucleus
ADAR1 is expressed at a medium to high level, while ADAR2 and ADAR3 are barely expressed[21]

Summary

Introduction

Adenosine deaminases acting on RNA (ADARs) are the primary factors underlying adenosine to inosine (A-to-I) editing in metazoans. ADAR1 interacts with DROSHA and DGCR8 in the nucleus and possibly outcompetes DGCR8 in primary miRNA binding, which enhances mature miRNA expression These functions are dependent on ADAR1’s editing activity, at least for a subset of targets. A significant knowledge gap in our understanding of ADAR1 function is its genome-wide binding profile To this end, we carried out the first global study of ADAR1 binding in human cells using the crosslinking immunoprecipitation (CLIP) method followed by high-throughput sequencing (CLIP-seq). While ADAR1 binding to Alu regions enables the discovery of new insights regarding A-to-I editing, its binding to non-Alu sites reveals a number of functional roles related to regulation of alternative 30 untranslated region (UTR) usage and primary miRNA processing in the nucleus. Our study expands the landscape of the functional roles of ADAR1 that contributes to a better understanding of this essential protein

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