Genome-Wide Identification of Human RNA Editing Sites by Parallel DNA Capturing and Sequencing

Abstract

Adenosine-to-inosine (A-to-I) RNA editing leads to transcriptome diversity and is important for normal brain function. To date, only a handful of functional sites have been identified in mammals. We developed an unbiased assay to screen more than 36,000 computationally predicted nonrepetitive A-to-I sites using massively parallel target capture and DNA sequencing. A comprehensive set of several hundred human RNA editing sites was detected by comparing genomic DNA with RNAs from seven tissues of a single individual. Specificity of our profiling was supported by observations of enrichment with known features of targets of adenosine deaminases acting on RNA (ADAR) and validation by means of capillary sequencing. This efficient approach greatly expands the repertoire of RNA editing targets and can be applied to studies involving RNA editing-related human diseases.

Organ-wide profiling in mouse reveals high editing levels of Filamin B mRNA in the musculoskeletal system

“…In mammals, ADAR1 and ADAR2 are the two active editing enzymes identified today [5]. While ADAR1 primarily edits non-coding regions and is required to mark endogenous RNAs as ‘self’ [6], ADAR2 seems more involved in editing coding regions of mRNAs [7]. …”

“…The pre-mRNAs encoding FLNA and FLNB undergo RNA editing leading to a glutamine (Q) to arginine (R) exchange at the identical position in either protein [7]. Editing of Flna RNA is conserved from birds to humans and is located in a highly interactive region of Filamins seemingly affecting multiple cellular functions.…”

Enigmatic In Vivo iduronate-2-sulfatase (IDS) mutant transcript correction to wild-type in Hunter syndrome

“…Pre-mRNA processing, involving the highly interconnected processes of 5' cap addition, splicing, polyadenylation and post-transcriptional modification can, together with mRNA decay, exert a profound influence on both the efficiency and fidelity of human gene expression [Buratowski, 2008;Preker et al, 2008;Seila et al, 2008;Moore and Proudfoot, 2009]. In addition, it has become increasingly clear that the posttranscriptional modification of pre-mRNAs by RNA editing is not an infrequent phenomenon and may make a significant contribution to human transcriptome diversity [Furey et al, 2004;Li et al, 2009].…”

Proteome diversification by adenosine to inosine RNA-editing

“…Hence, editing events in coding regions frequently lead to amino acid substitutions or alternative splicing events. [10][11][12] In this review we want to give an overview on the family of ADAR enzymes, focusing on recently identified RNA editing targets in coding regions. We will discuss the potential biological implications of these editing events in normal and pathological situations.…”