Abstract
BackgroundRNA editing encompasses a post-transcriptional process in which the genomically templated sequence is enzymatically altered and introduces a modified base into the edited transcript. Mammalian C-to-U RNA editing represents a distinct subtype of base modification, whose prototype is intestinal apolipoprotein B mRNA, mediated by the catalytic deaminase Apobec-1. However, the genome-wide identification, tissue-specificity and functional implications of Apobec-1-mediated C-to-U RNA editing remain incompletely explored.ResultsDeep sequencing, data filtering and Sanger-sequence validation of intestinal and hepatic RNA from wild-type and Apobec-1-deficient mice revealed 56 novel editing sites in 54 intestinal mRNAs and 22 novel sites in 17 liver mRNAs, all within 3′ untranslated regions. Eleven of 17 liver RNAs shared editing sites with intestinal RNAs, while 6 sites are unique to liver. Changes in RNA editing lead to corresponding changes in intestinal mRNA and protein levels for 11 genes. Analysis of RNA editing in vivo following tissue-specific Apobec-1 adenoviral or transgenic Apobec-1 overexpression reveals that a subset of targets identified in wild-type mice are restored in Apobec-1-deficient mouse intestine and liver following Apobec-1 rescue. We find distinctive polysome profiles for several RNA editing targets and demonstrate novel exonic editing sites in nuclear preparations from intestine but not hepatic apolipoprotein B RNA. RNA editing is validated using cell-free extracts from wild-type but not Apobec-1-deficient mice, demonstrating that Apobec-1 is required.ConclusionsThese studies define selective, tissue-specific targets of Apobec-1-dependent RNA editing and show the functional consequences of editing are both transcript- and tissue-specific.
Highlights
RNA editing encompasses a post-transcriptional process in which the genomically templated sequence is enzymatically altered and introduces a modified base into the edited transcript
This strategy permitted an evaluation of tissue-specific and dose-dependent changes in cytidine to uridine (C-to-U) RNA editing at different levels of Apobec-1 expression [15]
C-to-U mismatches found in both WT and Apobec-1-/- mice as well as sites with less than three reads were excluded from further analysis
Summary
RNA editing encompasses a post-transcriptional process in which the genomically templated sequence is enzymatically altered and introduces a modified base into the edited transcript. Mammalian C-to-U RNA editing represents a distinct subtype of base modification, whose prototype is intestinal apolipoprotein B mRNA, mediated by the catalytic deaminase Apobec-1. Among the mechanisms for RNA-DNA differences is RNA editing, in which genomically templated RNA sequences are enzymatically altered. The most prevalent type of editing involves a base change from adenosine to inosine (A-to-I), mediated by adenosine deaminases acting on (double-stranded) RNA (ADARs). A second, much less prevalent type of RNA editing involves deamination of cytidine to uridine (C-to-U) in single-stranded RNA, mediated by Apobec-1, a member of the APOBEC family of cytidine deaminases [8]. The prototype for mammalian C-to-U RNA editing is apolipoprotein B (apoB) RNA, where Apobec-1-mediated deamination of a CAA codon introduces a translational termination (UAA) codon in the edited transcript. ApoB mRNA editing is a critical adaptive pathway for lipid transport in both the mouse intestine and liver, and exhibits distinctive developmental and metabolic regulation [9], mediated via the expression and stoichiometric interactions of two dominant trans-acting proteins, Apobec-1 and Apobec-1 complementation factor (ACF), other proteins are implicated [9,10,11,12]
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