Email updates

Keep up to date with the latest news and content from Genome Biology and BioMed Central.

Open Access Research

Genome-wide identification and functional analysis of Apobec-1-mediated C-to-U RNA editing in mouse small intestine and liver

Valerie Blanc1, Eddie Park2, Sabine Schaefer3, Melanie Miller1, Yiing Lin4, Susan Kennedy1, Anja M Billing5, Hisham Ben Hamidane5, Johannes Graumann5, Ali Mortazavi2, Joseph H Nadeau3 and Nicholas O Davidson1*

Author Affiliations

1 Department of Medicine, Washington University St Louis, St Louis, MO 63110, USA

2 Department of Developmental and Cell Biology and Center for Complex Biological Systems, University of California Irvine, Irvine, CA 92697, USA

3 Pacific Northwest Research Institute, Seattle, WA 98122, USA

4 Departments of Surgery, Washington University St Louis, St Louis, MO 63110, USA

5 Proteomics Core, Weill Cornell Medical College in Qatar, Doha, Qatar

For all author emails, please log on.

Genome Biology 2014, 15:R79  doi:10.1186/gb-2014-15-6-r79

Published: 19 June 2014

Abstract

Background

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. However, the genome-wide identification, tissue-specificity and functional implications of Apobec-1-mediated C-to-U RNA editing remain incompletely explored.

Results

Deep 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.

Conclusions

These 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.