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

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.

Genome-wide analysis of differential RNA editing in epilepsy

“…2B; Supplemental Table S5). Consistent with previous observations (Blanc and Davidson 2011;Danecek et al 2012;Gu et al 2012;Blanc et al 2014), we observed that the majority (all = 77.3% and clustered = 80%) of the DRE sites resided in the 3 UTR of the gene , while 21.9% of all DRE sites and 11.1% of the clustered DRE sites resided in the protein coding regions of the gene (Fig. 2B).…”

C-to-U editing and site-directed RNA editing for the correction of genetic mutations

“…The few identified physiological C-to-U RNA editing targets include apolipoprotein B (apoB) pre-mRNA in intestinal cells and several recently validated, but uncharacterized mRNA targets; in an early study, 32 previously unknown APOBEC1 (apoB editing catalytic subunit 1) editing sites in the 3' untranslated regions (3' UTRs) of diverse mRNA transcripts were identified and validated (11). In addition, 56 novel editing sites in 54 intestinal mRNAs and 22 novel sites in 17 liver mRNAs in AU-rich segments of the 3' UTRs were also identified (12). Recently, 410 C-to-U RNA editing events across 275 transcripts were also found in bone marrow-derived macrophages, and nearly all (97%) of these C-to-U events were detected in the 3' UTRs (13).…”

Functional requirements of AID’s higher order structures and their interaction with RNA-binding proteins

“…The functional relevance of all of the A1-associated RBPs is not yet fully understood, but they may participate in a variety of RNA-processing events by A1. In fact, large-scale sequence analyses by two independent groups recently revealed novel A1-specific C-to-U editing signatures in the UTR of a dozen mRNAs (55,56). Therefore, the dimeric form of AID, like that of A1, may form an as-yet unidentified RNAediting complex(es) in association with its CSR-specific RBP Before the co-IP analysis, the cell lysates were either untreated or treated with RNase A or 500 mM NaCl.…”