Splicing controls tissue specific regulation of A-to-I editing sites in murine pre-mRNAs

Most metazoan mRNA-processing - including mRNA-splicing and adenosine to inosine (A-to-I) editing - occurs co-transcriptionally. During A-to-I editing a genomically encoded adenosine is deaminated to inosine by adenosine deaminases acting on RNA (ADARs). As inosine has different base-pairing characteristics, A-to-I editing affects various cellular processes ranging from the recoding of transcripts to the recognition of RNAs by the innate immune system. ADAR enzymes require double-stranded RNA for binding. These editing-competent stems are frequently formed between exons and introns, suggesting that editing and splicing require co-transcriptional coordination. Here, we use nascent RNA-seq to identify A-to-I editing events that occur co-transcriptionally. We identified almost 100,000 editing sites (~80% novel) that primarily locate to intronic regions. As A-to-I editing frequently depends on intronic sequences we reasoned that the efficiency of splicing is a major factor regulating editing. Indeed, inhibition of splicing changed the editing levels of hundreds of sites. Intronic and exonic editing levels primarily increase, suggesting that reduced splicing efficiency leads to an increased exposure of intronic and exonic sequences to ADAR enzymes. Consistently, we also observe changes in editing levels for mice where the alternative splicing factors NOVA1 or NOVA2 are depleted, suggesting that alternative splicing factors can act as editing modulators. Finally, we show that across tissues, intron retention rates correlate with editing levels. We therefore suggest that splicing efficiency contributes to tissue-specific differences in editing levels.