RNA editing generates cellular subsets with diverse sequence within populations

Abstract

RNA editing is a mutational mechanism that specifically alters the nucleotide content in transcribed RNA. However, editing rates vary widely, and could result from equivalent editing amongst individual cells, or represent an average of variable editing within a population. Here we present a hierarchical Bayesian model that quantifies the variance of editing rates at specific sites using RNA-seq data from both single cells, and a cognate bulk sample to distinguish between these two possibilities. The model predicts high variance for specific edited sites in murine macrophages and dendritic cells, findings that we validated experimentally by using targeted amplification of specific editable transcripts from single cells. The model also predicts changes in variance in editing rates for specific sites in dendritic cells during the course of LPS stimulation. Our data demonstrate substantial variance in editing signatures amongst single cells, supporting the notion that RNA editing generates diversity within cellular populations.

Single-cell transcriptomics reveals specific RNA editing signatures in the human brain

“…These observations suggest that the penetrance of editing at single sites in single brain cortex cells shows an "all or nothing" distribution and that the affected sites vary between single cells, an effect that is masked by the study of bulk tissues. The bimodal distribution of RNA editing levels was also recently shown for C-to-U editing levels in homogeneous populations of mice macrophages (Harjanto et al 2016).…”

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

“…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). C-to-U RNA editing of apoB pre-mRNA occurs at nucleotides 6666 and 6802 in the nucleus (14,15).…”

MultiEditR: An easy validation method for detecting and quantifying RNA editing from Sanger sequencing

“…Although the mean inaccuracy of C and T bases was significant, the magnitude of this difference was less than 5% ( Figure 1E-F). RNA editing is characterized by high variability in natural context (Harjanto et al 2016). In addition, when RNA editing is induced by targeted RNA editing tools, in which RNA editing level is presumably quite similar between cells, there is variability in the reported editing of 5% or more (Cox et al 2017;Vogel et al 2018).…”

“…The RNA editing activity of APOBEC1 is not limited to Apob mRNA. In fact APOBEC1 edits many more transcripts in both Apob expressing tissues and tissues where Apob is not present, leading to C-to-U RNA editing in hundreds of transcripts mainly in their 3'UTR (Blanc et al 2014;Harjanto et al 2016;Rayon-Estrada et al 2017;Rosenberg et al 2011). APOBEC1 Cto-U editing seems to have a role also in maintaining brain physiology in mice, rats and humans (Cole et al 2017;Kankowski et al 2018;Meier et al 2005), suggesting a critical role of C-to-U editing in the regulatory mechanism for brain homeostasis (Gagnidze et al 2018).…”