RNA editing of protein sequences: A rare event in human transcriptomes

We developed a robust computational statistical framework to identify RNA editing events from RNA-Seq data with high specificity. Our approach handles several outstanding challenges of genome-wide editing analyses, including the effect of editing on read alignment and the utilization of redundant reads. By applying this framework, we characterized the nuclear and cytosolic editomes of seven human cell lines. We found that 93.8-99.2% of the editing events are A-to-G (or A-to-I). Nuclear transcriptomes contain many more editing events than cytosolic transcriptomes. Most of the sites exhibiting nucleus-specific editing are in introns or novel intergenic transcripts that are preferentially localized in the nucleus regardless of their editing status, arguing against the role of editing in nuclear retention. In contrast, many sites that exhibit cytosol-specific editing show comparable nuclear and cytosolic expression, suggesting the differential subcellular compartmentalization of the edited and the unedited alleles. We found that RNA editing is globally associated with the modification of microRNA regulation in 3′ untranslated regions, whereas editing events in coding regions are rare and tend to be synonymous. Interestingly, A-to-G editing at derived alleles in the human lineage tends to result in reversion back to the ancestral forms at the RNA level. This suggests that editing can mediate RNA memory on evolutionary time-scales to maintain ancestral genetic information.high-throughput sequencing | nucleo-cytoplasmic localization A lthough high-throughput sequencing has facilitated the identification of genetic DNA variants, the identification of RNA editing is much more challenging owing to the uneven read distribution in RNA sequencing and the varied RNA editing rates. Errors in base calling and read alignment, the handling of redundant reads, and other systematic sequencing errors all hinder the single-nucleotide-level analysis of RNA editing. Early analyses of high-throughput sequencing data reported more than 10,000 exonic editing events, many of which were non-A-to-G (1). However, recent studies argued that many of these non-A-to-G editing events were false positives resulting from inappropriate bioinformatic analyses (2-4). To deal with multiple sources of potential errors, the existing tools for editing discovery (5-7) usually involve comprehensive pipelines packed with multiple read aligners, read simulations, and various filters. Meanwhile, many critical issues in editing discovery remain to be addressed more properly. For example, the existing methods remove a large number of redundant reads starting from the same positions, although in deep sequencing many redundant reads can result from true expression and are useful for estimating editing levels. Moreover, the effect of editing on read alignment has been commonly overlooked.Herein, we developed an efficient and robust computational statistical framework for RNA editing discovery. This framework considers the effect of editing on read alignment and hand...

Section: Resultscontrasting

confidence: 99%

Section: Discussioncontrasting

confidence: 51%

See 1 more Smart Citation

Characterization and comparison of human nuclear and cytosolic editomes

Chen

2013

“…A-to-G substitution is typically the most frequently occurring RNA variants detected in other RNA editing studies (22)(23)(24)(25). Curiously, we found that after T-to-C, A-to-G substitutions were the more frequent substitutions identified in our study (Fig.…”

Section: Rna Variation Is Similar In Drug-tolerant Cells and Other Casupporting

confidence: 72%

Single-cell analyses of transcriptional heterogeneity during drug tolerance transition in cancer cells by RNA sequencing

Lee

López-Díaz

Khan

et al. 2014

168

150

The acute cellular response to stress generates a subpopulation of reversibly stress-tolerant cells under conditions that are lethal to the majority of the population. Stress tolerance is attributed to heterogeneity of gene expression within the population to ensure survival of a minority. We performed whole transcriptome sequencing analyses of metastatic human breast cancer cells subjected to the chemotherapeutic agent paclitaxel at the single-cell and population levels. Here we show that specific transcriptional programs are enacted within untreated, stressed, and drugtolerant cell groups while generating high heterogeneity between single cells within and between groups. We further demonstrate that drug-tolerant cells contain specific RNA variants residing in genes involved in microtubule organization and stabilization, as well as cell adhesion and cell surface signaling. In addition, the gene expression profile of drug-tolerant cells is similar to that of untreated cells within a few doublings. Thus, single-cell analyses reveal the dynamics of the stress response in terms of cell-specific RNA variants driving heterogeneity, the survival of a minority population through generation of specific RNA variants, and the efficient reconversion of stress-tolerant cells back to normalcy.

“…In the last few years, genomic studies in humans have uncovered an astonishingly large number of RNA editing sites (4,(14)(15)(16)(17)(18)(19)(20). Although editing apparently occurs primarily in noncoding regions, especially in Alu repeat elements (15,19,20), the number of edited coding sites also exceeds 100 times the previously known number (14).…”

mentioning

confidence: 99%

Human coding RNA editing is generally nonadaptive

Zhang

2014

125

132

Impairment of RNA editing at a handful of coding sites causes severe disorders, prompting the view that coding RNA editing is highly advantageous. Recent genomic studies have expanded the list of human coding RNA editing sites by more than 100 times, raising the question of how common advantageous RNA editing is. Analyzing 1,783 human coding A-to-G editing sites, we show that both the frequency and level of RNA editing decrease as the importance of a site or gene increases; that during evolution, edited As are more likely than unedited As to be replaced with Gs but not with Ts or Cs; and that among nonsynonymously edited As, those that are evolutionarily least conserved exhibit the highest editing levels. These and other observations reveal the overall nonadaptive nature of coding RNA editing, despite the presence of a few sites in which editing is clearly beneficial. We propose that most observed coding RNA editing results from tolerable promiscuous targeting by RNA editing enzymes, the original physiological functions of which remain elusive.deleterious | neutral | synonymous