A-to-I RNA editing in the earliest-diverging Eumetazoan phyla

© The Author(s), 2017. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Molecular Biology and Evolution 34 (2017): 1890-1901, doi:10.1093/molbev/msx125.The highly conserved ADAR enzymes, found in all multicellular metazoans, catalyze the editing of mRNA transcripts by the deamination of adenosines to inosines. This type of editing has two general outcomes: site specific editing, which frequently leads to recoding, and clustered editing, which is usually found in transcribed genomic repeats. Here, for the first time, we looked for both editing of isolated sites and clustered, non-specific sites in a basal metazoan, the coral Acropora millepora during spawning event, in order to reveal its editing pattern. We found that the coral editome resembles the mammalian one: it contains more than 500,000 sites, virtually all of which are clustered in non-coding regions that are enriched for predicted dsRNA structures. RNA editing levels were increased during spawning and increased further still in newly released gametes. This may suggest that editing plays a role in introducing variability in coral gametes.This work was supported by the Australian Research Council (to PK), the European Research Council (grant 311257), the I-CORE Program of the Planning and Budgeting Committee in Israel (grants 41/11 and 1796/12), and the Israel Science Foundation (1380/14)

Trade-off between transcriptome plasticity and genome evolution in cephalopods

Author Posting. © The Author(s), 2017. This is the author's version of the work. It is posted here by permission of Cell Press for personal use, not for redistribution. The definitive version was published in Cell 169 (2017): 191-202, doi:10.1016/j.cell.2017.03.025.RNA editing, a post-transcriptional process, allows the diversification of proteomes beyond the genomic blueprint; however it is infrequently used among animals. Recent reports suggesting increased levels of RNA editing in squids thus raise the question of their nature and effects in these organisms. We here show that RNA editing is particularly common in behaviorally sophisticated coleoid cephalopods, with tens of thousands of evolutionarily conserved sites. Editing is enriched in the nervous system affecting molecules pertinent for excitability and neuronal morphology. The genomic sequence flanking editing sites is highly conserved, suggesting that the process confers a selective advantage. Due to the large number of sites, the surrounding conservation greatly reduces the number of mutations and genomic polymorphisms in protein coding regions. This trade-off between genome evolution and transcriptome plasticity highlights the importance of RNA recoding as a strategy for diversifying proteins, particularly those associated with neural function.NLB was supported by a post-doctoral scholarship from the Center for Nanoscience and Nanotechnology, Tel-Aviv University. The research of RU is supported by the Israel Science Foundation (772/13). The research of EYL was supported by the European Research Council (311257) and the Israel Science Foundation (1380/14). The research of JJCR was supported by the National Institutes of Health [1R0111223855, 1R01NS64259], the National Science Foundation (HRD- 1137725), and the Frank R. Lillie and Laura and Arthur Colwin Research Fellowships from the Marine Biological Laboratory in Woods Hole. The work of JJCR and EE was supported by grant No 094/2013 from the United States-Israel Binational Science Foundation (BSF).2018-04-0

Elevated RNA Editing Activity Is a Major Contributor to Transcriptomic Diversity in Tumors

Genomic mutations in key genes are known to drive tumorigenesis and have been the focus of much attention in recent years. However, genetic content also may change farther downstream. RNA editing alters the mRNA sequence from its genomic blueprint in a dynamic and flexible way. A few isolated cases of editing alterations in cancer have been reported previously. Here, we provide a transcriptome-wide characterization of RNA editing across hundreds of cancer samples from multiple cancer tissues, and we show that A-to-I editing and the enzymes mediating this modification are significantly altered, usually elevated, in most cancer types. Increased editing activity is found to be associated with patient survival. As is the case with somatic mutations in DNA, most of these newly introduced RNA mutations are likely passengers, but a few may serve as drivers that may be novel candidates for therapeutic and diagnostic purposes

Dynamic hyper-editing underlies temperature adaptation in <i>Drosophila</i>

<div><p>In <i>Drosophila</i>, A-to-I editing is prevalent in the brain, and mutations in the editing enzyme ADAR correlate with specific behavioral defects. Here we demonstrate a role for ADAR in behavioral temperature adaptation in <i>Drosophila</i>. Although there is a higher level of editing at lower temperatures, at 29°C more sites are edited. These sites are less evolutionarily conserved, more disperse, less likely to be involved in secondary structures, and more likely to be located in exons. Interestingly, hypomorph mutants for ADAR display a weaker transcriptional response to temperature changes than wild-type flies and a highly abnormal behavioral response upon temperature increase. In sum, our data shows that ADAR is essential for proper temperature adaptation, a key behavior trait that is essential for survival of flies in the wild. Moreover, our results suggest a more general role of ADAR in regulating RNA secondary structures <i>in vivo</i>.</p></div

Analysis of Intron Sequences Reveals Hallmarks of Circular RNA Biogenesis in Animals

Circular RNAs (circRNAs) are a large class of animal RNAs. To investigate possible circRNA functions, it is important to understand circRNA biogenesis. Besides human ALU repeats, sequence features that promote exon circularization are largely unknown. We experimentally identified circRNAs in C. elegans. Reverse complementary sequences between introns bracketing circRNAs were significantly enriched in comparison to linear controls. By scoring the presence of reverse complementary sequences in human introns, we predicted and experimentally validated circRNAs. We show that introns bracketing circRNAs are highly enriched in RNA editing or hyperediting events. Knockdown of the double-strand RNA-editing enzyme ADAR1 significantly and specifically upregulated circRNA expression. Together, our data support a model of animal circRNA biogenesis in which competing RNA-RNA interactions of introns form larger structures that promote circularization of embedded exons, whereas ADAR1 antagonizes circRNA expression by melting stems within these interactions

The degree and prevalence of A-to-I RNA editing are dynamically affected by temperature.

<p><b>(A)</b> Generation of editing list by combining the RADAR database (2,697 sites), Rennan's and Rosbash's datasets[<a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1006931#pgen.1006931.ref011" target="_blank">11</a>,<a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1006931#pgen.1006931.ref032" target="_blank">32</a>] (3,580 and 1,341 sites respectively) with novel hyper-editing sites detected by our method (30,190 sites). This resulted in a list of 32,974 unique sites, containing 11,097 editing sites in CDS. <b>(B)</b> Hyper-editing motif. The sequence near the hyper-editing sites is depleted of Gs upstream and enriched with Gs downstream as expected from ADAR targets. <b>(C)</b> Editing index, fraction of inosines among all expressed adenosines of all detected editing sites, show lower editing levels at 29°C. <b>(D)</b> Editing levels of significantly altered 55 editing sites in CDS. Each site is presented by a number which indicates its position in <a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1006931#pgen.1006931.s006" target="_blank">S1 Table</a>. <b>(E)</b> The distribution of hyper-editing detected sites, shows higher number of sites found at elevated temperature. <b>(F)</b> Average hyper-editing events per detected sites. Statistical significance between 18°C and 29°C was assessed by Student-t test (p<10⁻⁴). <b>(G)</b> Editing cluster's difference between temperatures. Left panel presents the average cluster length for each temperature. Right panel presents the average unique number of detected editing-sites for each temperature.</p

Functional analysis of hyper-edited genes.

<p>Functional analysis of hyper-edited genes.</p

EvoFold analysis of hyper-editing sites.

<p>EvoFold analysis of hyper-editing sites.</p

Editing sites at lower temperatures are edited more frequently and are more commonly flanked by complementary sequences.

<p><b>(A)</b> Mean conservation (PhastCons) score of hyper-edited sites. Position 0 indicates the position of editing site. Blue line denotes conservation mean for editing sites supported by more than one event, red line denoted conservation mean for editing sites supported by only one event, and black line represents background conservation of chosen randomly adenosines. Left figure represents all genome wide hyper-editing sites, while the right figure represents hyper-editing sites in coding regions (CDS). The information from the non-hyper-edited reads was included. <b>(B)</b> RNA secondary structure prediction using BLAST[<a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1006931#pgen.1006931.ref050" target="_blank">50</a>] tool (see <a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1006931#sec009" target="_blank">Methods</a>). Blue bars donate for predicted dsRNA structure involving the hyper-editing site, as we succeeded to match the editing regions with their anti-sense sequence. Red bars denote for matches found in the sense sequence, representing the control. Green bars denote for predicted dsRNA structure involving the hyper-editing site after converting the adenosine (A) to its edited form, guanosine (G). Violet bars represents the control for the converted adenosines. <b>(C)</b> Genomic locations of detected hyper-editing sites show increase in the number of exonic sites at 29°C.</p