Trade-off between Transcriptome Plasticity and Genome Evolution in Cephalopods

Liscovitch-Brauer, Noa; Alon, Shahar; Porath, Hagit T.; Elstein, Boaz; Unger, Ron; Ziv, Tamar; Admon, Arie; Levanon, Erez Y.; Rosenthal, Joshua J. C.; Eisenberg, Eli

doi:10.1016/j.cell.2017.03.025

Cited by 295 publications

(420 citation statements)

References 62 publications

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“…Positive selection: in a previous paper studying A-to-I RNA editing sites in cephalopods (Liscovitch-Brauer et al, 2017), the authors proved the positive selection on RNA editing events by showing that (a) The fraction of nonsynonymous editing events is higher than the genomic background; (b) The nonsynonymous editing levels are generally higher than the synonymous editing levels. In our study, we observed exactly the same pattern in Arabidopsis C-to-U RNA editome.…”

Section: Discussionmentioning

confidence: 98%

The chloroplast and mitochondrial C‐to‐U RNA editing in Arabidopsis thaliana shows signals of adaptation

Chu

Wei

2019

Plant Direct

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C‐to‐U RNA editing is the conversion from cytidine to uridine at RNA level. In plants, the genes undergo C‐to‐U RNA modification are mainly chloroplast and mitochondrial genes. Case studies have identified the roles of C‐to‐U editing in various biological processes, but the functional consequence of the majority of C‐to‐U editing events is still undiscovered. We retrieved the deep sequenced transcriptome data in roots and shoots of Arabidopsis thaliana and profiled their C‐to‐U RNA editomes and gene expression patterns. We investigated the editing level and conservation pattern of these C‐to‐U editing sites. The levels of nonsynonymous C‐to‐U editing events are higher than levels of synonymous events. The fraction of nonsynonymous editing sites is higher than neutral expectation. Highly edited cytidines are more conserved at DNA level, and the gene expression levels are correlated with C‐to‐U editing levels. Our results demonstrate that the global C‐to‐U editome is shaped by natural selection and that many nonsynonymous C‐to‐U editing events are adaptive. The editing mechanism might be positively selected and maintained and could have profound effects on the modified RNAs.

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Section: Discussionmentioning

confidence: 98%

The chloroplast and mitochondrial C‐to‐U RNA editing in Arabidopsis thaliana shows signals of adaptation

Chu

Wei

2019

Plant Direct

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“…Importantly, a recent study found that unlike other bilaterians, coleoids, i.e. all cephalopods except for nautiluses, diversify their proteomes to a hitherto unknown extent by RNA editing (Liscovitch‐Brauer et al, ). This recoding appears to be evolutionarily conserved and adaptive among coleoids and may be one reason for their sophisticated cognitive abilities.…”

Section: Evodevo Genomes and The Diversification Of Molluscsmentioning

confidence: 99%

The evolution of molluscs

2018

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Molluscs are extremely diverse invertebrate animals with a rich fossil record, highly divergent life cycles, and considerable economical and ecological importance. Key representatives include worm-like aplacophorans, armoured groups (e.g. polyplacophorans, gastropods, bivalves) and the highly complex cephalopods. Molluscan origins and evolution of their different phenotypes have largely remained unresolved, but significant progress has been made over recent years. Phylogenomic studies revealed a dichotomy of the phylum, resulting in Aculifera (shell-less aplacophorans and multi-shelled polyplacophorans) and Conchifera (all other, primarily uni-shelled groups). This challenged traditional hypotheses that proposed that molluscs gradually evolved complex phenotypes from simple, worm-like animals, a view that is corroborated by developmental studies that showed that aplacophorans are secondarily simplified. Gene expression data indicate that key regulators involved in anterior-posterior patterning (the homeobox-containing Hox genes) lost this function and were co-opted into the evolution of taxon-specific novelties in conchiferans. While the bone morphogenetic protein (BMP)/decapentaplegic (Dpp) signalling pathway, that mediates dorso-ventral axis formation, and molecular components that establish chirality appear to be more conserved between molluscs and other metazoans, variations from the common scheme occur within molluscan sublineages. The deviation of various molluscs from developmental pathways that otherwise appear widely conserved among metazoans provides novel hypotheses on molluscan evolution that can be tested with genome editing tools such as the CRISPR/Cas9 (clustered regularly interspaced short palindromic repeats/clustered regularly interspaced short palindromic repeats-associated protein9) system.

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“…Co-transcriptional and post-transcriptional processing, such as RNA splicing and RNA editing, can alter the structure and sequence of RNAs, leading to different transcripts produced from the same DNA sequence. RNA editing can be defined as any site-specific alteration in RNA sequences, that include insertion or deletion of nucleotides and base conversion, and is an effective mechanism to modifying and enrich genetic information beyond the genetic code (Bahn et al, 2012;Li et al, 2011;Liscovitch-Brauer et al, 2017;Qulsum et al, 2019). The predominant type of RNA editing in animals is the conversion of adenosine (A) to inosine (I), catalyzed by a family of adenosine deaminases (ADARs) acting on double strand RNA (Nishikura, 2006).…”

Section: Introductionmentioning

confidence: 99%

“…Another well documented type of RNA editing in humans is the deamination of cytidine leading to uridine (C-to-U), a RNA editing event catalyzed by the activation of APOBECs (Salter et al, 2016). However, it is still an enigma how the remaining ten nucleotide modifications found in humans (Li et al, 2011) and in cephalopods (Liscovitch-Brauer et al, 2017) transcriptomes can occur.…”

Section: Introductionmentioning

confidence: 99%

RNA editing in inflorescences of wild grapevine unveils association to sex and development

Ramos

Faísca-Silva

Coito

et al. 2020

Preprint

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RNA editing challenges the central dogma of molecular biology, by modifying the genetic information at the transcription level. Recent reports, suggesting increased levels of RNA editing in plants, raised questions on the nature and dynamics of such events during development. We here report the occurrence of distinct RNA editing patterns in wild Vitis flowers during development, with twelve possible RNA editing modifications observed for the first time in plants. RNA editing events are gender and developmental stage specific, identical in subsequent years of this perennial species and with distinct nucleotide frequencies neighboring editing sites on the 5' and 3' flanks. The transcriptome dynamics unveils a new regulatory layer responsible for gender plasticity enhancement or underling dioecy evolution in Vitis.

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Trade-off between Transcriptome Plasticity and Genome Evolution in Cephalopods

Cited by 295 publications

References 62 publications

The chloroplast and mitochondrial C‐to‐U RNA editing in Arabidopsis thaliana shows signals of adaptation

The chloroplast and mitochondrial C‐to‐U RNA editing in Arabidopsis thaliana shows signals of adaptation

The evolution of molluscs

RNA editing in inflorescences of wild grapevine unveils association to sex and development

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