Alon Shahar

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  • Preprint
    Trade-off between transcriptome plasticity and genome evolution in cephalopods
    ( 2017-03) Liscovitch-Brauer, Noa ; Alon, Shahar ; Porath, Hagit T. ; Elstein, Boaz ; Unger, Ron ; Ziv, Tamar ; Admon, Arie ; Levanon, Erez ; Rosenthal, Joshua J. C. ; Eisenberg, Eli
    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.
  • Article
    Profiling molecular and behavioral circadian rhythms in the non-symbiotic sea anemone Nematostella vectensis
    (Nature Publishing Group, 2015-06-17) Oren, Matan ; Tarrant, Ann M. ; Alon, Shahar ; Simon-Blecher, Noa ; Elbaz, Idan ; Appelbaum, Lior ; Levy, Oren
    Endogenous circadian clocks are poorly understood within early-diverging animal lineages. We have characterized circadian behavioral patterns and identified potential components of the circadian clock in the starlet sea anemone, Nematostella vectensis: a model cnidarian which lacks algal symbionts. Using automatic video tracking we showed that Nematostella exhibits rhythmic circadian locomotor activity, which is persistent in constant dark, shifted or disrupted by external dark/light cues and maintained the same rate at two different temperatures. This activity was inhibited by a casein kinase 1δ/ε inhibitor, suggesting a role for CK1 homologue(s) in Nematostella clock. Using high-throughput sequencing we profiled Nematostella transcriptomes over 48 hours under a light-dark cycle. We identified 180 Nematostella diurnally-oscillated transcripts and compared them with previously established databases of adult and larvae of the symbiotic coral Acropora millepora, revealing both shared homologues and unique rhythmic genes. Taken together, this study further establishes Nematostella as a non-symbiotic model organism to study circadian rhythms and increases our understanding about the fundamental elements of circadian regulation and their evolution within the Metazoa.
  • Article
    A-to-I RNA editing in the earliest-diverging Eumetazoan phyla
    (Oxford University Press, 2017-04-08) Porath, Hagit T. ; Schaffer, Amos A. ; Kaniewska, Paulina ; Alon, Shahar ; Eisenberg, Eli ; Rosenthal, Joshua J. C. ; Levanon, Erez ; Levy, Oren
    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.