Limits...
The majority of transcripts in the squid nervous system are extensively recoded by A-to-I RNA editing.

Alon S, Garrett SC, Levanon EY, Olson S, Graveley BR, Rosenthal JJ, Eisenberg E - Elife (2015)

Bottom Line: These studies on few established models have led to the general assumption that recoding by RNA editing is extremely rare.Here we employ a novel bioinformatic approach with extensive validation to show that the squid Doryteuthis pealeii recodes proteins by RNA editing to an unprecedented extent.Recoding is tissue-dependent, and enriched in genes with neuronal and cytoskeletal functions, suggesting it plays an important role in brain physiology.

View Article: PubMed Central - PubMed

Affiliation: George S Wise Faculty of Life Sciences, Department of Neurobiology, Tel Aviv University, Tel Aviv, Israel.

ABSTRACT
RNA editing by adenosine deamination alters genetic information from the genomic blueprint. When it recodes mRNAs, it gives organisms the option to express diverse, functionally distinct, protein isoforms. All eumetazoans, from cnidarians to humans, express RNA editing enzymes. However, transcriptome-wide screens have only uncovered about 25 transcripts harboring conserved recoding RNA editing sites in mammals and several hundred recoding sites in Drosophila. These studies on few established models have led to the general assumption that recoding by RNA editing is extremely rare. Here we employ a novel bioinformatic approach with extensive validation to show that the squid Doryteuthis pealeii recodes proteins by RNA editing to an unprecedented extent. We identify 57,108 recoding sites in the nervous system, affecting the majority of the proteins studied. Recoding is tissue-dependent, and enriched in genes with neuronal and cytoskeletal functions, suggesting it plays an important role in brain physiology.

Show MeSH
Editing tends to avoid potentially deleterious recoding events.Each squid ORF was aligned against the conserved domains in the ConservedDomain Database (CDD) (Marchler-Bauer etal., 2013), and the score for substituting each amino acid by allother types of amino acids was calculated (Boratyn et al., 2012). The substitution score is a positive ornegative integer, reflecting amino acid substitution which, compared tochance, occur frequently or infrequently in the alignment of the conserveddomains, respectively. (A) The average editing levels, usingdata from the GFL and OL tissues combined, as a function of the amino acidsubstitution score. The average editing levels for negative substitutionscores is significantly lower compared to what is expected by chance.(B) The distribution of the recoding sites as a function ofthe amino acid substitution score. Recoding sites tend to avoid largenegative substitution scores compared with random changes. (C)The average substitution score as a function of the editing levels, usingdata from the GFL and OL tissues combined. The higher the editing levels,the higher the average substitution score, indicating that highly editedsites are more likely to recode to amino acids that occur frequently inother species. Expected values and error bars were calculated by using themean values and standard deviation of 10,000 bootstrap runs, respectively.For A and C, the editing levels in all the siteswith the same recoding type were randomly shuffled. For B,adenosines were randomly modified in a way that preserves the sequencepreference and the total number of editing events. One asterisk mark p-value<0.05, two mark p-value<1e-4. Abbreviations: Giant fiber lobe(GFL), Optic lobe (OL).DOI:http://dx.doi.org/10.7554/eLife.05198.015
© Copyright Policy
Related In: Results  -  Collection

License
getmorefigures.php?uid=PMC4384741&req=5

fig4s3: Editing tends to avoid potentially deleterious recoding events.Each squid ORF was aligned against the conserved domains in the ConservedDomain Database (CDD) (Marchler-Bauer etal., 2013), and the score for substituting each amino acid by allother types of amino acids was calculated (Boratyn et al., 2012). The substitution score is a positive ornegative integer, reflecting amino acid substitution which, compared tochance, occur frequently or infrequently in the alignment of the conserveddomains, respectively. (A) The average editing levels, usingdata from the GFL and OL tissues combined, as a function of the amino acidsubstitution score. The average editing levels for negative substitutionscores is significantly lower compared to what is expected by chance.(B) The distribution of the recoding sites as a function ofthe amino acid substitution score. Recoding sites tend to avoid largenegative substitution scores compared with random changes. (C)The average substitution score as a function of the editing levels, usingdata from the GFL and OL tissues combined. The higher the editing levels,the higher the average substitution score, indicating that highly editedsites are more likely to recode to amino acids that occur frequently inother species. Expected values and error bars were calculated by using themean values and standard deviation of 10,000 bootstrap runs, respectively.For A and C, the editing levels in all the siteswith the same recoding type were randomly shuffled. For B,adenosines were randomly modified in a way that preserves the sequencepreference and the total number of editing events. One asterisk mark p-value<0.05, two mark p-value<1e-4. Abbreviations: Giant fiber lobe(GFL), Optic lobe (OL).DOI:http://dx.doi.org/10.7554/eLife.05198.015

Mentions: Recently, it was suggested that RNA editing is generally not advantageous in humans(Xu and Zhang, 2014), as nonsynonymousevents are less frequent than expected by chance (Xuand Zhang, 2014). Strikingly, for sites with high editing levels in squid, theopposite is true (Figure 4B and Figure 4—figure supplement 2A). Recodingevents favor creation of glycine and arginine, mainly at the expense of lysine (Figure 4—figure supplement 2B–D).Moreover, highly edited sites within conserved domains tend to recode to amino acidsthat occur frequently in other species at the same position (Figure 4—figure supplement 3), suggesting selectiontowards functional substitutions and against deleterious ones.


The majority of transcripts in the squid nervous system are extensively recoded by A-to-I RNA editing.

Alon S, Garrett SC, Levanon EY, Olson S, Graveley BR, Rosenthal JJ, Eisenberg E - Elife (2015)

Editing tends to avoid potentially deleterious recoding events.Each squid ORF was aligned against the conserved domains in the ConservedDomain Database (CDD) (Marchler-Bauer etal., 2013), and the score for substituting each amino acid by allother types of amino acids was calculated (Boratyn et al., 2012). The substitution score is a positive ornegative integer, reflecting amino acid substitution which, compared tochance, occur frequently or infrequently in the alignment of the conserveddomains, respectively. (A) The average editing levels, usingdata from the GFL and OL tissues combined, as a function of the amino acidsubstitution score. The average editing levels for negative substitutionscores is significantly lower compared to what is expected by chance.(B) The distribution of the recoding sites as a function ofthe amino acid substitution score. Recoding sites tend to avoid largenegative substitution scores compared with random changes. (C)The average substitution score as a function of the editing levels, usingdata from the GFL and OL tissues combined. The higher the editing levels,the higher the average substitution score, indicating that highly editedsites are more likely to recode to amino acids that occur frequently inother species. Expected values and error bars were calculated by using themean values and standard deviation of 10,000 bootstrap runs, respectively.For A and C, the editing levels in all the siteswith the same recoding type were randomly shuffled. For B,adenosines were randomly modified in a way that preserves the sequencepreference and the total number of editing events. One asterisk mark p-value<0.05, two mark p-value<1e-4. Abbreviations: Giant fiber lobe(GFL), Optic lobe (OL).DOI:http://dx.doi.org/10.7554/eLife.05198.015
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4384741&req=5

fig4s3: Editing tends to avoid potentially deleterious recoding events.Each squid ORF was aligned against the conserved domains in the ConservedDomain Database (CDD) (Marchler-Bauer etal., 2013), and the score for substituting each amino acid by allother types of amino acids was calculated (Boratyn et al., 2012). The substitution score is a positive ornegative integer, reflecting amino acid substitution which, compared tochance, occur frequently or infrequently in the alignment of the conserveddomains, respectively. (A) The average editing levels, usingdata from the GFL and OL tissues combined, as a function of the amino acidsubstitution score. The average editing levels for negative substitutionscores is significantly lower compared to what is expected by chance.(B) The distribution of the recoding sites as a function ofthe amino acid substitution score. Recoding sites tend to avoid largenegative substitution scores compared with random changes. (C)The average substitution score as a function of the editing levels, usingdata from the GFL and OL tissues combined. The higher the editing levels,the higher the average substitution score, indicating that highly editedsites are more likely to recode to amino acids that occur frequently inother species. Expected values and error bars were calculated by using themean values and standard deviation of 10,000 bootstrap runs, respectively.For A and C, the editing levels in all the siteswith the same recoding type were randomly shuffled. For B,adenosines were randomly modified in a way that preserves the sequencepreference and the total number of editing events. One asterisk mark p-value<0.05, two mark p-value<1e-4. Abbreviations: Giant fiber lobe(GFL), Optic lobe (OL).DOI:http://dx.doi.org/10.7554/eLife.05198.015
Mentions: Recently, it was suggested that RNA editing is generally not advantageous in humans(Xu and Zhang, 2014), as nonsynonymousevents are less frequent than expected by chance (Xuand Zhang, 2014). Strikingly, for sites with high editing levels in squid, theopposite is true (Figure 4B and Figure 4—figure supplement 2A). Recodingevents favor creation of glycine and arginine, mainly at the expense of lysine (Figure 4—figure supplement 2B–D).Moreover, highly edited sites within conserved domains tend to recode to amino acidsthat occur frequently in other species at the same position (Figure 4—figure supplement 3), suggesting selectiontowards functional substitutions and against deleterious ones.

Bottom Line: These studies on few established models have led to the general assumption that recoding by RNA editing is extremely rare.Here we employ a novel bioinformatic approach with extensive validation to show that the squid Doryteuthis pealeii recodes proteins by RNA editing to an unprecedented extent.Recoding is tissue-dependent, and enriched in genes with neuronal and cytoskeletal functions, suggesting it plays an important role in brain physiology.

View Article: PubMed Central - PubMed

Affiliation: George S Wise Faculty of Life Sciences, Department of Neurobiology, Tel Aviv University, Tel Aviv, Israel.

ABSTRACT
RNA editing by adenosine deamination alters genetic information from the genomic blueprint. When it recodes mRNAs, it gives organisms the option to express diverse, functionally distinct, protein isoforms. All eumetazoans, from cnidarians to humans, express RNA editing enzymes. However, transcriptome-wide screens have only uncovered about 25 transcripts harboring conserved recoding RNA editing sites in mammals and several hundred recoding sites in Drosophila. These studies on few established models have led to the general assumption that recoding by RNA editing is extremely rare. Here we employ a novel bioinformatic approach with extensive validation to show that the squid Doryteuthis pealeii recodes proteins by RNA editing to an unprecedented extent. We identify 57,108 recoding sites in the nervous system, affecting the majority of the proteins studied. Recoding is tissue-dependent, and enriched in genes with neuronal and cytoskeletal functions, suggesting it plays an important role in brain physiology.

Show MeSH