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Elife. 2015 Jan 8;4. doi: 10.7554/eLife.05198.

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

Author information

1
George S Wise Faculty of Life Sciences, Department of Neurobiology, Tel Aviv University, Tel Aviv, Israel.
2
Department of Genetics and Developmental Biology, Institute for Systems Genomics, University of Connecticut Health Center, Farmington, United States.
3
Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan, Israel.
4
Institute of Neurobiology, University of Puerto Rico Medical Sciences Campus, San Juan, Puerto Rico.
5
Sagol School of Neuroscience, 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.

KEYWORDS:

Doryteuthis pealeii; RNA editing; evolutionary biology; genomics; neuroscience; recoding

PMID:
25569156
PMCID:
PMC4384741
DOI:
10.7554/eLife.05198
[Indexed for MEDLINE]
Free PMC Article

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