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

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.

腺苷脱氨基作用介导的RNA编辑，可改写基因组蓝图所承载的遗传信息。当该编辑对信使RNA（mRNA）进行重编码时，可为生物体提供表达多种功能迥异的蛋白质同工型的可能。从刺胞动物到人类的所有真后生动物（eumetazoans），均表达RNA编辑酶。然而，全转录组筛选仅在哺乳动物中发现了约25个携带保守重编码RNA编辑位点的转录本，在果蝇（Drosophila）中也仅发现了数百个重编码位点。这些基于少数经典模型生物的研究，使得学界普遍认为RNA编辑介导的重编码现象极为罕见。本研究采用一种全新的生物信息学方法并开展了大量验证实验，证实美洲大赤鱿（Doryteuthis pealeii）通过RNA编辑进行蛋白质重编码的程度远超此前认知。本研究在其神经系统中鉴定出57108个重编码位点，覆盖了绝大多数被分析的蛋白质。该重编码过程具有组织特异性，且在具有神经元功能与细胞骨架功能的基因中显著富集，提示其在大脑生理活动中发挥重要作用。