How octopuses, squid, and cuttlefish defy genetics central dogma

Octopuses, squid, and cuttlefish often do not follow the genetic instructions in their DNA to the letter. Instead, they use enzymes to pluck out specific adenosine RNA bases (some of As, out of the As, Ts, Gs, and Us of RNA) that codes for proteins and replace them with a different base, called Inosine. 

This process—called "RNA editing"—is rarely used to recode proteins in most animals, but octopuses and their kin edit RNA base pairs in over half of their transcribed genes. When researchers did experiments to quantify and characterize the extent of this RNA editing across cephalopod species, they found evidence that this genetic strategy has profoundly constrained evolution of the cephalopod genome.

Researchers have found that octopuses use RNA editing to rapidly adapt to temperature changes and that the majority of RNA transcripts in squid neurons contain these. In the new study, researchers hoped to find out how commonplace these edits are, how they evolved along the cephalopod lineage, and how such extraordinary editing capabilities affect the evolution of the cephalopod genome.

Vertebrate cells are capable of RNA editing, but we use it very rarely. Humans have 20,000 genes but only a few dozen conserved RNA editing sites that are likely encoding functional proteins. Squids also have about 20,000 genes but have at least 11,000 active RNA editing sites affecting the proteome, many of which are conserved, according to this study's estimates. "Basically, this is a mechanism to make proteins that are not encoded in the DNA. They are not present in the genomic sequence," says study co-author Eli Eisenberg, a biophysicist at Tel Aviv University in Israel. "With these cephalopods, this is not the exception. This is the rule. The rule is that most of the proteins are being edited."