Squid and octopus genomes preserve broad domains while DNA loops vary
Genome contacts in squid, cuttlefish and octopus show two scales of organisation: relatively conserved broad domains and smaller loops that vary with species and biological setting. A peer-reviewed study combines comparative maps with a targeted squid-embryo deletion linked to distant gene activity. These observations map regulatory flexibility without resolving the evolution of complex cephalopod brains or behaviour.
Squid, cuttlefish and octopus genomes bring different stretches of DNA into contact in three-dimensional space. A single peer-reviewed study compared these contacts with gene activity and DNA accessibility across tissues and developmental stages. Broad contact domains were comparatively conserved, even though cephalopod chromosomes have undergone extensive rearrangement. The comparison covered the squid Euprymna scolopes, the cuttlefish Sepia officinalis and the octopus Octopus bimaculoides.[1]
Smaller loops change with species, tissue and development
Within that larger structure, many smaller chromatin loops varied by species, tissue or developmental stage. Chromatin is DNA packaged with proteins; a loop can bring regions far apart along the DNA sequence into spatial proximity. Some larger loops in the octopus may reflect chromosome fusions and rearrangements. The authors present that relationship as an evolutionary interpretation of the comparative patterns.[1]
A squid-embryo deletion changes distant gene activity
The team also used CRISPR gene editing to remove a candidate regulatory sequence within the Quaking B gene in Euprymna berryi, a related squid species. Among the edited embryos, some had shortened arms or smaller optic brain regions, alongside changes in the activity of distant genes. Changes within the conserved loop did not remain statistically significant after correction for multiple comparisons. Outcomes varied among embryos, and this targeted experiment does not establish how complex cephalopod brains or behaviour evolved.[1]
