Genome complexity: 3-D change changes body morphology (Introduction)

by David Turell , Tuesday, May 30, 2023, 17:02 (543 days ago) @ David Turell

From shark to skate:

https://www.quantamagazine.org/how-3d-changes-in-the-genome-turned-sharks-into-skates-2...

"Now researchers have discovered how skates evolved their distinctive profile: Rearrangements in the skate’s DNA sequence altered the 3D structure of its genome and disrupted ancient connections between key developmental genes and the regulatory sequences that governed them. Those changes in turn redrafted the animal’s body plan.

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"By comparing the genome of the little skate to the genomes of other vertebrates, the researchers determined that the skate genome has generally remained very similar to that of their vertebrate ancestors at the sequence level. However, there were a few notable rearrangements that would have affected the genome’s 3D structure. In the DNA of individuals, such rearrangements can cause diseases by throwing off gene regulation. The discovery led the researchers to wonder whether the rearrangements in skates might have similarly disrupted the original genetic instructions for their body plan.

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"In vertebrates, sets of functionally related genes and their enhancers are physically grouped together in three dimensions in units called topologically associating domains, or TADs. Boundary regions help to ensure that enhancers only act on genes in the same TAD.

"However, when major genome rearrangements occur — like the ones that the team was seeing in the skate’s DNA — boundaries can be lost, and the relative positions of genes on chromosomes can change. As a result, “some enhancers can provide instructions to the wrong gene,” explained Dario Lupiáñez, an evolutionary biologist at the Max Delbrück Center in Berlin and one of the senior authors of the study.

"It seemed possible that the changes in the 3D architecture of the skate genome might have disrupted the ancient blocks of genes the skates inherited from their sharklike ancestors, affecting the genes’ function.

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"It suggested that the disruption of the ancestral TAD had produced the skate’s distinctive fins by activating PCP genes in a new part of the body.

“'This rearrangement of the TAD basically changes the entire environment of the gene and brings new enhancers into the vicinity of the gene,” Lupiáñez said.

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"In the picture of skate evolution that the researchers have reconstructed, at some point after the skate lineage diverged from sharks, they acquired a mutation in an enhancer that made their hoxa genes active in both the front and the back of their pectoral fins. And within the new tissues growing along the anterior of the fin, genome rearrangements caused the PCP pathway to be activated by enhancers in a different TAD, which had the further effect of making the fin extend forward and fuse with the animal’s head.

“'By forming the winglike structure, [the skates] are able now to inhabit a whole different ecological niche, the bottom of the ocean,” Amemiya explained.

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“'This is a completely new way to think about evolution,” he said. Structural rearrangements “can cause a gene to be activated in a place where it should not be.” He added: “This can be a mechanism of disease, but it can also serve as a driver of evolution.'”

Comment: the 3-D arrangement of DNA is very important since the same genes can be driven into new actions. It may help explain our small genome.