2023-04-12 19:18:33
A study by the Higher Council for Scientific Research (CSIC) reveals the genetic mechanism that explains how rays evolved to develop wing-like finsorganisms that are also very relevant for understanding the evolution of the traits that made us human, such as limbs.
Precisely, the genetic cause behind the shape of its fins has been the object of the study carried out by CSIC researchers at the Andalusian Center for Developmental Biology (CABD), in Seville, and at the Barcelona Biomedical Research Institute (IRBB), according to the entity in a statement.
The results, published in the journal Nature, confirm that alterations in the three-dimensional structures that DNA forms when it folds about himself, known as topologically associated domains (TAD, for its acronym in English), determine the genes that are activated and deactivated at a certain moment in evolution.
The researchers point out that genomic changes that alter TADs may be a driver of evolution. Until recently, the study of the evolution of the genome focused mainly on the coding regions, that is, on those parts that contain the genes that give rise to proteins.
However, this new study focuses on the role of TADs and non-coding regions. “This is a new way of understanding how genomes evolve“, comments the geneticist of the Max Delbrück Center for Molecular Medicine (Germany) and one of the main authors of the study Darío Lupiáñez.
More than 450 million years ago, the genome of a primitive fishthe ancestor of all vertebrate animals, doubled twice. The expansion of genetic material prompted the rapid evolution of more than 60,000 vertebrates, including humans. One of our most distant vertebrate relatives are rays, organisms that are very relevant to understanding the evolution of the traits that made us human, such as limbs.
For it, researchers have studied a type of stingray (Leucoraja erinacea) which, due to the similarity of this species with ancestral vertebrates, “allows us to compare its characteristics with those of other species to determine what is novel and what is ancestral during evolution,” explains CABD biologist and one of the first authors, Christina Paliou.
A turning point for evolutionary genomics
In 2017, the late CABD researcher José Luis Gómez-Skarmeta, an essential figure in evolutionary genomics in our country, brought together scientists from all over the world to study the evolution of the stingray. His interest was to investigate how genomes evolve structurally and functionally to promote the appearance of new traits.
That moment was crucial for the field of evolutionary genomics. Scientists got a whole new insight into how the DNA of each cellwhich can measure up to two meters, folds into a cell nucleus that is only 0.005 centimeters in diameter.
These new studies showed that the DNA packaging in the nucleus is far from random., rather it is organized into 3D structures called TADs, which contain genes and their regulatory sequences. “These 3D structures ensure that the appropriate genes are turned on and off at a given time, in the right cells,” explains Juan Tena, one of the lead authors of the study.
Center geneticist Max Delbrück and one of the first authors, Rafael Acemel, conducted experiments using Hi-C technology to elucidate the 3D structure of the TADs. But interpreting the results was challenging, as the scientists needed the complete genome of the skate as a reference point. “At the time, the reference consisted of thousands of little pieces of DNA sequence that were completely out of order, which didn’t help much,” he stressed.
To overcome this difficulty, the scientists used long read sequencing technology, together with the Hi-C data, to assemble the pieces of the DNA like a puzzle and assign the disordered sequences to the chromosomes of the line. With this new reference, reconstructing the 3D structure of the TADs was finally possible.
With this new genome they were able make comparisons with the genomes of closest relativeslos sharks, in order to identify TADs altered during the evolution of rays. These altered TADs included genes for the Wnt/PCP pathway, which is important for fin development.
They also identified a specific variation in a non-coding sequence near the Hox genes, which also regulate fin development. “This specific sequence can activate several Hox genes in the front part of the ray finswhich is not the case in other fish or tetrapod animals,” says Paliou.
Subsequently, the scientists performed functional experiments that confirmed that these molecular changes contributed to the evolution of the characteristic fin shape of rays.
TADs drive evolution
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Previous studies had shown that changes in the TADs can affect gene expression and cause disease. In this new study, the scientists show that TADs are also involved in the evolution of traits in certain species.
“TADs are important for gene regulation, as they 40% of them are conserved in all vertebrates, while the remaining 60% have evolved in one way or another. This mechanism of evolution could be relatively frequent and explain many other interesting features of species that we observe in nature. This is an important finding, as it suggests that the 3D structure of the genome influences its evolution”concludes Lupiáñez.
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