2023-04-24 14:45:24
The dance of a stingray on the ocean floor is graceful: its huge front fins flap like wings as it glides under the sand. Precisely, the genetic cause behind the shape of their fins has been the subject of a study that reveals how rays evolved to develop wing-shaped fins.
The study is the work of specialists from the Barcelona Biomedical Research Institute (IRBB) and the Higher Council for Scientific Research (CSIC) at the Andalusian Center for Developmental Biology (CABD), in Seville, Spain.
The results confirm that alterations in the three-dimensional structures that DNA forms when it folds in on itself, known as topologically associated domains (TADs), determine which genes are turned on and off at a given time 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,” says Darío Lupiáñez, a geneticist at the Max Delbrück Center for Molecular Medicine (Germany) and one of the lead authors of the study.
More than 450 million years ago, the genome of a primitive fish, the ancestor of all vertebrate animals, doubled twice. The expansion of genetic material fueled 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.
To do this, the researchers have studied a type of stingray (Leucoraja erinacea) that, 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 the evolution”, explains Christina Paliou, biologist at CABD and one of the first authors of the study.
Una Raya. (Photo: Claire Fackler/CINMS/NOAA)
A turning point for evolutionary genomics
In 2017, the late CABD researcher José Luis Gómez-Skarmeta, an essential figure in evolutionary genomics in Spain, brought together scientists from all over the world to study the evolution of the skate. His interest was to investigate how genomes evolve structurally and functionally to promote the appearance of new traits.
That moment was pivotal for the field of evolutionary genomics. The scientists gained completely new insight into how the DNA of each cell, which can be up to two meters long, folds into a cell nucleus just 0.005 centimeters in diameter. These new studies showed that the packaging of DNA in the nucleus is far from random, but rather 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.
Rafael Acemel, a geneticist at the Max Delbrück center and one of the first authors of the study, 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.” To overcome this difficulty, the scientists used long-read sequencing technology, along with Hi-C data, to assemble the DNA pieces like a puzzle and map the jumbled sequences to the chromosomes of the streak. With this new reference, reconstructing the 3D structure of the TADs was finally possible.
With this new genome they were able to make comparisons with the genomes of their closest relatives, 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’s fins, which does not happen 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
Previous studies have shown that changes in 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, since 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, since it suggests that the 3D structure of the genome influences its evolution”, concludes Lupiáñez.
The study is titled “The little skate genome and the evolutionary emergence of wing-like fin appendages”. And it has been published in the academic journal Nature. (Source: CSIC)
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