A stingray’s dance on the ocean floor is graceful: its huge front flippers flap like wings as it glides under the sand. Precisely, the genetic cause behind the shape of its fins has been the subject of study carried out by CSIC researchers at the Centro Andaluz de Biologia do Desenvolvimento (CABD), in Seville, and at the Instituto de Investigações Biomédicas de Barcelona (IRBB).
The results, published in the journal Natureconfirm that changes in the three-dimensional structures that DNA forms when it folds back on itself, known as topologically associated domains (TADs), determine which genes are turned on and off at a given point in evolution.
Changes in the three-dimensional structures of DNA determine which genes are turned on and off in evolution
The researchers point out that genomic changes that alter TADs may be a factor in 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 main authors of the study.
More than 450 million years ago, the genome of a primitive fish, the ancestor of all vertebrate animals, doubled. The expansion of genetic material has 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 features that made us human, such as limbs.
Rays are one of the most distant vertebrate relatives of humans.
For this, the researchers studied a type of stingray (Leucoraja erinacea) which, due to the similarity of this species with ancestral vertebrates, “allows you to compare its characteristics with those of other species to determine what is new and what is ancestral during evolution.” , explains Christina Paliou, a biologist at the CABD and one of the first authors.
A turning point for evolutionary genomics
In 2017, the late CABD researcher José Luis Gómez-Skarmeta, a leading figure in evolutionary genomics, brought together scientists from around the world to study the evolution of skateboarding. His interest was in investigating how genomes evolve structurally and functionally to promote the emergence of new traits.
That moment was crucial for the field of evolutionary genomics. Scientists gained a completely new view of 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 have shown that DNA packaging in the nucleus is far from random, but organized into 3D structures called TADs, which contain genes and their regulatory sequences.
These structures ensure that the appropriate genes are turned on and off at a given time.
Juan Tena, co-lead author
“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 study’s lead authors.
Rafael Acemel, a geneticist at the Max Delbrück Center and one of the first authors, conducted experiments using Hi-C technology to elucidate the 3D structure of TADs. But interpreting the results was a challenge, as the scientists needed the complete skateboard genome as a reference point. “At the time, the reference consisted of thousands of small pieces of DNA sequence that were completely out of order, which wasn’t very helpful.”
The researchers used long-read sequencing to describe the complete skate genome.
To overcome this difficulty, the scientists used long-read sequencing technology, along with Hi-C data, to assemble the pieces of DNA like a jigsaw puzzle and map the confusing sequences to the chromosomes in the sequence. With this new reference, it was finally possible to reconstruct the 3D structure of the TADs.
With this new genome they were able to make comparisons with the genomes of their closest relatives, sharks, 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 close to the Hox genes, which also regulate fin development.
“This specific sequence can activate several Hox genes on the front part of stingray fins, which does not happen in other fish or tetrapod animals,” says Paliou. Later, scientists performed functional experiments that confirmed that these molecular changes contributed to the evolution of the characteristic shape of ray fins.
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.
The 3D structure of the genome influences its evolution
Darío Lupiáñez, molecular geneticist and author of the study
TADs are important for gene regulation, as 40% of them are conserved across all vertebrates, while the remaining 60% have evolved in one way or another. This evolutionary mechanism may be relatively frequent and explain many other interesting features of species that we observe in nature.
“This is an important discovery, as it suggests that the 3D structure of the genome influences its evolution”, concludes Lupiáñez.
Reference:
Marlétaz, F. et al. “The small skate genome and the evolutionary emergence of wing-like fin appendages”. Nature (2023)