A recent study has unveiled the unique three-dimensional structure of turtle genomes, revealing a configuration that stands out from all other known animal genomes.
DNA, composed of long sequences of nucleotides, is a treasure trove of genetic information that serves as a guide for living beings—essentially the blueprint of life. However, the way this blueprint is organized significantly influences how it is interpreted and utilized.
During cell division, DNA strands wrapped around proteins—known as chromatin—form tightly packed chromosomes. After a cell splits, these chromosomes relax, and the chromatin becomes less condensed. The manner in which these chromatin fibers fold and loop impacts the activation of genes. Research led by a team from Iowa State University sheds new light on this intricate process, which may have important biomedical implications.
“The three-dimensional configuration of folded chromatin is crucial for gene regulation. The spatial positioning of chromatin within the nucleus influences its function. Changes in chromatin folding can impact genome function as well as developmental pathways, driving evolution and adaptation to varying conditions,” stated Nicole Valenzuela, a professor specializing in ecology, evolution, and organismal biology at Iowa State University. “The intricacies of chromosome folding remain somewhat elusive. Although we’ve gained significant insights, we have only begun to scratch the surface.”
The spatial arrangement and shape of chromosomes during the interphase stage of the cell cycle, following division, are vital for gene function, as they facilitate contact between distant regions—like enhancer sequences and gene promoters. DNA that is easily accessible within active chromatin regions is more prone to expression, whereas DNA situated within the less accessible repressed chromatin remains inactive.
By examining how often various regions of DNA interact with one another, researchers have created models of the different structural configurations of chromatin found in humans and other commonly examined species, such as mice and birds. Turtles can now be added to this list, thanks to the efforts of Valenzuela’s research team. In a recent publication in Genome Research, the researchers detailed their findings on the genomes of two turtle species, revealing a surprising chromatin arrangement previously unseen in other organisms.
A distinctive arrangement
Chromosomes feature a central part known as a centromere, and their ends are capped with repetitive DNA sequences called telomeres. In humans, chromosomes exist in separate regions within the cell nucleus, while in certain animals, like marsupials, chromosomes gather to allow centromere interaction. In other species, such as birds, they cluster primarily to bring telomeres into proximity. Notably, turtles are the only animals studied so far where telomeres and centromeres are positioned closely together. These variations in folding and organization result in unique gene regulation specific to different lineages.
“This arrangement may represent the ancestral state of amniotes, the group from which mammals, birds, and reptiles diverged in distinct ways. Turtles might be showing us a glimpse into our evolutionary beginnings, providing insights into the development of vertebrate genomes,” Valenzuela explained.
By enhancing our understanding of the three-dimensional genome structure in turtles and its response to environmental factors, researchers aim to uncover the genetic foundations of traits that could benefit human medicine. For example, some turtles can endure extended periods without oxygen, which might inspire treatments for stroke patients. Similarly, insight into how certain turtles withstand extreme cold could improve cryopreservation techniques for human tissues.
“We strive to comprehend why different lineages exhibit both similarities and differences, identifying shared features and distinct traits,” Valenzuela noted, emphasizing her focus on turtle biology. “By reconstructing the evolutionary progression of these changes, we can gain a clearer picture of how the organization and folding of DNA influence the traits we are interested in, gene regulation, and the evolution of vertebrate genomes. Furthermore, understanding how turtle chromatin structures react to external factors will aid conservation efforts by anticipating how environmental changes could impact their biology.”
The research received partial funding from two grants provided by the National Science Foundation.
Looking ahead
Valenzuela’s lab plans to continue investigating the spatial organization of turtle genomes. Future objectives include studying additional turtle species. While the current research focused on spiny softshell and northern giant musk turtles, Valenzuela’s team has already collected data from four more turtle species for further examination. Additionally, she hopes to compare turtle genomes with those of crocodiles, lizards, and snakes to determine if similar chromatin arrangements exist among them.
To delve deeper into the functionality of turtle chromatin folding, Valenzuela plans to study liver organoids—small, lab-grown cell clusters resembling liver tissue—that her lab has created for three turtle species.
More advanced mapping techniques will also enhance future studies, yielding high-resolution data for producing detailed chromatin maps and exploring how the three-dimensional chromatin architecture changes over time and in response to different environments.
“To effectively connect genotype to phenotype, we need to achieve this level of complexity,” she added.