A new wrinkle in turtles: Their genomes fold in a unique way, researchers find

As cells divide and replicate, DNA strands coiled around proteins -- chromatin -- are in tightly bundled chromosomes. After division, the chromosomes loosen and chromatin is less compact. How and where the chromatin fiber folds and loops onto itself affects what genes are activated. Findings from an Iowa State University-led research team offer new insight into this process that may have potential biomedical uses.

"The three-dimensional structure of the chromatin when it's folded matters for gene regulation. Where chromatin physically sits in the nucleus matters. The evolution of chromatin folding patterns alters genome function and developmental programs that drive phenotypic evolution and adaptation to changing environments," said Nicole Valenzuela, professor of ecology, evolution and organismal biology at Iowa State University. "Chromosome folding remains a bit of a black box. We've learned a lot about it, but it's still just the tip of the iceberg."

The shape and location of chromosomes during the post-division interphase of the cell cycle impacts gene function because it brings non-adjacent regions into contact, such as enhancer sequences and gene promoters. DNA readily available for interaction within active chromatin regions is more likely to be expressed, whereas DNA within less accessible repressed chromatin is silenced.

By analyzing how often different parts of DNA molecules contact each other, scientists have modeled the varying physical configurations of the chromatin in humans and many commonly researched animals, including mice and birds. Add turtles to the list, thanks to a research team Valenzuela helped lead. In a recent paper in Genome Research, the researchers described their study of the genomes of two species of turtles, which showed a surprising chromatin arrangement that hasn't been observed in other organisms.

A novel alignment

Chromosomes have a thinner junction point called a centromere and at their ends are protected by repetitive sequences of DNA called telomeres. In humans, chromosomes remain in separate territories inside the cell nucleus. But in the cells of some animals, like marsupials, chromosomes cluster so their centromeres can interact. In other animals, like birds, they cluster so telomeres are in contact. Turtles are the only animal studied so far where telomeres and centromeres are aligned to be near each other. These differences in folding and position translate into lineage-specific gene regulation.

"It's possible this is the ancestral condition of amniotes, from which mammals, birds and reptiles evolved in different patterns. The turtles may be showing us what existed at the beginning, shedding light on the evolution of vertebrate genomes," Valenzuela said.

Learning more about the three-dimensional genome structure of turtles and how it responds to environmental conditions could help explain the genetic basis of traits that could be leveraged for biomedical uses in humans. For instance, some turtles can survive weeks without oxygen, which could lead to treatment of strokes. Figuring out how some turtles can withstand extreme cold could benefit cryogenic preservation of human tissues.

"We want to understand more about why different lineages are different in some aspects and why they're the same in others, what parts we share and what parts differ," said Valenzuela, whose research focuses on turtles. "If we can reconstruct the evolutionary history of the changes that have taken place, we will be able to tell much more about how the differences in the packaging of the DNA and the folding of chromosomes might be affecting the traits we're interested in, how genes are regulated and how vertebrate genomes evolve. And understanding how turtle chromatin structure responds to external conditions also will benefit conservation efforts by helping predict the potential effect of environmental change on their biology."

The study was funded in part by two grants from the National Science Foundation.

Digging deeper

Studying the spatial organization of turtle genomes will continue to be an emphasis for Valenzuela's lab, she said.

Future plans include examining additional turtle species. The current study concerned the spiny softshell and northern giant musk turtles, but Valenzuela's research group has already collected the data to look at the genomic structure of four more species of turtles. She'd also like to compare turtles to crocodiles, lizards and snakes to see if their chromatin arranges in similar patterns.

To dig deeper on the function of turtles' chromatin folding, Valenzuela will study the liver organoids her lab developed for three species of turtles -- tiny, lab-grown balls of cells that mimic a simplified version of liver tissue.

More sophisticated mapping methods also will yield richer results, including higher-resolution data that produces even more detailed chromatin maps and techniques for studying how the 3-D chromatin structure changes over time and in different environments.

"To really do genotype-to-phenotype mapping, we have to get to this level of complexity," she said.