When the genome shuffles but the animal doesn't change: a new approach to understanding gene regulation

Imatge de Oikopleura dioica

In the animal kingdom, variations in gene expression patterns during development can trigger new phenotypes and enhance evolution and adaptation. Genome restructuring is one of the evolutionary mechanisms that allow the creation of biodiversity. Despite being a widely documented phenomenon, it is still not understood how a genome maintains its gene regulation after such rearrangements, a question that remains open in evolutionary biology.

Oikopleura dioica is a small planktonic marine chordate widely distributed in the world's oceans. Although different populations show an extreme degree of genomic mixing—with genome translocations and reorganizations—the animal maintains a virtually identical morphology throughout. This contrast has made the species an exceptional model to study how gene regulatory networks remain stable amidst great structural variability in the genome.

Reading the genome in action

Researchers Nuria Torres-Águila and Maria Rosselló, from the Institute for Biodiversity Research of the University of Barcelona (IRBio), funded with a competitive grant PR IRBio 2024, have applied the Assay for Transposase-Accessible Chromatin using sequencing (ATAC-seq) technique to embryos of O. dioica from the Barcelona population. This methodology allows the identification of regions of the genome that are “open” and accessible to the transcription machinery, which activates genes, offering a unique key window to understand when and how genes are activated during development.

The team has successfully established the working protocol —including the optimization of the cell dissociation protocol with ACME;— and has obtained the first data on chromatin opening at the incipient embryonic tailbud stage, when cell fate specifications begin.

Researchers from the Institute for Research on Biodiversity (IRBio) of the University of Barcelona have implemented the ATAC-seq technique for the first time in Oikopleura dioica, a marine organism with one of the most restructured genomes in the animal kingdom. The results open the door to understanding how gene regulation mechanisms are conserved despite drastic changes in the organization of the genome.

A first step to compare populations with reorganized genomes

These results establish the methodological foundations necessary to be able to apply this technique in other populations of Oikopleura dioica and compare how the genome is regulated between lineages with such different chromosomal organizations. Understanding this mechanism could provide new knowledge about how organisms maintain their biological identity.

Grants that drive careers.

The researchers highlight that these PR-IRBio grants promote collaboration between groups that has allowed them to grow professionally in the management and coordination of projects, such as in bioinformatics analysis and nucleus purification techniques. These new learnings and skills will be key in their future research paths.
The project has also served as the basis for the design of a new study focused on the evolutionary impact of genomic rearrangements in O. dioica.

Finally, this collaboration between groups and the execution of this project is key in the academic future of both researchers as it demonstrates their leadership capacity, a very important skill in order to apply for more senior research positions.

@IRBio