Single-Molecule Tracing Reveals Hidden Diversity in Worm Genome Organization

For the cell to function, this enormous amount of genetic material must be organized so that it does not become tangled, while genes remain accessible for reading, copying and repair. Researchers at the University of Basel have now discovered three distinct types of large chromosomal domains that help organize DNA within the nuclei of the roundworm Caenorhabditis elegans, a finding that challenges earlier assumptions about how genomes are arranged in this widely used model organism. Scientists have long known that chromosomes are not randomly distributed inside the nucleus.

Microscopy studies revealed distinct structures resembling small neighborhoods within the nuclear space, while molecular studies identified two major organizational principles: topologically associating domains, or TADs, in which neighboring stretches of DNA frequently interact with one another, and larger compartments in which TADs are grouped together. According to Professor Susan Mango, who led the study, there had long been a gap between what could be seen under the microscope and what molecular measurements suggested about DNA organization. Previous research had suggested that, unlike in vertebrates, TADs were largely absent from C. elegans.

However, those studies relied on measurements averaged across thousands of DNA molecules, an approach that could obscure individual structures. First author Dania Camila Pulido-Barrera took a different route. Using a microscopy-based technique called chromatin tracing, she examined individual DNA molecules one by one and grouped them according to their three-dimensional folding patterns.

When thousands of molecules are averaged together, important differences can disappear, she explained; looking at single molecules revealed structures that had previously remained hidden. The team applied this approach to chromosomes during early embryonic development in C. elegans, tracing individual DNA molecules to see how they fold and are organized within the nucleus. They identified three distinct types of large chromosomal domains within heterochromatin, the densely packed regions of the genome.

These domains differ not only in their three-dimensional structure but also in the mechanisms through which they form. One type closely resembles the TADs found in vertebrates. Another houses a set of genes critical for making ribosomes, the cellular factories that produce proteins.

This so-called 5S eICID domain is distinct from the well-known nucleolus and also behaves differently from the TAD-like domains. The big surprise, Pulido-Barrera noted, was the diversity: the researchers discovered different ways in which large regions of DNA can be organized within the cell nucleus. The findings, published in Nature Structural & Molecular Biology, challenge the previous assumption that C. elegans lacks large, clearly defined TAD-like domains on its autosomes.

They also suggest that fundamental principles of chromosome organization are more widespread across the animal kingdom than previously thought. The study leaves open what these structures actually do. Mango emphasized that the big question now is what function the different domains serve, what happens when they are disrupted, and how disruption affects gene regulation.

The research team plans to continue using C. elegans to investigate these questions, and the new study reinforces the model organism's suitability for such work. For now, the results stand as a reminder that averaging measurements across many molecules can mask biologically meaningful variation, and that single-molecule approaches can uncover genome structures that population-level methods miss.

Subject of Research: Single-molecule chromatin tracing of genome organization in C. elegans embryos

Article Title: Genome organization: More diverse than previously thought

Article References: Genome organization: More diverse than previously thought. Original publication (Bibliographic details unavailable.)

Image Credits: AI Generated

DOI: Not provided

Keywords: genome organization, chromatin tracing, TADs, heterochromatin, C. elegans, nucleus, embryonic development, chromosomes, gene regulation, University of Basel, single-molecule microscopy, 5S eICID