Despite countless advances in the field of genetics, some processes happening in our DNA still remain a mystery – one which scientists are working hard to solve in its entirety – and the most recent breakthrough allows them to see those loops in more detail than ever.
Indeed, the scientists at the European Molecular Biology Laboratory (EMBL) have managed to observe how a human cell archives the process in which chromosomes form a compact X-shaped structure with two rod-like copies when preparing for transport to daughter cells during cell division, per a report by News Medical on March 24.
Setting out to solve condensin mutations
Specifically, Kai Beckwith, a former postdoc in EMBL Heidelberg’s Ellenberg Group and currently an associate professor at the Norwegian University of Science and Technology (NTNU), wanted to solve the problem of mutations in the structure of condensins.
These are large protein complexes binding DNA during cell division and extruding it to create loops of varying sizes, the mutations of which can lead to severe chromosome segregation defects and, ultimately, cell death, cancer formation, or rare developmental disorders called ‘condensinopathies.’
So far, observing how this looping process takes place on the cellular scale and contributes to chromosome structure has been rather difficult, as Andreas Brunner, a postdoc in the Ellenberg Group and lead author of the new paper, pointed out. In his words:
“This is because methods for visualizing DNA with high resolution are usually chemically harsh and require high temperatures, which together disrupt the native structure of DNA.”
High-res chromatin tracing method at work
However, using the newest method, the team carefully removed one strand of DNA in cells at various stages of cell division while keeping the chromosome structure intact. This enabled them to apply targeted sets of DNA-binding labels to observe the nanoscale structure of the uncovered DNA strand.
As such, the innovative technique, which they dubbed LoopTrace, allowed the scientists to directly observe DNA in cells during division as it progressively formed loops and folds. Commenting on this significant scientific achievement, Beckwith explained:
“Andreas and I were now able to visualize the structure of chromosomes as they started to change shape. (…) This was crucial for understanding how the DNA was folded by the condensin complexes.”
Following this development, the researchers saw that DNA forms loops in two stages during cell division. First, it creates stable large loops, which then subdivide into smaller, transient, nested loops, increasing their compaction incrementally at each stage, the process enabled by two types of condensin proteins.
As Beckwith emphasized:
“We realized that these condensin-driven loops are much larger than previously thought and that it was very important that the large loops overlap to a significant extent. (…) Only these features allowed us to recapitulate the native structure of mitotic chromosomes in our model and understand how they can be segregated during cell division.”
Ultimately, the new chromatin tracing model based on the overlapping loop structure in the long DNA molecules confirmed that the physical repulsion between these loops is sufficient for them to stack up and generate the rod-shaped chromosomes observed under the microscope.
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