During cell division, our genetic material is concentrated in the chromosomes and packed tightly with the help of auxiliary structures. New analyzes now confirm that the chromatin in the chromosomes is coiled up in spiral turns. The density and size of the coils depends, among other things, on the position in the genome and the gene density on the DNA, as the researchers determined using the example of barley chromosomes. The spiral structure of chromatin refutes non-helical models of chromosome structure and confirms helical models, according to which the chromatin in metaphase chromosomes in metaphase chromosomes is probably arranged in a spiral manner in all higher organisms. Whether the spirals of the sister chromatids turn in the same direction or in opposite directions is flexible and varies depending on the species.
The DNA is the carrier of our genetic information and thus a kind of reference library for all our cells. It is correspondingly extensive: the DNA from a single human cell alone is around two meters long, and in some plants there is almost 100 meters of DNA in each cell. This is normally loosely tangled in lumps in the cell nucleus. Before each cell division, however, the genetic material has to be converted into a compact “transport form”: the chromosomes. How exactly this neat packaging of the DNA takes place was unclear for a long time. In recent years, however, scientists have gained more insight into these mechanisms. Accordingly, so-called condensin proteins lay the DNA in loops and folds, bringing it step by step into a condensed form. This compact DNA is then further packaged with the participation of so-called histone proteins in the chromatin of the chromosomes. Only through this mechanism can the DNA be compressed tens of thousands of times and tied together into compact chromosomes.
Spiral or non-helical fold?
Up until now, however, there has been a dispute as to how the chromatin is arranged in the chromosomes. Some models assume that in the metaphase of mitosis, the chromatin is arranged in a spiral in each sister chromatid, called the chromonema. In contrast, non-helical models assume that the chromatin is folded within the chromatids without forming a spiral. “Textbook depictions suggest that chromosome ultrastructure is well understood. But that is not the case,” says senior author Veit Schubert from the Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) in Gatersleben. It is true that microscopic analyzes suggested a spiral winding in various plant cells, in chickens and also in human cell cultures. However, other studies could not find this spiral structure. Direct visualization of the coiled chromonema to confirm the spiral model was lacking.
The team led by Schubert and first author Ivona Kubalova has now succeeded in doing this. For their study, the scientists used high-resolution microscopy techniques, conformational detection (Hi-C) on isolated mitotic chromosomes and a special fluorescent labeling of individual DNA sections to visualize the superordinate structure of the chromatin in the chromosomes. They used the genome of cultivated barley (Hordeum vulgare) as a model organism because its genome, which has a total of 4.88 billion base pairs, forms particularly large chromosomes. In addition, the condensed metaphase chromosomes in this plant can be isolated and examined particularly well.
Spiral chromonema confirmed
The analyzes showed that the chromatin in the chromosomes of barley is indeed spirally wound. “The convoluted chromatid organization and its organizational unit, the chromonema, were independently confirmed using different methods,” says Schubert. Using conformational mapping, they were also able to determine how many turns this chromatin spiral has; “We found that the barley chromosomes, which are between 522 and 675 megabases long, have between 18 and 23 turns, depending on their size,” the scientists report. “A single helical turn comprises 20 to 38 megabases of DNA and forms a fiber around 400 nanometers thick, which we call a chromonema,” says Schubert’s colleague Amanda Camara. In barley, the spiral turns of the sister chromatids are each rotated in the same direction, while the spirals in human cells and some other plants show mirror-image turns. “In some plant genera, the direction of rotation can even switch at the centromere and different parts of the arms,” say the researchers.
According to Schubert and his team, this indicates that the control mechanisms do not always act uniformly throughout the chromosome. “It appears that the helical direction of rotation of the chromonema is flexible rather than strictly determined,” the scientists write. The tightness of the turns also seems to be linked to the gene density on the DNA. “This suggests a possible involvement of epigenetic processes, mainly through histone modifications, which can locally regulate the structure of chromosomes at mitosis,” the team said. At the centromere of the chromosomes – the middle of the “X” – the chromatin also forms smooth, parallel strands instead of spirals, as the analyzes revealed. The same applies to the nucleolus organizer regions located on the short arms of some chromosomes, which are important for the formation of the nucleoli. They are also constricted and structured in parallel.
The researchers hypothesize that this structure represents a general mechanism for the formation of condensed mitotic chromosomes that is applicable to all eukaryotes with a wide range of genome sizes. “We expect that after our study, the chromonema-based organization of chromosomes will be confirmed in a larger number of plant and animal species with large chromosomes,” says Camara.
Source: Ivona Kubalova (Leibniz Institute for Plant Genetics and Crop Plant Research (IPK), Gatersleben) et al., Nucleic Acids Research, doi: 10.1093/nar/gkad028