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How Two Meters of DNA Is Packaged Into a Human Cell

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The "Marie Kondo" of molecular biology

Cells are fascinating molecular factories. In one cell, a particular gene might be "turned on", so that the DNA code can be transcribed into mRNA and then translated into a protein that serves the cells function. In other cells, the very same gene might be "turned off", because it isn't required for that cell's particular purpose in an organism. Regardless of whether the gene is turned "on" or "off", the DNA encoding all genes is present in every single cell. That's a lot of information, and when you consider that a cell's nucleus – the organelle that contains the DNA code – is approximately six micrometers in size, it's clear that efficient storage is necessary.

DNA is packaged tightly into chromosomes, which resemble a string of beads under a microscope. From end to end, the chromosome of a human cell is approximately two meters long. While that may seem sizable, the crown for the largest genome discovered thus far belongs to a humble Japanese flower, Paris japonica, which is a staggering 149 billion nucleotides in size.

Across the animal kingdom, a specific family of proteins is responsible for folding DNA into loops. Arguably the Marie Kondo of the molecular biology world, these protein complexes – known as structural maintenance of chromosomes (SMCs) – are present in plants, bacteria and animals. In eukaryotic cells, SMCs include condensin, cohesin and a complex known as Smc5/6.

Scientists know that these complexes accomplish their organizational tasks through an association with chromosomal DNA. However, the molecular processes by which this is achieved has remained somewhat of a mystery – until now.

Professor Jan-Michael Peters, scientific director of the Research Institute of Molecular Pathology in Vienna has been studying cohesin in his laboratory for some time. "Genome folding has been studied since the 1970s and cohesin for 25 years, but that cohesin can fold DNA has only been proposed a few years ago and been experimentally demonstrated two years ago. How cohesin performs this function has remained a mystery but has been subject to numerous speculations," he says. In collaboration with Professor Peter Hinterdorfer, chair of biophysics and head of applied experimental biophysics at the University of Linz, Peters and colleagues address this question for the first time experimentally. Their work is published in the journal Cell.

Visualizing the cohesin complex

To visualize the workings of cohesin, the research team adopted a method known as atomic force microscopy. This technique is both unusual and remarkable, the researchers say. "Unlike other microscopes, it does not make use of light (photons) or electrons (like in electron microscopy) to generate images. Instead, it uses an ultrathin tip, which in ideal cases ends in a single atom, to 'touch’ the sample," explains Benedikt Bauer, postdoctoral researcher in the Peters lab. By "touching" the sample, it is possible to sense differences in the height of molecules, using this information to reconstruct an image. "It is like a blind person using a stick to detect things around them," Bauer adds. Years of training is required to obtain the high-speed atomic force microscopy recordings necessary to explore cohesin's properties.

Using this method, the scientists were able to visualize the cohesin complex and deduce its workings. It is shaped like a wishbone, comprising two extremities that connect via a hinge. The hinge makes the first contact with DNA and is able to bind to it with assistance from a protein called Nipped-B-like protein, or NIPBL. Next, the arms of the cohesin protein fold, and the hinge is able to swing in a fashion that hands the DNA over to the protein's extremities, meaning that another binding site can attach to the DNA.

The NIPBL protein maintains the contact between the arm's binding site and the DNA. In this way, the DNA is kept in place until cohesin's hinge can regain its original position, where it is available to grab another section of the DNA. Over repetitive cycles, this folds DNA into looped structures.

The researchers liken this process to the folding of a climbing rope, whereby you extend one of your arms to grab a part of the rope that is further away and bring the rope to your second hand. This second hand keeps the rope gripped while you once again reach for a more distant part of the rope. In cells, the energy required for cohesin's folding task comes from adenosine triphosphate (ATP).

Due to the small size of the cohesin protein and DNA, some of the team's model is based on indirect observations. Peters explains, "More work will therefore be required to test our model. In this sense, our work has some resemblance to work in astrophysics, where conclusions about the universe are also based on indirect evidence."

Cohesin's potential role in gene regulation

Understanding the methods by which DNA is packaged and folded is integral to exploring genome evolution and provides insights into gene regulation. "Complexes related to cohesin exist also in bacteria and are thought to fold their DNA, too," says Peters. "We therefore suspect that these complexes and their DNA folding activity evolved before bacteria and our cells (eukaryotic cells) separated, and that these complexes enabled the development of large DNA genomes. Understanding DNA folding by these complexes is therefore of very general interest for different fields, ranging from immunology to evolution."

Mutations in cohesin and NIPBL contribute to the rare disease Cornelia de Lange Syndrome that results in severe defects during development. "Cohesin mutations are also frequently found in human tumors, in particular in Ewing sarcoma, bladder cancer and the blood cancer acute myeloid leukemia," Peters says.

The exact role of the mutations in tumor development is not well understood, but it is possible that they contribute to tumorigenesis via gene regulation alterations. "By providing insight into how cohesin functions, our work has the potential to help explain how cohesin mutations contribute to these diseases," Peters notes.

The next step for the team is to further test their model and understand how the process characterized in this study is controlled inside of cells. They also wish to explore cohesin's role in gene regulation, recombination in the immune system and other "possibly unknown" functions.

Jan-Michael Peters and Benedikt Bauer were speaking to Molly Campbell, Science Writer for Technology Networks.

Reference: Bauer B, Davidson I, Canena D, et al. Cohesin mediates DNA loop extrusion by a ‘swing and clamp’ mechanism. Cell. doi: 10.1016/j.cell.2021.09.016.