How rings and loops organize our DNA

12-04-2018

How are the meters of DNA arranged in our cell nucleus such that all individual genes can do their job? Chromosome biologist Benjamin Rowland of the Netherlands Cancer Institute has just started a new research project funded by the European Research Council (ERC) to find out how a minuscule ring ensures that the DNA is structured in the right way.

Gene regulation

Genes must pass on their information to the cell at the right time. This determines the behaviour of a cell in our body. If that goes wrong, people get sick. Genes are on or off, but they do not do that on their own.

Benjamin Rowland: 'Genes are carefully controlled by regulatory elements that also lie on the DNA, but they are often a long distance away from the gene. How can they regulate a gene from such a distance? This is possible because the DNA is folded into loops, so that distant parts of the DNA are brought close together. These loops are built by a ring-shaped protein complex called cohesin.' How cohesin makes loops and hereby organizes DNA is one of the main open questions in biology. With his ERC Consolidator Grant, Rowland wants to figure that out over the next five years. This month, Rowland starts with his project.

Rings

Cohesin was discovered about 20 years ago by the Oxford professor Kim Nasmyth, with whom Rowland would later become a post doc. Cohesin and the related condensin are ring-shaped protein complexes that each, in their own way, ensure that the DNA is organized in the correct manner. They do so in simple organisms such as yeast, but also in more complex ones such as humans. Rowland's research group investigates these rings, which have been revealing their secrets, step by step, over recent years. Because cohesin and condensin are so similar, new knowledge about one ring can also be used to learn about the other.

Shortening the DNA

Meters of DNA that fit into a cell nucleus of about 10 microns in diameter: how is that possible? Rowland: 'The DNA is divided over bite-sized pieces known as chromosomes. But each chromosome is still one long DNA strand of a few centimetres: about 10,000 times too long to simply fit in the cell. Cohesin and condensin both turn out to play a crucial role in structuring the DNA. When they were discovered, we already knew that they were important to the organism, but it is only over the last three or four years that we've come to understand just how important.'

Rings and loops structure the DNA (copyright Benjamin Rowland)

Cell division

Cohesin has two roles. First it was discovered that the ring plays an important role in cell division. After all 46 chromosomes are copied, they consist of two identical halves: one for each daughter cell. Cohesin rings keep the two copies firmly together until they are pulled apart and the cell can divide in two. Chromosomes have their iconic X-shape because the cohesin rings in the middle remain in place for the longest time. Condensin plays a different role, as it makes the chromosomes short and compact, which is also essential for a successful cell division. If cohesin or condensin does not function properly, the DNA is not accurately distributed over two daughter cells. This can lead to cancer or other detrimental diseases.

Loops in the DNA

But cohesin also does something else: it makes loops in the DNA that increase in size as long as cohesin is on the DNA. This is what Benjamin Rowland's group, in collaboration with Elzo de Wit's group, also in the Netherlands Cancer Institute, demonstrated experimentally last year. They have hereby confirmed a famous hypothesis that was launched in 2001 by the discoverer of cohesin, but that had never been demonstrated in a lab: the loop extrusion model. They also showed that the cell constantly makes loops that are then lost again. All of this keeps the DNA in motion so that genes can be turned on and off.

Discovering the mechanism

The researchers know the components of cohesin. They also know which molecule can open the ring, although its mechanism is still unknown. And they know the - severe - consequences when cohesin does not function properly. But how it all really works remains a black box and that needs to change in the coming years. Rowland: 'What is the driving force that leads to the formation of the loops? Does cohesin move along the DNA strand and does it provide the energy by itself? It is a good possibility, but the simple fact is that we just don't know. What role do individual components of the protein complex play? And do the loops in the DNA become larger because more cohesin rings are used, or because cohesin increases its speed?'

Interdisciplinary

'The cool thing about this research is that it is really interdisciplinary', says Rowland. 'We want to know everything about how these processes work, so we use all kinds of techniques to get to our answers. Because these techniques are often very new and specialized, we collaborate with many research groups both inside and outside the Netherlands Cancer Institute.'

A selection of methods and techniques: the researchers look at chromosomes with a super-resolution microscope, use a technique that shows which pieces of DNA interact with other pieces, and do genetic screens that pinpoint which gene is responsible for a process. And then they use biochemistry to figure out the precise mechanism. Rowland: 'With the Consolidator Grant, the ERC finances researchers who have successfully led their own research group for a couple of years. You are assessed by the scientific community. I think it's quite fantastic that eight anonymous referees apparently all really like our research.'