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.
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.
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)
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
'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.'