Publication highlights

Go inside our research

Explore a selection of research case studies from the past five years.

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Intro

Researchers at the Crick are tackling the big questions about human health and disease, and new findings are published every week.

Our faculty have picked some of the most significant papers published by Crick scientists, all of which are freely available thanks to our open science policy.

Highlights

Chromosome shape changes over time

X doesn’t always mark the spot: researchers challenge idea of chromosome shape

An international group of researchers from the Crick, Imperial College London, Waseda University and the Cancer Institute of the Japanese Foundation for Cancer Research have redrawn the idea of chromosome shape, finding that they’re not always stable X-shaped structures but are constantly in flux as cell division takes place. They live-imaged chromosomes over time, observing that they become continuously shorter and thicker, and that they are aiming for a 'final roundness' - a ratio of length and width that's the most physically stable. Using computer simulations, they showed that longer chains reach far longer to reach a stable length, suggesting that they aren't in a steady state at cell division, whereas shorter chains reach a steady state almost straight away. The team conclude that the length of time chromosomes spend in mitosis dictates whether they will all reach a final shape or not.

Progressive chromosome shape changes during cell divisions

Published in EMBO Reports

Published

DNA double helix

How genetic copies stick together during replication: sister chromatid cohesion via other mehanisms

Sister chromatids of DNA are held together by a ring-shaped protein complex called cohesin, and scientists have long pondered how the DNA-copying machinery manages to navigate genetic strands while encountering cohesin rings. After finding that the replisome can travel through the cohesin ring, a multidisciplinary team of researchers at the Crick investigated sister chromatid cohesion in more detail. They often observed that cohesin hugged just a single DNA copy after replication, and that a structure called the 'cohesin loader' appears to intervene and bring the second chromatid into the ring. They also showed that sometimes more cohesin molecules are used, bringing together the chromatids in a two-step process involving additional cohesin molecules to those present before replication.

Biochemical reconstitution of sister chromatid cohesion establishment during DNA replication

Published in Molecular Cell

Published

DNA double helix

How genetic copies stick together during replication: cohesin throws its hat into the ring

Sister chromatids of DNA are held together by a ring-shaped protein complex called cohesin, and scientists have long pondered how the DNA-copying machinery manages to navigate genetic strands while encountering cohesin rings. A multidisciplinary team of researchers at the Crick use a biological reconstitution method to explore this. When they loaded cohesin onto DNA and added the replisome, in some cases they witnessed the replisome travelling through the ring. Additionally, the more replisome components they added, the more efficiently the complex passed through the rings, despite its increased size. Finally, the team showed that the components responsible for helping the replisome pass through the cohesin ring where DNA polymerase enzymes. In a complimentary paper, they also showed that there are other ways for the replisome to bypass cohesin rings.

Replisome passage through the cohesin ring

Published in Cell

Published

Diagram

A new take on cell signalling decisions

When we think about cell signalling, be it developmental transitions, or be it the sequential events that make up the cell growth and division cycle, we think of regulators. Typically, a kinase is thought to exert control over downstream events, such as the cyclin-dependent kinase (CDK), which has master control over cell cycle progression. Researchers at the Crick revisit how CDK phosphorylates each of its many cell cycle targets at the right time. Not merely a decision by the kinase, they realise that the substrates themselves contribute to deciding when their phosphorylation time has come. ‘Substrate control’ likely more widely forms part of cell signalling decisions.

Evidence of substrate control of Cdk phosphorylation during the budding yeast cell cycle

Published in Cell Reports

Published

Loop capture explained using rope (DNA) and carabiner (cohesin)

New mechanism identified to keep DNA organised

Researchers in the Chromosome Segregation Laboratory and the Mechanobiology and Biophysics Laboratory have proposed a new model for how loops in DNA are created in order to keep DNA strands organised. A ring-shaped protein called cohesin is responsible for embracing two sister DNA strands, and also for creating loops within each strand. A popular theory for how cohesin forms these DNA loops is called ‘loop extrusion’. This idea is based on lab experiments where cohesin wraps around a strand of DNA and pulls the loop through the ‘ring’. Crick researchers tested this theory in live cells, by creating yeast with mutated cohesin that couldn’t extrude DNA loops. To their surprise, the DNA was still able to form loops. This resulted from two places on the same DNA being entrapped by a cohesin ring, in which the researchers call the ‘loop capture’ mechanism.

An extrinsic motor directs chromatin loop formation by cohesin

Published in The EMBO Journal

Published

Mechanical disengagement of the cohesin ring

Mechanical disengagement of the cohesin ring

In healthy cell division, the replicated DNA forms sister chromatids that must remain connected until separation later in the process. It’s only then that X-shaped chromosomes must be segregated symmetrically: each sister chromatid (one half of the X) is pulled to the opposite edges of the dividing cell by microtubules - protein filaments that generate force – to give rise to two daughter cells with an equal amount of genetic material. A ring-shaped protein called cohesin physically links sister chromatids and, like an elastic band, resists the forces generated by microtubules. Not only is the absence of cohesion lethal, but mutations in it can lead to cancer and incurable developmental disorders.

In this research by the Molodtsov and Uhlmann groups, the force that the cohesin complex can withstand is revealed. Using optical tweezers, the researchers pulled apart the DNA molecules tied by cohesin, showing that one cohesin ring is capable of embracing two DNAs and can resist up to 20 piconewtons of force, and when it breaks, it always opens at its weakest point: the hinge domain. These findings reveal that 40 cohesins are sufficient to oppose the tension generated in mitosis, whilst larger forces release the sisters. For the first time, this work lifts the veil on cohesin’s physical properties, bringing us closer to understanding how it is dysregulated in disease.

Mechanical disengagement of the cohesin ring

Published in Nature Structural and Molecular Biology

Published

How condesin packs up chromosomes

Condensin stitches up pieces of DNA to weave the fabric of a chromosome

Long DNA molecules form the basis of our lives, and these must be intricately packed into chromosomes to be passed on from one cell generation to the next.

Key to DNA compaction is a ring-shaped protein complex called condensin. How condensin achieves this miraculous task remained mysterious. A popular idea is that condensin extrudes DNA loops, much like threading pieces of string through the eye of a needle. However, chromosomal DNA exists in a form that is likely too bulky to slide through the eye. In search for an alternative mechanism, Crick researchers made pure condensin and examined how it engages with DNA in a test tube. This approach revealed the striking ability of condensin to sequentially entrap two DNA molecules that find each other by pure chance. The researchers even watched this process happen in front of their own eyes using a specialized microscope. Collaborators from Hokkaido University in turn found compelling evidence for the new capture mechanism inside chromosomes of living cells. Together, these results change our way of thinking about chromosomes: condensin stitches up pieces of DNA to weave the fabric of a chromosome.

Establishment of dsDNA-dsDNA interactions by the condensin complex

Published in Molecular Cell

Published

The link between DNA replication and faithful chromosome segregation

Faithful chromosome segregation to daughter cells involves an additional critical feature, namely that the two newly synthesised products of DNA replication, the sister chromatids, stay connected to one another. This process, known as sister chromatid cohesion, allows the cell division machinery to recognise replication products for faithful segregation into daughter cells during cell divisions. Sister chromatid cohesion is mediated by cohesin, a ring-shaped protein complex that topologically entraps the two sister DNAs. The process requires modification—in this case acetylation—of conserved cohesin lysine residues. The Uhlmann lab, in collaboration with John Diffley’s group, has now shown how this process is linked to DNA replication. Reconstitution in a test tube of replication-coupled cohesin acetylation reveals that flaps or nicks, transient DNA structures which form during DNA replication, are transient molecular clues that direct cohesin acetylation next to where cohesin likely co-entraps the replication products. These important results give the first detailed explanation of how DNA replication is linked to sister chromatid cohesion establishment.

A replication fork determinant for the establishment of sister chromatid cohesion

Published in Cell

Published

DNA entry into and exit out of the cohesin ring by an interlocking gate mechanism

Building on our successful biochemical reconstitution of topological cohesin loading onto DNA, we completed the reconstitution of both dynamic loading as well as unloading. We realised that both loading and unloading follow a very similar trajectory through sequential ATPase and kleisin gates, only one of which can be open at any one time. This formed the basis for our unified DNA passage proposal both into and out of the ring.

View the publication

Published in Cell

Published

A structure-based mechanism for DNA entry into the cohesin ring

Cohesin is a ring-shaped protein complex that topologically entraps DNA to fulfil key functions in chromosome architecture. In a collaborative and multidisciplinary approach, we used cryo-EM, biochemical and biophysical techniques to describe how ATP-fuelled structural changes of the cohesin complex drive the DNA entry reaction into the cohesin ring. This solves one of the outstanding riddles in molecular biology.

View the publication

Published in Molecular Cell

Published