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

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

A cartoon of a section of chromatin in the nucleus with replication origins in three different states.

Collapsing forks and checkpoints in DNA replication

The DNA replication checkpoint is essential for maintaining genome stability. Without it, when DNA copying restarts after a stall, too many replication origins—the starting points for copying—are mistakenly activated, ultimately leading to cell death. Researchers at the Crick showed, in human cells lacking this checkpoint, that excessive DNA synthesis from surplus origins consumes the vital replication proteins PCNA and RFC, preventing normal restart of stalled copying at replication forks. Without the protection of PCNA and RFC, the ends of the forks are attacked by a protein called HLTF, causing irreversible damage. Removing HLTF helps cells survive even in the absence of the checkpoint, which has implications for how resistance to anti-checkpoint cancer therapies may arise.

The DNA replication checkpoint prevents PCNA/RFC depletion to protect forks from HLTF-induced collapse in human cells

Published in Molecular Cell

Published

Diagrams of the human MCM and DNA

How are human MCM double hexamers loaded onto DNA?

The MCM helicase enzyme separates the two strands of the double helix, enabling DNA replication, with two copies of MCM (a “double hexamer”) marking where replication can start. We have a clear understanding of how double hexamers are loaded in yeast, but not in human cells. Researchers from the Crick reconstituted double hexamer loading with purified human proteins and determined the atomic structures. They found that, unlike in yeast, loading of a human double hexamer is sufficient to start opening DNA. Two alternate loading pathways exist to load human double hexamers. Loading factors that are essential in yeast only play a dispensable, regulatory role in the human system. Thus, while the double-hexamer loaders are conserved throughout evolution, how they function is different. This work begins to unravel how human cells regulate initiation of DNA replication, ensure that their genome is duplicated only once, and prevent chromosome instability and cancer.

MCM double hexamer loading visualized with human proteins

Published in Nature

Published

Cryo-EM structure of the ATPase motor, MCM, bound to the DNA double helix.

How do eukaryotic cells start bidirectional replication?

The ring-shaped MCM helicase enzyme is loaded around double-stranded DNA as a structure called a 'double hexamer' which is inactive before DNA is replicated. Upon activation, two split MCM single hexamers transition to encircling single-stranded DNA, establishing divergent replication forks. Researchers at the Crick investigated how this happens, by visualising helicase activation under the electron microscope. They found that Mcm10, the factor promoting initiation, wedges itself in between two MCM rings so that the double hexamer is broken in two. Mcm10 also constricts the MCM ring pore, forcing one of the two DNA strands to escape. These mechanisms ensure that chromosomes are replicated only once per cell cycle, preventing chromosome instability and cancer.

Unwinding of a eukaryotic origin of replication visualized by cryo-EM

Published in Nature Structural and Molecular Biology

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

Why do so many p53-positive tumours have whole genome duplication?

Whole-genome duplication (WGD) is a frequent event in cancer evolution and an important driver of aneuploidy—having an abnormal number of chromosomes. The role of the p53 tumour suppressor in WGD has been enigmatic: p53 can stop aneuploid cells from proliferating, acting as a barrier to WGD, but it can also promote mitotic bypass—a key step in WGD in which replication of DNA is uncoupled from the normal next step of cell division (mitosis).

In tumours containing normal p53, WGD is frequently associated with excessive amounts of the protein cyclin E1. The Diffley lab has now shown that too much cyclin E1 causes replicative stress, which arrests the cell cycle after DNA replication but before the cell divides. p53 then drives a process that promotes mitotic bypass, which would normally be a red flag to the cell, triggering a retreat into the safety of senescence. However, the excess cyclin E overrides senescence, allowing cells to complete endoreduplication. P53 therefore contributes to cancer evolution and hence progression by promoting WGD.

Cyclin E-induced replicative stress drives p53-dependent whole-genome duplication

Published in Cell

Published

Unravelling key step in DNA replication

Researchers in the Costa and Diffley labs have visualised the full process of the DNA double helix being untwisted and opened using cryo EM. The team observed that, after embracing the DNA, two enzymes drift away from each other in a process that deforms the double helix, initiating the process of DNA opening.

Mechanism of replication origin melting nucleated by CMG helicase assembly

Published in Nature

Published

Cell division in high resolution

Researchers in the Costa and Diffley labs have used high resolution cryo-electron microscopy techniques to observe replicative helicase activation following loading onto DNA. As a prelude to cell division, the genome must be duplicated, and replicative helicases play a fundamental part in this, unwinding DNA and exposing the single-stranded template for the replicative polymerases. The team characterised the role of the key enzymes involved in selectively activating the replicative helicases at the right time and in the right places on DNA, an important step forward in understanding exactly how DNA replication works in both health and disease.

Structural mechanism for the selective phosphorylation of DNA-loaded MCM double hexamers by the Dbf4-dependent kinase

Published in Nature Structural and Molecular Biology

Published

Mechanism of head-to-head MCM double-hexamer formation revealed by cryo-EM

The MCM replicative helicase is loaded onto duplex DNA as a double hexamer. Here we use time-resolved cryo-EM to show that ORC binds to its high affinity binding site to load the first MCM hexamer. ORC then releases this site and it, or another ORC molecule then binds the B2 element, which contains a degenerate ORC binding site. This binding is stabilised by a novel interaction between the Orc6 subunit of ORC and the N-terminus of the MCM hexamer. ORC then recruits and loads the second hexamer by the same mechanism as the first hexamer. We employed newly developed in silico reconstitution approaches to describe the full context of the helicase loading reaction, studied on a near-native, chromatinised origin of replication. This study radically changes our approach to investigating chromosome replication with cryo-EM.

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Published in Nature

Published

Bidirectional eukaryotic DNA replication is established by quasi-symmetrical helicase loading

This paper shows that loading of the MCM double hexamer is a quasi-symmetrical reaction: two ORC molecules bound at two opposing sites of different affinity each recruit and load a single hexamer. The distance between the ORC binding sites is not critical. Subsequent work has provided further evidence for this from cryo-EM.

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Published in Science

Published

Phosphopeptide binding by Sld3 links Dbf4-dependent kinase to MCM replicative helicase activation

Here we showed that Sld3, which we previously identified as being one of two essential cyclin dependent kinase (CDK) substrates in replication, is a phosphopeptide binding protein which binds specifically to Mcm4 and Mcm6 when they have been phosphorylated by Dbf4 dependent kinase (DDK). Sld3 then directly recruits Cdc45 to MCM and, via CDK phosphorylation, recruits the remaining firing factors. We had previously shown that Sld3 is also one of two targets of the DNA damage checkpoint kinase involved in inhibiting origin firing in response to DNA damage. Thus, Sld3 plays key roles with all three kinases that regulate replication (CDK, DDK, Rad53).

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Published in EMBO Journal

Published

The mechanism of eukaryotic CMG helicase activation

This paper provided the first view of how the inactive MCM double hexamer is converted to two active CMG helicases. We showed MCM remains bound to ADP after loading; firing factors trigger ADP-ATP exchange; ATP rebinding causes double hexamer splitting, initial DNA melting and CMG formation. Active helicases then translocate N-terminus first.

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Published in Nature

Published

Chromatin controls DNA replication origin selection, lagging-strand synthesis, and replication fork rates

In this and the accompanying paper (Yeeles et al. 2017 Mol Cel 65, 105-116) we describe the reconstitution of full chromatin replication. We first identified all of the factors required for complete and rapid replication of naked DNA. Then we identified and characterised factors required to replicate chromatinised templates. We showed FACT is essential for chromatin replication, whilst nucleosome remodellers and histone acetylases help chromatin replication. In addition, chromatin enforces origin specificity and Okazaki fragment processing. Finally, we found that histones are efficiently transferred to nascent DNA.

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Published in Molecular Cell

Published