Eukaryotic replication and chromatin

A single-molecule approach to reveal the dynamics of Eukaryotic DNA replication in chromatin.

Research overview

Replisome in the context of chromatin
Replisome in the context of chromatin

The copying, or replication, of DNA is one of the central processes that take place in all living organisms. Our understanding of DNA replication has made gigantic leaps forward since the discovery of the double helical form of DNA by Watson and Crick in 1953. We know many of the structures and functions of the proteins and enzymes involved. Many of these discoveries have been made by studying DNA replication in simple systems, such as viruses or bacteria. These continue to yield valuable insights, but recently, advances in the reconstitution of the yeast replisome have made it possible to gain insights into eukaryotic replication.

DNA replication is carried out at very high accuracy by nanometer-scale, multi-protein complexes known as replisomes. In eukaryotic organisms such as ourselves, the replisome consists of some twenty different proteins. Eukaryotic replication occurs in the context of chromatin: the meters of DNA in eukaryotic organisms are tightly packed into a higher-order structure called chromatin in order to fit in the tiny nucleus. The basic compaction unit of this condensed structure is a DNA-protein complex termed nucleosome which consists of a small piece of DNA wrapped around a core of so-called histone proteins. This compaction adds an extra layer of complexity to the replication process.

Our research focuses on understanding the molecular processes that underlie eukaryotic DNA replication in the context of chromatin, with the particular aim of gaining spatiotemporal insight into their dynamics by using our single-molecule biophysical expertise in replication and chromatin while integrating it with state-of-the-art molecular biology and biochemistry.

Approach

Eukaryotic replisome
Eukaryotic replisome

Despite tremendous advances in understanding chromatin replication achieved by experiments in genetics, cell biology, structural biology, and biochemistry, a detailed mechanistic understanding of how the replisome interacts with nucleosomes, histone chaperones, and chromatin remodelers still remains. The possibility of reconstituting an active yeast replisome in vitro in our lab (originally described by the Diffley laboratory in 2015) has opened up a new perspective, because when integrated with reconstituted forms of chromatin it provides the means to study chromatin replication in a precise, carefully controlled manner.

However, to really understand how the different processes that maintain robust chromatin replication occur in space and time requires probing the stoichiometry and dynamics of the individual proteins involved. Doing so requires a complementary approach to bulk biochemistry that can be found in single-molecule techniques. These high-resolution techniques, which include single-molecule fluorescence and single-molecule force spectroscopy, monitor individual biochemical processes under physiological conditions in real time and have demonstrated their value in revealing the dynamics of large protein complexes.

Researchers currently involved in these projects

  • Humberto S├ínchez
  • Kaley McCluskey
  • Daniel Ramirez Montero
  • Richard Janissen
  • Edo van Veen
  • Theo van Laar

Current collaborators

  • John Diffley Lab (Francis Crick Institute, UK)
  • Francesca Mattiroli Lab (Hubrecht Lab)
  • John van Noort Lab (Leiden University)
  • Alexandra Lusser Lab (University of Innsbruck Medical School, Austria)