Structural biology of chromosome folding and dysregulation in disease

The elucidation of the structure of DNA in 1953 kick-started the revolution in life science research and marked the beginning of modern molecular biology. While we do know the structure of DNA at atomic level resolution, it is still mysterious how DNA is packaged in the cell. Human genomic DNA that, if it were stretched out, would reach over two meters in total. In a cell, all this DNA needs to be compacted into a micron-sized nucleus. One basic unit of coiling DNA is the nucleosome, which has for decades been viewed as the first step in condensation of the DNA. However, it is now clear that the main function of nucleosomes is not to enable large-scale genome packaging. Instead, higher-order genome folding is mediated by Structural maintenance of chromosomes (SMC) proteins, an ancient class of ATPases that is found in all domains of life. SMC proteins are large, ring-shaped proteins that act by DNA loop extrusion. While the details are currently unknown, the consequences are that SMC proteins organise DNA into large, dynamic loops.

It is becoming increasingly apparent that this chromosome folding reaction is important for many of the most fundamental aspects of genome biology: control of gene regulation by distant regulatory elements, genome replication and repair as well as chromosome segregation during mitosis and meiosis. There are indications that mutation of cohesin subunits plays an important role in a number of cancers and 'cohesinopathies'.

We here propose to address two key aspects of this genome folding reaction catalysed by cohesin, on such SMC protein complex. We aim to understand: 1. The structural mechanism of how cohesin catalyses 3D genome folding, and 2. The mechanism that allows cohesin to be deployed during a number of different genome transactions.

To achieve these goals, we need to understand better the structure of cohesin holocomplexes and how they interact with DNA and catalyse folding. We also need to address how cohesin interacts with regulators that allow specific deployment during different genome transactions.

The different protein subunits of the cohesin complex are mutated in many 'Cohesinopathies' that range from cancer to developmental disorders. More specifically, cohesin dysregulation during meiosis in oocytes can lead to mis-segregation of chromosomes resulting in cells with the wrong number of chromosomes, a hallmark of Down's syndrome (Trisomy 21) and a leading cause of age-related aneuploidy and infertility. Mutations in the cohesin complex are associated with genetic diseases such as Cornelia de Lange and Roberts syndrome which result in severe development defects. Cohesin mutations also can result in genomic instability due to mis-processing of chromosome loops, dysregulation of chromosome replication, repair or segregation. Mis-processing of loops may be at the origin of extrachromosomal DNA loops that overexpress oncogenes and have been identified with high frequency in half of all solid tumor cancers.

We therefore need a much better understanding of the molecular mechanisms of cohesin function, regulation and deployment in different chromatin transactions. This will allow us to better understand how mutations contribute to disease. This in turn will allow us to better understand the molecular mechanisms underlying different diseases and to potentially develop new approaches in treatment against cohesin-related cancer and Cohesinopathies. The long-standing challenge will be to understand how the molecular mechanism of genome folding leads to hierarchical genome organisation, and how such organisation leads to emergent properties of genome function (such as long-range gene regulation) and how dysregulation contributes to disease.

The cohesin complex is a multisubunit, dynamic molecular machine comprised of four core subunits, SMC1, SMC3, SCC1 and SA1/2 as well as a number of regulatory factors that are required for DNA loading and translocation (SCC2/SCC4), to stabilise cohesin on DNA (PDS5 and ESCO1 acetylation) and that enable cohesin release (WAPL). The long-term goal is to understand the molecular mechanism by which cohesin entraps DNA and catalyses loop extrusion and that allows cohesin deployment in a number of important genome transactions.

We have recently determined structures of a series of cohesin subcomplexes, mostly using xray crystallography. To understand how accessory factors control cohesin function one needs to capture the complex in defined compositional and conformational states. We here propose to use a structural, biochemical and cell biological biology approach to better understand the structures of larger cohesin complexes bound to different accessory factors. We will also create and test defined mutations (in vitro and vivo) for effects on biological function.

The different protein subunits of the cohesin complex are mutated in many 'Cohesinopathies' that range from cancer to developmental disorders. More specifically, cohesin dysregulation during meiosis in oocytes can lead to mis-segregation of chromosomes resulting in cells with the wrong number of chromosomes, a hallmark of Down's syndrome (Trisomy 21) and is a leading cause of age-related aneuploidy and infertility. Mutations in the cohesin complex are associated with genetic diseases such as Cornelia de Lange and Roberts syndrome which result in severe development defects. Cohesin mutations also can result in genomic instability due to mis-processing of chromosome loops, dysregulation of chromosome replication, repair or segregation. Our work will form the basis for a more detailed understanding of cohesin function and dysregulation in disease.