Project P20

About

The cohesin complex is crucial for the spatial arrangement of chromatin in the cell nucleus and involved in many fundamental processes including cell division, DNA replication, DNA repair and gene expression. How cohesin regulates gene expression is not well understood. Cohesin is a ring-shaped protein complex, which can entrap two chromatin fibers for example during replication or sister chromatid cohesion. Besides these more canonical functions, cohesin generates also chromatin loops during interphase in a process called loop extrusion. In this process cohesin walks along the chromatin fiber to extrude kilobase- to megabase-sized loops depending on the organism. Loop extrusion and the resulting folding of chromatin can influence gene expression most-likely by altering promoter-enhancer contacts. However, the underlying mechanism is not fully understood as depletion of cohesin only results in the downregulation of a subset of genes. To fully understand the role of cohesin in gene expression, we first need to re-evaluate the role of cohesin in chromatin folding to distinguish direct from indirect effects. Recently, we could reconstitute chromatin domains from S. cerevisiae by using a genome-wide in vitro reconstitution approach, which is free of interfering processes like transcription or replication. Upon reconstitution of regular, in vivo-like nucleosome positioning with ATP-dependent chromatin remodeling enzymes (remodelers), we could reconstitute chromatin domains in vitro. This showed that nucleosome positioning plays an important role in the 3D chromatin organization. Here, we will use this approach to define now the direct impact of cohesin function on the 3D chromatin organization and how cohesin activity is regulated by remodelers. Long-term, this re-evaluation will allow us to get a better understanding of how cohesin and the 3D chromatin organization contribute to changes in gene expression.