Measuring Chromatin-nucleolus Interactions in Living Cells

Chromatin organization plays an important role in cellular processes. How chromatin is organized in the cell nucleus is crucial for genome function, such as gene expression. It has been shown by sequencing-based approaches that membraneless nuclear bodies, such as nucleoli and nuclear speckles can interact with chromatin and shape chromatin organization. The coupling constants of these chromatin-nuclear body interactions are important inputs for building chromatin organization models in the cell nucleus yet are not measured experimentally in living cells. Here, we measured the coupling constants of chromatin-nucleolus interactions in living human cells using an approach combining real-time genomic-locus dynamics, the Langevin equation, and a polymer model. We specifically labeled genomic loci on different chromosomes using CRISPR-Sirius, a CRISPR-based live-cell chromatin imaging technique and tracked the real-time dynamics of loci associated with nucleoli. Using the Langevin equation and polymer model, we can obtain effective force constants of chromatin-nucleolus interactions for different genomic loci associated with nucleoli and investigate their chromosome and genomic-region dependencies, which sheds light on chromatin-nuclear body interactions and provides insights into chromatin organization and nuclear architecture.