Simulation and quantitative analysis of spatial centromere distribution patterns

A prominent feature of eukaryotic chromosomes are centromeres, which are specialized regions of repetitive DNA required for faithful chromosome segregation during cell division. In interphase cells centromeres are non-randomly positioned in the three-dimensional space of the nucleus in a cell-type specific manner. The functional relevance and the cellular mechanisms underlying this observation are unknown, and quantitative methods to measure distribution patterns of centromeres in 3D space are needed. Here we have developed an analytical framework that combines robust clustering metrics and advanced modeling techniques for the quantitative analysis of centromere distributions at the single cell level. To identify a robust quantitative measure for centromere clustering, we benchmarked six metrics for their ability to sensitively detect changes in centromere distribution patterns from high-throughput imaging data of human cells, both under normal conditions and upon experimental perturbation of centromere distribution. We find that Ripley’s K Score has the highest accuracy with minimal sensitivity to variations in centromeres number, making it the most suitable metric for measuring centromere distributions. As a complementary approach, we also developed and validated spatial models to replicate centromere distribution patterns, and we show that a radially shifted Gaussian distribution best represents the centromere patterns seen in human cells. Our approach creates tools for the quantitative characterization of spatial centromere distributions with applications in both targeted studies of centromere organization as well as in unbiased screening approaches.