TopoLoop: A new tool for chromatin loop detection in live cells via single-particle tracking

Abstract

We present a novel method for identifying topological features of chromatin domains in live cells using single-particle tracking and topological data analysis (TDA). By applying TDA to particle trajectories, we can effectively detect complex spatial patterns, such as loops, that are often missed by traditional time series analysis. Using simulations of polymer bead–spring chains, we have validated the accuracy of our method and determined its limitations for detecting loops. Our approach offers a promising avenue for exploring the topological complexity of chromatin in living cells using TDA techniques.