Universal contact statistics of looped polymers resolve cohesin density and stoichiometry in vivo

Loop extrusion by cohesin complexes is central to genome organization, yet the stoichiometry of extrusion in vivo remains unresolved. Resolving this requires a quantitative link between microscopic loop density and macroscopic Hi-C contact statistics. We develop a perturbation theory for polymers decorated with quenched loops and measured under a finite Hi-C capture radius. The theory predicts a universal scaling law for the contact probability P ( s ): its logarithmic derivative displays a distinct minimum at genomic distance , determined solely by the loop–gap period T (inverse loop density) and the effective fragment length . This two-parameter reduction is validated by molecular-dynamics simulations of active loop extrusion and recapitulates short-scale features of Hi-C data. Applying the framework to mammalian datasets, we infer a conserved density of 6 ± 1 cohesin-mediated loops per megabase. Comparison with independent cohesin counts reveals near one-to-one correspondence between loops and complexes, providing quantitative evidence for monomeric loop extrusion. Our results establish a universal physical principle for short-scale chromatin folding and show how polymer theory bridges genome architecture with the molecular mechanisms that shape it.