Chromatin Dynamics are Highly Subdiffusive Across Seven Orders of Magnitude

Abstract

Chromatin dynamics control the timescales of essential biological processes including DNA damage repair and activation of gene promoters by distal enhancers. Prior chromatin dynamics studies have reported widely varying degrees of subdiffusion, likely due to technical limitations. Here, we integrate MINFLUX--a recently developed single particle tracking method capable of achieving microsecond time resolution--with traditional tracking methodologies. We tracked chromatin dynamics across seven orders of magnitude in time in both human and mouse cells and found strongly subdiffusive dynamics ( [~] 0.3). These dynamics are only mildly sensitive to perturbations of transcription, histone acetylation, and topoisomerase II, while loop extrusion has a constraining effect. Search times under these observed dynamics are extremely short for nearby loci (1 {micro}m). These findings have important implications for processes involving two locus contacts such as enhancer-promoter search and double-strand break repair.