Chromatin architecture mapping by multiplex proximity tagging

Chromatin plays a pivotal role in genome expression, maintenance, and replication. To better understand chromatin organization, we developed a proximity-tagging method to map molecules that associate in 3D space. Using this method-PCP (proximity copy paste)-we mapped the positioning and connectivity of individual nucleosomes in Saccharomyces cerevisiae. We show that chromatin is predominantly organized into regularly spaced nucleosome arrays that can be positioned or delocalized. PCP can also map long-range, multi-way interactions, and we provide direct evidence supporting a model that metaphase chromosomes are compacted by cohesin loop clustering. Analyzing single-molecule nuclease footprinting data, we define distinct chromatin states within a mixed population to show that non-canonical overlapping di-nucleosomes are a stable feature of chromatin. PCP is a versatile method, allowing the detection of the connectivity of individual molecules locally and over large distances to be mapped at high resolution in a single experiment.