Super-resolution chromatin tracing reveals domains and cooperative interactions in single cells

Abstract

The spatial organization of chromatin is pivotal for regulating genome functions. We report an imaging method for tracing chromatin organization with kilobase- and nanometer-scale resolution, unveiling chromatin conformation across topologically associating domains (TADs) in thousands of individual cells. Our imaging data revealed TAD-like structures with globular conformation and sharp domain boundaries in single cells. The boundaries varied from cell to cell, occurring with non-zero probabilities at all genomic positions, but preferentially at CTCF/cohesin sites. Surprisingly, cohesin depletion, which abolished TADs at the population-average level, did not diminish domain structures in single cells, but eliminated preferential domain boundary positions. Moreover, we observed wide-spread, cooperative, multi-way chromatin interactions, which remained after cohesin depletion. These results provide critical insight into the mechanisms underlying chromatin domain and hub formation.