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

TLDR

The spatial organization of chromatin is pivotal for regulating genome functions. The study introduces an imaging method to trace chromatin organization at kilobase‑ and nanometer‑scale resolution across topologically associating domains in thousands of individual cells. The authors employed a high‑resolution imaging technique to map chromatin conformation across TADs in thousands of single cells. The imaging revealed globular TAD‑like structures with sharp, variable boundaries preferentially at CTCF/cohesin sites, and showed that cohesin depletion eliminated boundary preference but not TAD‑like structures or cooperative multiway interactions, providing insight into chromatin domain and hub formation.

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 nonzero probabilities at all genomic positions but preferentially at CCCTC-binding factor (CTCF)- and cohesin-binding sites. Notably, cohesin depletion, which abolished TADs at the population-average level, did not diminish TAD-like structures in single cells but eliminated preferential domain boundary positions. Moreover, we observed widespread, cooperative, multiway chromatin interactions, which remained after cohesin depletion. These results provide critical insight into the mechanisms underlying chromatin domain and hub formation.