Gene

Cell biology

Cohesin

Demography

Biology

Enhancer

Cell nucleus

Genomic organization

Chromosome conformation capture

Nucleus

Computational biology

ChIA-PET

Genetics

Chromatin

Genome

CTCF

Mathematics

Population

Domain (mathematical analysis)

Sociology

Transcription factor

Mathematical analysis

Cell

Biophysics

Nucleosome

Gene expression

Science

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.

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