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

• Published in: Science (American Association for the Advancement of Science) Vol. 362; no. 6413
• Main Authors: Bintu, Bogdan, Mateo, Leslie J., Su, Jun-Han, Sinnott-Armstrong, Nicholas A., Parker, Mirae, Kinrot, Seon, Yamaya, Kei, Boettiger, Alistair N., Zhuang, Xiaowei
• Format: Journal Article
• Language: English
• Published: United States The American Association for the Advancement of Science 26.10.2018
• Subjects: Binding sites; Biological activity; Boundaries; CCCTC-Binding Factor - chemistry; Cell Cycle Proteins - chemistry; Cell lines; Chromatin; Chromatin - chemistry; Chromatin - ultrastructure; Chromosomal Proteins, Non-Histone - chemistry; Cohesin; Cohesins; Cohesion; Deoxyribonucleic acid; Depletion; DNA; Domains; Fluorescence; Fluorescence in situ hybridization; Functional morphology; Gene expression; Gene regulation; Gene sequencing; Genome, Human; Genomes; Genomics; HCT116 Cells; High resolution; Humans; Image resolution; In Situ Hybridization, Fluorescence; Loci; Nuclei; Nuclei (cytology); Population; Protein Binding; Protein Domains; Segments; Single-Cell Analysis - methods
• ISSN: 0036-8075; 1095-9203; 1095-9203
• DOI: 10.1126/science.aau1783

The genome is organized within the nucleus as three-dimensional domains that modulate DNA-templated processes. Bintu et al. used high-throughput Oligopaint labeling and imaging to observe chromatin dynamics inside the nuclei of several different mammalian cell lines. After combining the datasets, single-cell matrices revealed chromatin arranged in topologically associating domains (TADs). Removing cohesin resulted in a loss of aggregate TADs among populations of cells, but specific TADs were still detected at the single-cell level. Furthermore, higher-order organization was detected, suggestive of cooperative interactions within the genome. Science , this issue p. eaau1783 Chromatin imaging reveals topologically associating domain–like structures with spatially segregated conformations. 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.