biostudies-literatureCattoni DIEuropean Research Council1753https://www.ebi.ac.uk/biostudies/studies/S-EPMC5700980biostudies-literatureUnknown8(1)At the kilo- to megabase pair scales, eukaryotic genomes are partitioned into self-interacting modules or topologically associated domains (TADs) that associate to form nuclear compartments. Here, we combine high-content super-resolution microscopies with state-of-the-art DNA-labeling methods to reveal the variability in the multiscale organization of the Drosophila genome. We find that association frequencies within TADs and between TAD borders are below ~10%, independently of TAD size, epigenetic state, or cell type. Critically, despite this large heterogeneity, we are able to visualize nanometer-sized epigenetic domains at the single-cell level. In addition, absolute contact frequencies within and between TADs are to a large extent defined by genomic distance, higher-order chromosome arNature communicationsSingle-cell absolute contact probability detection reveals chromosomes are organized by multiple low-frequency yet specific interactions.PMC5700980260787609989Marti-Renom MACavalli GDi Stefano MFiche JBValeri AHoubron CChamousset DSexton TCattoni DIGeorgieva MChang JMCardozo Gizzi AMNollmann MGonzalez IDejardin SBantignies FfalseSingle-cell absolute contact probability detection reveals chromosomes are organized by multiple low-frequency yet specific interactions.At the kilo- to megabase pair scales, eukaryotic genomes are partitioned into self-interacting modules or topologically associated domains (TADs) that associate to form nuclear compartments. Here, we combine high-content super-resolution microscopies with state-of-the-art DNA-labeling methods to reveal the variability in the multiscale organization of the Drosophila genome. We find that association frequencies within TADs and between TAD borders are below ~10%, independently of TAD size, epigenetic state, or cell type. Critically, despite this large heterogeneity, we are able to visualize nanometer-sized epigenetic domains at the single-cell level. In addition, absolute contact frequencies within and between TADs are to a large extent defined by genomic distance, higher-order chromosome ar2017-01-01T00:00:00Z2017 Nov2026-04-16T07:18:34.433Z2019-03-27T03:02:50ZS-EPMC57009802917043410.1038/s41467-017-01962-x