Single-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 architecture, and epigenetic identity. We propose that TADs and compartments are organized by multiple, small-frequency, yet specific interactions that are regulated by epigenetics and transcriptional state.This research was supported by funding from the European Research Council under the 7th Framework Program (FP7/2010-2015, ERC grant agreement 260787 to M.N. and FP7/2007-2013, and ERC grant agreement 609989 to M.A.M.-R.). M.A.M.-R. and G.C. acknowledge support from the European Union's Horizon 2020 research and innovation program under grant agreement 676556. This work has also benefited from support by the Labex EpiGenMed, an «Investments for the future» program, reference ANR-10-LABX-12-01, the Spanish Ministry of Economy and Competitiveness (BFU2013-47736-P to M.A.M.-R.), and from “Centro de Excelencia Severo Ochoa 2013-2017”, SEV-2012-0208 to the CRG. 3D-SIM experiments were performed at Montpellier Resource Imaging. We acknowledge the France-BioImaging infrastructure supported by the French National Research Agency (ANR-10-INBS-04, «Investments for the future»)

3D structures of individual mammalian genomes studied by single-cell Hi-C

The folding of genomic DNA from the beads-on-a-string like structure of nucleosomes into higher order assemblies is critically linked to nuclear processes. We have calculated the first 3D structures of entire mammalian genomes using data from a new chromosome conformation capture procedure that allows us to first image and then process single cells. This has allowed us to study genome folding down to a scale of <100 kb and to validate the structures. We show that the structures of individual topological-associated domains and loops vary very substantially from cell-to-cell. By contrast, A/B compartments, lamin-associated domains and active enhancers/promoters are organized in a consistent way on a genome-wide basis in every cell, suggesting that they could drive chromosome and genome folding. Through studying pluripotency factor- and NuRD-regulated genes, we illustrate how single cell genome structure determination provides a novel approach for investigating biological processes