Single-cell Hi-C reveals unique chromatin reorganization at oocyte-to-zygote transition

Chromatin is reorganized and reprogrammed after fertilization to produce a totipotent zygote with the potential to generate a new organism. In mammals, the maternal genome inherited through the oocyte and the paternal genome provided by sperm coexist as separate haploid nuclei in interphase of the first cell cycle. How these two epigenetically distinct genomes are spatially organized remains poorly understood. Existing chromosome conformation capture-based methods are inapplicable to oocytes and zygotes due to paucity of material. To study the three-dimensional organization of chromatin in rare cell types, we developed a simplified single-cell Hi-C (sscHi-C) protocol that provides 100-fold more contacts per cell than a previous method. Using sscHi-C, we show that chromatin architecture is uniquely reorganized during the oocyte-to-zygote transition. We found that major features of chromosome organization, compartments, domains and loops are all present in individual cells, with noticeable cell-to-cell variation and differences between male and female nuclei in zygotes. Compartments detected in male nuclei are notably absent from female nuclei, indicating these are the first mammalian interphase nuclei lacking this higher-order structure. While compartments in single cells closely resemble compartments from the cell population, TADs manifest themselves as contact domains (CDs) that differ from cell to cell, nevertheless averaging into TADs in pooled data. Finally, scaling of contact probability with genomic separations suggests that chromosome conformations in oocyte and zygote nuclei are fundamentally different and each are distinct from the global organization of chromosomes in other interphase cells. We conclude that chromatin organization of zygote nuclei is unique and can serve as the chromatin "ground state" of a totipotent cell. Overall design: We generated 98 HiC libraries from single oocytes (includes comparison of NSN and SN oocytes + two different experimental conditions), 82 libraries from nuclei of zygotes (comparison of maternal vs paternal nuclei + 2 experimental conditions), 2 libraries of bulk K562 cells compared to 34 libraries of single K562 cells and 2 libraries of bulk MEL cells (with 2 different fixation conditions).