Single-cell chromatin studies provide insights into how chromatin structure relates to functions of individual cells. However, balancing high-resolution and genome wide-coverage remains challenging. We describe a computational method for the reconstruction of large 3D-ensembles of single-cell (sc) chromatin conformations from population Hi-C that we apply to study embryogenesis in Drosophila. With minimal assumptions of physical properties and without adjustable parameters, our method generates large ensembles of chromatin conformations via deep-sampling. Our method identifies specific interactions, which constitute 5–6% of Hi-C frequencies, but surprisingly are sufficient to drive chromatin folding, giving rise to the observed Hi-C patterns. Modeled sc-chromatins quantify chromatin heterogeneity, revealing significant changes during embryogenesis. Furthermore, >50% of modeled sc-chromatin maintain topologically associating domains (TADs) in early embryos, when no population TADs are perceptible. Domain boundaries become fixated during development, with strong preference at binding-sites of insulator-complexes upon the midblastula transition. Overall, high-resolution 3D-ensembles of sc-chromatin conformations enable further in-depth interpretation of population Hi-C, improving understanding of the structure-function relationship of genome organization.

单细胞染色质研究提供了有关染色质结构如何与单个细胞功能相关的见解。然而，平衡高分辨率和全基因组覆盖仍然具有挑战性。我们描述了一种计算方法，用于重建来自 Hi-C 群体的单细胞 (sc) 染色质构象的大型 3D 集合，我们将其应用于研究果蝇胚胎发生. 在对物理特性进行最小假设且没有可调参数的情况下，我们的方法通过深度采样生成大量染色质构象。我们的方法确定了特定的相互作用，这些相互作用占 Hi-C 频率的 5-6%，但令人惊讶的是足以驱动染色质折叠，从而产生观察到的 Hi-C 模式。建模的 sc 染色质量化染色质异质性，揭示胚胎发生过程中的显着变化。此外，当没有可感知的种群 TAD 时，>50% 的建模 sc 染色质在早期胚胎中保持拓扑关联域 (TAD)。域边界在发育过程中变得固定，在中囊胚转变时强烈偏好绝缘体复合物的结合位点。总体，