On January 21, 2025, the research team led by Prof. Xiaoliang Sunney Xie at Changping Laboratory / Peking University Biomedical Pioneering Innovation Center (BIOPIC) published a research paper titled “Droplet-based high-throughput 3D genome structure mapping of single cells with simultaneous transcriptomics” in Cell Discovery. This study developed a high-throughput scHi-C technology (dscHi-C) along with its transcriptome co-assay (dscHi-C multiome) based on droplet microfluidics platform. The researchers also demonstrated that dscHi-C is robust, sensitive, and scalable for applications in cell lines and tissues.

The advancement of single-cell 3D genome technologies, particularly sequencing-based single-cell Hi-C techniques, has enabled the investigation of 3D genome heterogeneity and cell-type specificity at single-cell resolution. However, existing scHi-C methods generally face limitations in cell throughput. Although high-throughput approaches employing combinatorial indexing strategies have been reported, they remain constrained by the following technical barriers: complex and time-consuming experimental workflows; reliance on custom-designed reagents; low detectability and data sparsity, with an average detection of only ~5,000 chromatin contacts per cell. These challenges critically hinder the application of scHi-C technologies in large-scale single-cell atlas studies. In this study, researchers developed dscHi-C, a droplet-based high-throughput single-cell Hi-C technology and along with its transcriptome co-assay (dscHi-C multiome).

Figure 1. The development of dscHi-C

Utilizing dscHi-C, we profiled chromatin structural changes during mouse brain aging across three developmental stages (3, 12, and 23 months), analyzing 32,777 single cells and yielding a median of 78,220 unique contacts. The results revealed multiscale reorganization of chromatin interaction patterns during aging, characterized by a global weakening of A/B compartmentalization alongside enhanced insulation of local topologically associated domain (TAD) boundaries. Concurrently, increased long-range and inter-chromosomal interactions were observed. Pathway enrichment analysis demonstrated that genes exhibiting compartment shifts in neurons were enriched in sensory perception, pheromone response, and DNA demethylation related pathways, while those in glial cells were significantly associated with innate immune responses, including inflammatory activation and cytokine production. These findings elucidate the regulatory role of 3D genome dynamics in brain aging and underscore the capability of dscHi-C in resolving three-dimensional chromatin architecture heterogeneity within complex tissues.

Figure 2. Chromatin remodeling associated with mouse brain aging

Subsequently, the researchers successfully developed a high-throughput single-cell multi-omics technology for three-dimensional genomes and transcriptomes—dscHi-C multiome—based on the dscHi-C technique (see Figure 3a). Improvements were made in both chromatin contacts detection and RNA capture, which further enhanced the detection rate (see Figures 3b and c). The application of the dscHi-C multiome technology in studying the relationship between three-dimensional chromatin architecture and gene expression was then demonstrated in mouse cortex (see Figures 3d and e). The advancement of high-throughput single-cell Hi-C technology has established a methodological foundation for elucidating the spatiotemporal relationships between epigenetic mechanisms and gene regulation in development and disease. This technology has the potential for in-depth application in areas such as neurodegenerative diseases, embryonic development, and the analysis of tumor microenvironment heterogeneity, thereby advancing mechanistic research and the development of therapeutic strategies in the era of precision medicine.

Figure 3. dscHi-C multiome reveals the relationship between chromatin structure and gene expression in the mouse cortex

Dr. Honggui Wu, and Ph.D. Candidate Maoxu Wang at the Peking University Biomedical Frontier Innovation Center/School of Life Sciences, are co-first authors of this paper. Professor Xiaoliang Sunney Xie from the Changping Laboratory / Peking University Biomedical Pioneering Innovation Center is the corresponding author. Associate investigator Yinghui Zheng from Xiaoliang Sunney Xie’s team made significant contributions to this paper. This research was supported and funded by the Changping Laboratory.

Paper link：https://www.nature.com/articles/s41421-025-00770-8