Recent advances in single-cell bioinformatics for inferring higher-order chromatin contact maps

DNA, a large molecule located in the nucleus, carries essential genetic information, including gene loci and cis-regulatory elements. Despite its extensive length, DNA is compactly stored within the limited space of the nucleus due to its hierarchical three-dimensional (3D) organization. In this structure, DNA is organized into territories known as topologically associated domains (TADs). Within each TAD, numerous chromatin loops link promoters and enhancers across the genome. These loops and the interactions between promoters and enhancers are dynamically regulated, thereby controlling gene transcription activities. With the rapid advancements in single-cell genomics technologies, TAD boundaries and chromatin loops can now be observed at the level of individual cells, allowing researchers to explore cellular heterogeneity in tissues. This review will summarize the state-of-the-art bioinformatics methods recently developed to analyze single-cell Hi-C and epigenomics datasets, which infer higher-order chromatin interactions within the 3D genome. Additionally, we will discuss the biological applications of these tools and future directions for comprehensively investigating epigenomic heterogeneity across different species, developmental stages, and disease states. [BMB Reports 2025; 58(12): 485-493].