Every gene everywhere all at once: High-precision measurement of 3D chromosome architecture with single-cell Hi-C

Abstract

The three-dimensional (3D) structure of chromosomes influences essential biological processes such as gene expression, genome replication, and DNA damage repair and has been implicated in many developmental and degenerative diseases. In the past two centuries, two complementary genres of technology-microscopy, such as fluorescence in situ hybridization (FISH), and biochemistry, such as chromosome conformation capture (3C or Hi-C)-have revealed general principles of chromosome folding in the cell nucleus. However, the extraordinary complexity and cell-to-cell variability of the chromosome structure necessitate new tools with genome-wide coverage and single-cell precision. In the past decade, single-cell Hi-C emerges as a new approach that builds upon yet conceptually differs from bulk Hi-C assays. Instead of measuring population-averaged statistical properties of chromosome folding, single-cell Hi-C works as a proximity-based "biochemical microscope" that measures actual 3D structures of individual genomes, revealing features hidden in bulk Hi-C such as radial organization, multi-way interactions, and chromosome intermingling. Single-cell Hi-C has been used to study highly dynamic processes such as the cell cycle, cell-type-specific chromosome architecture ("structure types"), and structure-expression interplay, deepening our understanding of DNA organization and function.

Keywords: DNA folding; chromatin structure; epigenetic regulation; genome architecture; spatial omics.

FIGURE 1

Single-cell Hi-C provides a holistic high-resolution view into the 3D structure of our genetic blueprint. (Left) DNA fluorescence in situ hybridization (FISH) provided the first look into genome organization in the cell nucleus by directly measuring 3D coordinates (i.e., x, y, and z) of various genomic loci (or entire chromosomes, in the case of chromosome painting) but is limited by the optical resolution and spectrum (i.e., the number of loci). (Right) Chromosome conformation capture (3C or Hi-C) indirectly measures nuclear architecture through 3D proximity between genomic loci (i.e., “contact map”). Bulk Hi-C measures the average 3D proximity (probability (P) that two loci are within a certain 3D distance (d)) among a large population of cells and, therefore, cannot produce true 3D structures (dashed line). In particular, the “all-to-all” inter-chromosomal contacts in bulk Hi-C provide conflicting spatial constraints, while chromatin domains (three are depicted here) would be seemingly isolated from each other. In contrast, single-cell Hi-C offers a new concept of a “biochemical microscope.” 3D proximity of a single cell can be converted into actual 3D coordinates of the whole genome, yielding high-resolution structures without the need for specialized equipment.