DNA is not randomly distributed within the nucleus but is packaged with proteins into chromatin, which is precisely folded into complex three-dimensional structures. However, scientists have not fully understood how this complex three-dimensional (3D) organization is regulated or how it changes over time.

Now, a research team led by Prof. LI Xiang from the Institute of Genetics and Developmental Biology (IGDB) of the Chinese Academy of Sciences (CAS) has developed SpaceA, a spatial 3D genomics technology that enables high-confidence, in situ profiling of long-range chromatin interactions within tissue sections.

The technology combines two approaches, allowing researchers to investigate higher-order chromatin architecture while preserving the spatial context of cells in tissues. These are microfluidic spatial barcoding, which uses tiny fluid channels to assign molecular identifiers to different locations within a tissue, allowing researchers to determine where particular chromatin interactions occur, and a SPRITE-like ligation-free contact detection strategy, which detects interactions between chromatin regions without physically joining DNA fragments.

The study was published in Developmental Cell on October 6.

In recent years, single-cell 3D genomics technologies have greatly advanced the understanding of chromatin conformation. However, these methods cannot preserve the spatial positions of cells within tissues, making it difficult to study how genome architecture regulates gene expression in native cellular environments. Recently developed spatial 3D genomics technologies have adopted ligation-based Hi-C strategies, which preferentially detect short-range chromatin interactions within 10 megabases (Mb).

To address these limitations, the researchers applied SpaceA to nine mouse embryo sections spanning four developmental stages, from embryonic days 11.5 to 14.5 (E11.5 to E14.5), generating approximately 4 TB of deeply sequenced data to characterize the changes in chromatin conformation during embryonic development.

Using SpaceA, the researchers found that A/B compartments underwent a dramatic transition at E12.5 to E13.5, coinciding with profound transcriptomic changes.

The team also discovered a distinct chromatin assembly mechanism in the embryonic liver that operates independently of classical A/B compartment determination. Mid-range interactions (10–40 Mb) were significantly enhanced, interactions between adjacent compartments were strengthened, and long-range interchromosomal interactions (>40 Mb) were weakened.

Microscopy revealed heterochromatin adhesion in liver cell nuclei, providing further evidence of this distinct chromatin structure, which was accompanied by a global decline in gene expression. This pattern differs from the classical model in which gene expression is promoted through A/B compartment switching or intracompartmental interactions.