Regulation associated modules reflect 3D genome modularity associated with chromatin activity

ABSTRACT The 3D genome has been shown to be organized into modules including topologically associating domains (TADs) and compartments that are primarily defined by spatial contacts from Hi-C or other experiments. There exists a gap to investigate whether and how the spatial modularity of the chromatin is related to the functional modularity resulting from the chromatin activity. Increasing evidence shows a tight interplay between histone modifications and 3D chromatin organization. As the histone modifications reflect the chromatin activity, it is tempting to infer the spatial modularity of the genome directly from the histone modification patterns, which would establish the connection between the spatial and functional modularity of the genome. However, uncovering the 3D genomic modules using histone modifications has not been well explored. Here, we report that the histone modifications show a modular pattern (referred to as regulation associated modules, RAMs) that reflects the spatial modularity of the chromatin structure. We found that enhancer-promoter interactions and extrachromosomal DNAs (ecDNAs) occur more often within the same RAMs than within the same TADs, indicating stronger insulation of the RAM boundaries and a modularization of the 3D genome at a scale better aligned with the chromatin activity. Consistently, compared to the TAD boundaries, in silico predictions showed that deletions of RAM boundaries perturb the chromatin structure more severely and somatic variants in the cancer samples are more enriched in the RAM boundaries. These observations suggest that RAMs reflect a modular organization of the 3D genome at a scale better aligned with chromatin activity, providing a bridge connecting the structural and functional modularity of the genome.