Principles of 3D compartmentalization of the human genome

Chromatin is organized in the nucleus via CTCF loops and compartmental domains. Here, we compare different cell types to identify distinct paradigms of compartmental domain formation in human tissues. We identify and quantify compartmental forces correlated with histone modifications characteristic of transcriptional activity and previously underappreciated roles for distinct compartmental domains correlated with the presence of H3K27me3 and H3K9me3, respectively. We present a computer simulation model capable of predicting compartmental organization based on the biochemical characteristics of independent chromatin features. Using this model, we show that the underlying forces responsible for compartmental domain formation in human cells are conserved and that the diverse compartmentalization patterns seen across cell types are due to differences in chromatin features. We extend these findings to Drosophila to suggest that the same principles are at work beyond humans. These results offer mechanistic insights into the fundamental forces driving the 3D organization of the genome.

Automated summary

Chromatin is organized in the nucleus via CTCF loops and compartmental domains, with distinct paradigms of compartmental domain formation identified in different cell types in human tissues. The forces driving compartmental domain formation in human cells are conserved, with diverse compartmentalization patterns attributed to differences in chromatin features. This study offers mechanistic insights into the fundamental forces driving the 3D organization of the genome, extending findings to suggest similar principles at work beyond humans.