Identification of Two Subsets of Subcompartment A1 Associated with High Transcriptional Activity and Frequent Loop Extrusion

SIMPLE SUMMARY: Genomic DNA is folded into chromatin interaction patterns contributing to logical control of gene expression in mammalian cells, but how these highly ordered structures form is not yet fully understood. To assess to what extent functional gene activity is relative to the positioning of genes within the 3D nuclear landscape, we analyzed genome-wide gene expression and chromatin conformation capture data together in five distinct types of cells. We observed that 3D chromatin repositioning frequently occurs during cell differentiation, and these chromatin relocations are significantly associated with changes in gene expression levels. A set of genomic loci with extraordinarily high gene density participates in the establishment of common subcompartment A1 across the genome in all these five cells. By contrast, regulatory genomic segments enriched in cell type-specific genes are engaged in the formation of variable A1. Both subsets of subcompartment A1 bearing the strongest euchromatin signals harbor topological domains with frequent intradomain interactions to facilitate gene regulation. Thus, our study links the gene transcriptional levels with their subcompartment positioning, suggesting a key role of both constitutive and regulatory transcriptional activity in the 3D genome organization. ABSTRACT: Three-dimensional genome organization has been increasingly recognized as an important determinant of the precise regulation of gene expression in mammalian cells, yet the relationship between gene transcriptional activity and spatial subcompartment positioning is still not fully comprehended. Here, we first utilized genome-wide Hi-C data to infer eight types of subcompartment (labeled A1, A2, A3, A4, B1, B2, B3, and B4) in mouse embryonic stem cells and four primary differentiated cell types, including thymocytes, macrophages, neural progenitor cells, and cortical neurons. Transitions of subcompartments may confer gene expression changes in different cell types. Intriguingly, we identified two subsets of subcompartments defined by higher gene density and characterized by strongly looped contact domains, named common A1 and variable A1, respectively. We revealed that common A1, which includes highly expressed genes and abundant housekeeping genes, shows a ~2-fold higher gene density than the variable A1, where cell type-specific genes are significantly enriched. Thus, our study supports a model in which both types of genomic loci with constitutive and regulatory high transcriptional activity can drive the subcompartment A1 formation. Special chromatin subcompartment arrangement and intradomain interactions may, in turn, contribute to maintaining proper levels of gene expression, especially for regulatory non-housekeeping genes.