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

Three-dimensional genome organization has been increasingly recognized as an important determinant of the precise regulation gene expression in mammalian cells, yet relationship between transcriptional activity and spatial subcompartment positioning is still not fully comprehended. Here, we first utilized genome-wide Hi-C data to infer eight types (labeled A1, A2, A3, A4, B1, B2, B3, B4) mouse embryonic stem cells four primary differentiated cell types, including thymocytes, macrophages, neural progenitor cortical neurons. Transitions subcompartments may confer changes different types. Intriguingly, identified two subsets defined by higher density characterized strongly looped contact domains, named common A1 variable respectively. We revealed that which includes highly expressed genes abundant housekeeping genes, shows a ~2-fold than where type-specific are significantly enriched. Thus, our study supports model both genomic loci with constitutive regulatory high can drive formation. Special chromatin arrangement intradomain interactions may, turn, contribute maintaining proper levels expression, especially for non-housekeeping genes.