The nuclear matrix protein HNRNPU maintains 3D genome architecture globally in mouse hepatocytes

Abstract

The eukaryotic chromosomes are folded into higher-order conformation to coordinate genome functions. Besides long-range chromatin loops, recent chromosome conformation capture (3C)-based studies indicated the higher level of chromatin structures including compartments and topologically associating domains (TADs), which may serve as units of genome organization and functions. However, the molecular machinery underlying these hierarchically three-dimensional (3D) chromatin architectures remains poorly understood. Via high-throughput assays including in situ Hi-C, DamID, ChIP-seq and RNA-seq, we investigated roles of the Heterogeneous Nuclear Ribonucleoprotein U (HNRNPU), a nuclear matrix (NM)-associated protein, in the 3D genome organization. Upon the depletion of HNRNPU in mouse hepatocytes, the coverage of lamina-associated domains (LADs) in the genome increases from 53.1% to 68.6%, and a global condensation of chromatin was observed. Furthermore, disruption of HNRNPU leads to compartment switching on 7.5% of the genome, decreases of TAD boundary strengths at borders between A (active) and B (inactive) compartments, and reduce of chromatin loop intensities. Long-range chromatin interactions between and within compartments or TADs are also significantly remodeled upon HNRNPU depletion. Intriguingly, HNRNPU mainly associates with active chromatin, and 80% of HNRNPU peaks coincide with the binding of CTCF or RAD21. Collectively, we demonstrated that HNRNPU functions as a major factor maintaining the 3D chromatin architecture, suggesting important roles of NM-associated proteins in genome organization.