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

HNRNPU regulates chromatin compartment organization. (A) Hi-C contact maps of Chromosome 19 in (left) shCtrl- and (right) shU-treated cells at 200-kb resolution. Compartments A (red) and B (blue) are shown by PC1 eigenvectors. (B) (Left) Log₂ (shU/shCtrl) of Chromosome 19 binned at 200-kb resolution. (Right) Log₂ (shU/shCtrl) of 40-kb bins (lower left) and averaged by compartments (upper right) in a 15.9-Mb region. (C,D) Statistics of interaction changes between (C) and within (D) compartments. (Top) Schematic view of regions examined. (Middle) Cumulative distribution of obs/exp values of interactions between compartments. P-values were obtained by two-factor ANOVA. (Bottom) Box plots showing the pairwise fold changes of interactions. Results from two replicates are presented. (E) Percentages of compartment switching between shCtrl- and shU-treated cells. (F) The relationships between compartment switching and the lamina association (based on lamin B1 DamID data). (G) Box plots showing expression changes with compartment switching. P-values were obtained by Wilcoxon rank-sum test.