Fig. 1: Effect of Eµ deletion on Igh chromatin structure.

a Schematic representation of the Igh locus highlighting Eµ (red oval, indicated by black arrow), IGCR1 (purple oval) and 3′CBE (blue and purple). Gene segments (V_H, D_H and J_H) are indicated as colored rectangles. The 3′ Igh domain comprises 260 kb between IGCR1 and 3′CBE. Proximal and distal refer to variable gene segments (V_H) close or far away from 3′ Igh domain, respectively. b, c cHi-C profiles of the 3′ Igh domain on wild-type (WT) and Eµ-deficient (Eµ^−/−) Igh alleles. The genomic interval of the 3′ Igh domain (b, chr12: 113200001-113500000, mm10) and entire Igh locus (c, chr12: 113200001-116000000, mm10) are illustrated for both WT (left panel) and Eµ^−/− (middle panel) alleles. Heatmaps indicate normalized interaction frequencies. Noteworthy interacting regions are demarcated by a black dash rectangle. High cross-linking frequency reflecting loops between Eµ and 3′CBE (Eµ/3′CBE) or IGCR1 (Eµ/IGCR1) are indicated by black ovals. Difference interaction map between WT and Eµ^−/− Igh alleles is shown on the right. Color code represents decreased (blue) or increased (red) interactions on Eµ^−/− alleles. The cHi-C analysis of clone Eµ^−/− #1 is presented in the middle panel, whereas data from clone Eµ^−/− #2 is depicted in Supplementary Fig. 1c. cHi-C data were visualized with software cooltools. Experiment was independently repeated twice with similar results. d Virtual 4C representation of cHi-C analysis using the 3′CBE as the viewpoint. Interacting reads within the 20 kb 3′CBE region (chr12:113210001-113230000) were extracted from cHi-C data (c) for WT and Eµ^−/− alleles and mapped within the entire Igh locus (chr12:113200001-116000000). Differential 4C analysis, contrasting Eµ^−/− and WT Igh alleles, highlights alterations in 3′CBE-associated interactions, denoted by increased (red) or reduced (blue) connections. IGCR1 and Eµ are indicated by black arrows and the 3′CBE anchor is indicated by the red arrow. ChIP-Seq profiles of CTCF and Rad21 derived from WT or Eµ^−/− pro-B cell lines are shown above virtual 4C maps. Experiment was independently repeated twice with similar results. See also Supplementary Fig. 1, Data 1, 2.