Extended Data Fig. 4. Wapl overexpression remodels the chromatin structure in the recombinase deficient pro-B cell line (D345).
(a) Flow cytometric analysis showing the D345 pro-B cell line with (left) or without (right) infection with Wapl-BFP lentivirus. The percentages of BFP+ and BFP- cells are indicated. BFP+ cells are sorted for experiments. (b) Normalized tracks for RNA-Seq across the Wapl locus are shown with IGV. “FC” represents fold change, and the Poisson test was applied with the P value indicated (n = 2). (c) Average Hi-C contact plots (n = 2) derived from BFP control and Wapl overexpressed D345 cells. Color shading refers to: compartments: pink, TADs and loops: green, and close interactions: yellow. (d) Quantitative comparison of TAD strength derived from Hi-C data of BFP control and Wapl overexpressed D345 cells. Similar analysis and the same cutoffs as in Fig. 3a were used. Representative genes from the top-ranked changed TADs are displayed. (e) Hi-C contact frequency heat maps (pooled from 2 biological replicates) showing the Igh TAD in BFP control and Wapl overexpressed D345 pro-B cells. A difference map (Wapl OE minus BFP control) for the same region is shown on the right; regions with increased and decreased interactions in old are colored red and blue, respectively. Schematics on top represent the Igh locus to scale; colors represent different parts of the locus as indicated to the right of the figure. (f) CellRadar (https://karlssong.github.io/cellradar/) plot derived from transcriptional changes identified in comparison of young and old pro-B cells (blue), Ebf1+/+ and Ebf1+/− pro-B cells (orange), and BFP control and Wapl overexpressed D345 cells. Differentially expressed genes (DEGs) with log2 fold change > 1 and P-value < 0.01 were used as input for young and old pro-B cells (blue), and Ebf1+/+ and Ebf1+/− pro-B cells. DEGs with P-value < 0.01 were used as input for BFP control and Wapl overexpressed D345 cells because of the limited number of DEGs by a more stringent cutoff.