Fig. 3
Allelic specificity of enhancer–promoter interaction in IGH-DUX4 haplotype versus wild-type haplotype in Nalm6. a Chromatin interaction plot from Hi-C data at the DUX4 region (72 kb) on 10q26 and the IGH region (1.4 Mb) plotted by the ProteinPaint program43. Different y-axis scale was used at DUX4 and IGH region for plotting RNA-seq, H3K27ac, ATAC-seq, and Capture-C. The Eμ-DUX4 interaction and Eμ-Igμ promoter interaction are marked as a blue and green box, respectively. In Capture-C data, the colored arcs represent regions interacting with Eμ, with thickness indicating interaction intensity. Yellow arcs show known Eμ-Igμ interactions. The two translocated DUX4 copies were marked at DUX4L13 region, because this region is best matched to our assembled IGH-DUX4 haplotype. Details are in Methods section. b Diagrams of Eμ-DUX4 interaction and Eμ-Igμ promoter interaction in different alleles. The genomic distances were estimated based on Chromium WGS data and the knowledge that the functional Igμ is from the active IGH allele which undergoes VDJ recombination3. Details are in Methods section. c Comparison of supporting read pairs for Hi-C/H3K27ac HiChIP, the reads coverage for Capture-C between Eμ-DUX4 interaction and Eμ-Igμ promoter interaction. Multiple mapping issue at DUX4 regions was considered. The details are described in Methods section
