Fig. 1: The patterns of chromatin accessibility in pediatric B-ALL.

a Multi-omics data for 61 patients analyzed in this study. Diagnosis (D) and relapse (R) samples from 11 B-ALL subtypes were analyzed, including hyperdiploidy, ETV6::RUNX1, TCF3::PBX1, KMT2A, BCR::ABL1, BCR::ABL1-like, ZNF384, PAX5alt, TCF3::HLF, hypodiploidy and MEF2D. Cases with unclassified subtype were grouped into B-other. NA not available. b The percentages of accessible chromatin regions (ACRs) located in indicated genome regions of B-ALL samples (n = 75). c Venn diagram shows the overlap between ACRs detected in B-ALL and B-cell progenitors (pre-pro B cells and pro B cells). d Violin plot presents the recurrence of ACRs in B-ALLs. The ACRs were grouped into four groups as showed in (c). Significant difference was observed among the four groups (p < 2.2e−16, Kruskal–Wallis test). Box plots show the median number as centers, with upper and lower hinges represent 75th and 25th percentile, and whiskers extend to largest and smallest values no more than 1.5*IQR. (B-ALL only: n = 585,248; B-ALL\Pre-pro B overlap: n = 26,385; B-ALL\Pro B overlap; B-ALL\Pre-pro B\Pro B overlap: n = 103,534). e Gene set enrichment analysis shows that 2332 protein coding genes regulated by 252,028 higher accessible ACRs in B-ALL were enriched in tumor associated biological processes. Only terms with FDR < 0.001 are displayed. The node size represents the enriched FDR values, and the edge represents overlap between two gene sets. Clusters of functionally related categories were manually grouped and labeled in different colors. f Wiggle plot shows regions with increased chromatin accessibility in B-ALLs as compared to B-cell progenitors. ACRs with ±1 kb centered the TSS of representative cosmic genes are showed. Only subtypes with more than three cases are included and two samples are randomly selected and showed for each subtype. The ACR present higher accessible in B-ALL upstream TSS of IL7R are highlighted in light-yellow. g Wiggle plot shows the chromatin accessibility in the blood enhancer cluster (BENC) region (chr8:126,712,193–128,412,193). The positions of enhancers (A–I) are indicated in the BENC track on the top. The tracks showing ACRs in this region are organized as in (f). Two enhancers from the BENC cluster showing increased accessibility in B-ALLs are highlighted in light-yellow.