Extended Data Fig. 2: Genomic loci displaying differential intra-TAD activity in T-ALL.
From: Three-dimensional chromatin landscapes in T cell acute lymphoblastic leukemia
a) Hi-C interaction heat maps (first row) showing the IKZF2 locus (black circle). Second row shows heat maps of log2 (fold-change) interactions compared to T cell 1. b) H3K27ac ChIP-seq tracks for IKZF2 locus in T cells and CUTLL1, NOTCH1 ChIP-seq tracks for CUTLL1. Tracks represent fold-enrichment over input where applicable and counts-per-million reads otherwise. Grey area indicates TAD containing IKZF2. Number replicates: T cells H3K27ac n = 2; CUTLL1 H3K27ac n = 2; CUTLL1 NOTCH1 n = 1. c) Quantifications for intra-TAD activity (left; as highlighted in a) and expression of IKZF2 (right). Statistical evaluation for intra-TAD activity was performed using paired two-sided t test of average per interaction-bin for IKZF2 TAD between T cells (n = 3) and T-ALL (n = 6), followed by multiple testing correction. Log2 FPKM of IKZF2 expression for T cells (n = 13) and T-ALL (n = 6) samples; statistical evaluation was performed using edgeR followed by multiple testing correction. d) Hi-C interaction heat maps (first row) showing the CYLD locus (black circle). Second row shows heat maps of log2 (fold-change) interactions when compared to T-cell 1. e) H3K27ac ChIP-seq tracks for CYLD locus in T cells and CUTLL1, NOTCH1 ChIP-seq tracks for CUTLL1. Tracks represent fold-enrichment over input where applicable and counts-per-million reads otherwise. Grey area indicates TAD containing CYLD. Number replicates: T cells H3K27ac n = 2; CUTLL1 H3K27ac n = 2; CUTLL1 NOTCH1 n = 1. f) Quantifications for intra-TAD activity (left; as highlighted in D)) and expression of CYLD (right). Statistical evaluation for intra-TAD activity was performed using paired two-sided t test of average per interaction-bin for CYLD TAD between T cells (n = 3) and T-ALL (n = 6), followed by multiple testing correction (see methods). Log2 FPKM of CYLD expression for T cells (n = 13) and T-ALL (n = 6); statistical evaluation was performed using edgeR followed by multiple testing correction. Boxplot information can be found as additional Source Data.
