Looping of genes flanking TAL1 suggest coregulation with TAL1 expression and involvement in T-ALL. (A) 4C-microarray interaction patterns obtained across the human TAL1 locus in K562 cells using TAL1 promoter 1b as the “bait”. Y-axis is the frequency of interactions expressed as a proportion of the “bait” signal for each microarray tile. Bars on the x-axis show the location of each tile across the TAL1 locus and its flanking genes. Looping interactions between TAL1 promoter 1b and the gene bodies of the TAL1, PDZK1IP1, and STIL are highlighted (black lines). The scale (in kb) is shown at the bottom left. (i) Schematic organization of the TAL1 hub with schematic interactions between the hub core, TAL1, and its flanking genes highlighted by the light gray arrows. (ii) The 4C interaction peak (−81) located in STIL intron 1 at the site of the TAL^d breakpoints found in patients with T-ALL. The extents of known TAL^d deletions are also shown by the horizontal gray bar (dotted gray portion represents a region of 8 kb known to contain breakpoints near the 5′ end of TAL1). (B) PDZK1IPI, STIL, and CMPK1 transcript levels (with SEs) in GATA1 knockdown samples 48 and 96 hours after transfection are shown relative to levels in the luciferase control samples. ACTB and TUBB were used as gene expression controls. (C) Bar diagrams of TAL1 promoter/STIL intron 1 (−81/TAL^d) looping interactions detected by 3C in K562 cells 96 hours after siRNA transfection with either GATA1 (KD) or with luciferase (LUC). P value is indicated for relative ligation frequencies which are significantly reduced between P^TAL1 and TAL^d at 96 hour of GATA1 knockdown when compared with the corresponding LUC control. (D) ChIP-quantitative PCR occupancy for Pol II at the STIL and CMPK1 promoters 96 hours after transfection with GATA1 (black) or luciferase (gray) siRNA. Control was the TBP promoter (Figure 2F). (E-F) Comparison of looping interactions at the TAL1 locus in 2 T-ALL cell lines: HPB-ALL (TAL1 nonexpressing) and Jurkat (TAL1 expressing). Ligation frequencies were normalized against ERCC3 ligation frequencies. The location of the Jurkat −7 enhancer²¹  ∼500 bp downstream of −8 is shown in panel E. P values are indicated for interactions which are significantly higher in Jurkat cells. (C,E,F) Interaction frequencies are shown with SEs. Location of the 3C “bait” region (TAL1 promoter 1b) is denoted by vertical gray arrows. *P < .05; **P < .01; ***P < .001; ****P < .0001.