Transcription factor cooperativity at a GATA3 tandem DNA sequence determines oncogenic enhancer-mediated activation.
The TAL1 oncogene driving T-cell lymphoblastic leukemia (T-ALL) is frequently activated through a mutated cis-regulatory element, whereby small indels create a binding site for the transcription factor MYB. Unravelling how noncoding mutations create oncogenic enhancers is key to understanding cancer biology and can provide important insights into fundamental mechanisms of gene regulation. Utilising a CRISPR-Cas9 screening approach, we identified GATA3 as the key transcriptional regulator of enhancer-mediated TAL1 overexpression. CRISPR-Cas9 engineering of the mutant enhancer revealed a tandem GATA3 site that is required for binding of GATA3, acquisition of an open chromatin state and recruitment of MYB. Reciprocally, MYB binding to its motif is required for GATA3 recruitment, consistent with a transcription factor cooperativity model. Importantly, we show that GATA3 stabilises a TAL1-MYB interaction and that complex formation requires GATA3 binding to DNA. Our work sheds light on the mechanisms of enhancer-mediated oncogene activation, where key TFs cooperate to achieve maximal transcriptional output and thereby support leukemogenesis. Overall design: ATAC-Seq on JURKAT cell line expressing endogenous GFP-tagged TAL1 with different modification of TAL1 enhancer by CRISPR (wildtype (WT), mutation of the TAL1 enhancer-repaired (MuTER), GATA3 binding sites 2 and 3 disrupted (2m3m)), and KOPT-K1 cell line as a control with low TAL1 expression.