CTCF Mediated Enhancer and Promoter Interaction Regulates Differential Expression of TAL1 Oncogene in Normal and Malignant Hematopoiesis

Abstract 281

The key hematopoietic transcription factor TAL1/SCL is essential for the specification of hematopoietic stem cells (HSCs) and differentiation along myeloid and erythroid lineages. However, ectopic activation of TAL1 gene is the most frequent gain-of-function mutation associated with childhood T-cell acute lymphoblastic leukemia (T-ALL) in approximately 60% of patients. To understand underlying epigenetic mechanisms of TAL1 activation in normal and in malignant hematopoiesis, we performed ChIP, ChIP-seq, and chromatin conformation capture assays to investigate chromatin structure profile which correlates with transcriptional activation, at the TAL1 locus comparing erythroid progenitors, K562 and CD36+ cells, with T-ALL cells, Jurkat and Rex cells. We found distinct epigenetic landscape and chromatin organization across the TAL1 locus in these two different types of hematopoietic cells. Although H3K4me3 is enriched at the TAL1 promoter in both erythroid progenitors and in T-ALL cells, the erythroid specific +51 enhancer is marked by active histone modifications only in erythroid progenitors, but not in T-ALL cells. Furthermore, we demonstrated that +51 enhancer interacts with the TAL1 promoter 1a via a long range chromatin loop in vivo in erythroid CD36+ and K562 cells. The recruitment of hSET1 HMT complex facilitates this enhancer/promoter chromatin interaction and depletion of hSET1 leads to loss of H3K4 methylation, enhancer/promoter interaction, RNA PolII loading, and TAL1 transcription at both the TAL1 promoter 1a and the +51 enhancer. In addition, loss of SET1 in CD34+ HSCs exhibited a significant reduction in the formation of CFU-E and BFU-E colonies. In contrast, neither H3K4 methylation nor enhancer/promoter interaction was detected at the +51 enhancer in T-ALL cells. Finally, we investigated the role of insulator protein CTCF in the regulation of TAL1 expression in normal and in malignant cells. We found that regardless of similar CTCF binding patterns at the TAL1 locus in erythroid progenitors and T-ALL cells, CTCF elements flanking the TAL1 locus mediate a long-range loop that encloses TAL1 promoter and enhancer in the same chromatin domain in erythroid progenitors, whereas in T-ALL Jurkat cells the CTCF site located between the promoter 1a and the +51 enhancer forms a repressive loop that expels the +51 enhancer from the same domain with the promoter 1a. Overall, our study demonstrates that a novel long range intrachromosomal interaction between the TAL1 promoter 1a and the +51 enhancer regulated and organized by hSET1 histone methyltransferase and insulator protein CTCF controls TAL1 promoter activity in normal versus malignant hematopoiesis.