Three-dimensional organisation of the Runx1 locus

The proper regulation of gene expression is crucial for cell-fate and lineage determination of hematopoietic stem cells (HSCs). Dysregulated expression of genes that drive haematopoietic differentiation can cause blood disorders, including leukaemia. Connecting hematopoietic genes with their regulatory elements is central to correct gene regulation, and is orchestrated by chromatin modifiers, including the genome organising protein complex, cohesin. The developmental transcription factor RUNX1/AML1 is a well-known leukaemia-associated gene. Runx1 is an important regulator of haematopoiesis in vertebrates; it is crucial for early myeloid differentiation, and plays a vital role in adult blood development. Genetic disruptions to the RUNX1 gene are frequently associated with Acute Myeloid Leukaemia (AML). Despite the well-established role of RUNX1 in haematopoiesis and disease contribution, the cis-regulatory mechanisms that modulate RUNX1 require further elucidation. Gene regulatory elements, such as enhancers, located in non-coding DNA are likely to be important for Runx1 transcription. My PhD studies provided insight into mouse Runx1 enhancer functions and highlighted the features of conserved human enhancers. I also used circular chromosome conformation capture sequencing (4C-seq) to identify DNA interactions with the previously identified +24 RUNX1 enhancer, which is essential for HSC expression of RUNX1. Using cohesin-deficient K562 leukaemia cells, my work shows that cohesin is required for the +24 enhancer (also known as eR1) to anchor an insulated neighbourhood that shields RUNX1 from outside influences. Striking results from this work show that the +24 Runx1 enhancer is a significant cohesin-dependent organiser of Chromosome 21 during megakaryocyte differentiation. In summary, my PhD studies identified a bouquet of enhancer-anchored connections that regulate RUNX1 transcription in leukaemia cells at steady state and during differentiation, and explain why cohesin loss dysregulates the expression of this important leukaemogenic gene