Runx1 binds as a dimeric complex to overlapping Runx1 sites within a palindromic element in the human GM-CSF enhancer

Abstract

Runx1 is a developmentally regulated transcription factor that is essential for haemopoiesis. Runx1 can bind as a monomer to the core consensus sequence TGTGG, but binds more efficiently as a hetero-dimer together with the non-DNA binding protein CBFβ as a complex termed core binding factor (CBF). Here, we demonstrated that CBF can also assemble as a dimeric complex on two overlapping Runx1 sites within the palindromic sequence TGTGGCTGCCCACA in the human granulocyte macrophage colony-stimulating factor enhancer. Furthermore, we demonstrated that binding of Runx1 to the enhancer is rigidly controlled at the level of chromatin accessibility, and is dependent upon prior induction of NFAT and AP-1, which disrupt a positioned nucleosome in this region. We employed in vivo footprinting to demonstrate that, upon activation of the enhancer, both sites are efficiently occupied. In vitro binding assays confirmed that two CBF complexes can bind this site simultaneously, and transfection assays demonstrated that both sites contribute significantly to enhancer function. Computer modelling based on the Runx1/CBFβ/DNA crystal structure further revealed that two molecules of CBF could potentially bind to this class of palindromic sequence as a dimeric complex in a conformation whereby both Runx1 and CBFβ within the two CBF complexes are closely aligned.

MicroRNA-378-mediated suppression of Runx1 alleviates the aggressive phenotype of triple-negative MDA-MB-231 human breast cancer cells

“…Therefore, motif analyses were performed to determine the presence of the most commonly observed Runx1 core DNA binding motif TGTGGT in the promoter region (+/− 2 kb from the transcription start site) of PPARGC1B (Fig. 4A) [60, 61]. These initial investigations revealed three such sites, indicating the potential for Runx1 to bind and regulate the miR-378 host gene PPARGC1B (Fig.…”

Improved eye- and skin-color prediction based on 8 SNPs

“…AML1 can improve its DNA binding capacity by forming a complex with a non-DNA binding protein (CBF beta) (30). AML1 recognizes the DNA sequence TGPyG G T, where Py stands for pyrimidine (T or C) (30). The bold G indicates the position of rs12896399.…”

Genetic regulation of the RUNX transcription factor family has antitumor effects

“…Notably, the doxycycline-dependent increase in the expression levels of RUNX2 and RUNX3 was detectable at 48 hours of incubation ( Figure 3A and Supplemental Figure 7A), suggesting that RUNX2 and RUNX3 might compensate for the loss of RUNX1 expression. Although the expression levels of well-established RUNX1-target genes (IL3, CSF2, and CSF2RB) (31)(32)(33) were decreased at 24 hours after RUNX1 knockdown, their expression levels were reciprocally increased at 48 hours after RUNX1 knockdown and accompanied by RUNX2 and RUNX3 stimulation ( Figure 3A). Forced expression of RUNX1, RUNX2, or RUNX3 suppressed the expression of RUNX2 and RUNX3, RUNX1 and RUNX3, or RUNX1 and RUNX2, respectively (Supplemental Figure 7B).…”