ChIP-seq analysis revealed MEF2D-MRE and crystallographic characterization of MEF2D-DNA_MRE engagement. (A) Venn diagram illustrating the overlap between DNA regions bound by MH fusion or WT MEF2D, as identified by ChIP-seq analysis with anti-FLAG antibodies in CD34⁺ cells sorted from human cord blood. (B) MEF2D-MRE sequence. Motif analysis summarized the MEF2 DNA motifs found in the regions bound by MH or WT MEF2D. The ChIP-seq analysis with stable expression of MH fusion helped to uncover a consensus binding site in MH-driven transcriptional deregulation. (C) Density heatmap of MH and MEF2D binding peaks. Heatmap is shown for a region extending from −2 kb to 2 kb relative to the peak summit. Top, peaks with increased binding of MH compared with WT MEF2D. Bottom, peaks with decreased binding of MH compared with WT MEF2D. (D) Side view of the MEF2D_2-95-DNA_MRE complex. The crystal structure is shown in cartoon representation. The DNA-binding motifs R3/K4/K5 and R15/K23/K31 in the MEF2D are shown in ball and stick representations. The DNA nucleotides TATTTATA (ie, the MRE core) are labeled. The 2 subunits in MEF2D dimer are colored in magenta and cyan, respectively. (E) Vertical view of the MEF2D-DNA engagement. The protein is rendered according to the electrostatic charge in the surface, in which the positive and negative charges are shown in blue and red, respectively. (F) MEF2D tetramer and MRE crosslinking. Four MEF2D subunits are colored in magenta, cyan, yellow, and green, respectively. D63/L67/T70 in the tetrameric interface (boxed) are labeled and shown in stick representation.