Fig. 3.

HIC1 binding at the 2q13 locus. a The rs7594852-C allele creates a stronger binding site for the hypermethylated in cancer 1 (HIC1) protein. The sequence logo of the HIC1-binding motif shows the DNA binding preferences of HIC1. Tall nucleotides above the dashed line indicate DNA bases that are preferred by HIC1, whereas bases below the dashed line are disfavored. The y-axis indicates the relative free energies of binding for each nucleotide at each position. The height of each nucleotide can be interpreted as the free energy difference from the average (ΔΔG) in units of gas constant (R) and temperature (T). The DNA sequence flanking the rs7594852-C allele is shown directly below, with the alternative rs7594852-T allele shown at the bottom. The rs7594852-T allele changes the HIC1 binding site sequence from C (most favored) to T (less favored). b UC Santa Cruz Genome Browser screenshot depicting the rs7594852 locus. The purple (CKAP2L) and black (IL1A) graphics at the top indicate the locations of exons (columns), untranslated regions (rectangles), and introns (horizontal lines), with arrows indicating the direction of transcription. The red vertical line indicates the position of rs7594852, which overlaps strong signals obtained from chromatin immunoprecipitation sequencing (ChIP-seq) experiments (indicating histone modification by mono-, di-, or trimethylation of histone H3 on lysine 4; H3K4) in trophoblast cultured cells, placental amnion, or fetal placenta. c Experimental validation of allele-dependent binding of human purified recombinant HIC1 protein with a c-Myc/DDK tag to rs7594852 and flanking sequence via electrophoretic mobility shift assay (EMSA). Arrows indicate allele-dependent binding of HIC1 (bottom arrow) and a supershift of the protein–DNA complex induced by the binding of the anti-DDK antibody to the complex (top arrow). The presence of multiple bands in lanes 3 and 4 is likely due to the presence of multiple HIC1 isoforms. Source data are provided as a Source Data file