Fig. 3: rs398206 displays allele-preferential binding to YY1. | Nature Communications

Fig. 3: rs398206 displays allele-preferential binding to YY1.

From: Massively parallel reporter assays of melanoma risk variants identify MX2 as a gene promoting melanoma

Fig. 3: rs398206 displays allele-preferential binding to YY1.The alternative text for this image may have been generated using AI.

a Quantitative mass-spectrometry of rs398206 using nuclear extract of UACC903 and 21 bp double-stranded DNA probes with A (risk) or C (protective) alleles. A-allele specific interacting proteins are shown in the bottom right quadrant, and C-allele specific interactors in the top left quadrant. Using label-swapping of high(H)-mass or low(L)-mass label, the A-bound/C-bound ratio is shown on the x-axis, and the C-bound/A-bound ratio on the y-axis. Proteins passing the inter-quartile >3 cutoff for both axes are color-coded for consistent (red circle) and inconsistent (yellow circle) direction from label-swapping. Names of consistently identified proteins are shown. b YY1 binding motif is shown as a position weight matrix at the top (motif obtained from HOCOMOCO database and plotted using weblogo3). The genomic sequence surrounding rs398206 is shown at the bottom with the risk-associated A allele matching the consensus YY1-binding motif. Genomic positions are hg19. c–d EMSAs using 21 bp double-stranded DNA probes with a or c alleles of rs398206 and nuclear extract from UACC2331 melanoma cells (c) or purified recombinant YY1 protein (d). Antibody super-shift using anti-YY1 antibody is shown at the last lanes of c, where the A-specific band (arrows) is diminished. Representative sets from three replicates (c) and one replicate (d) are shown. Source data are provided as a Source Data file.

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