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[Preprint]. 2023 Oct 6:2023.10.05.561076. [Version 1] doi: 10.1101/2023.10.05.561076

Figure 4. Allele- and cell-type specific differential nuclear protein affinities of the prioritized SNPs rs57494551 and rs4938572 on the shared DDX6-CXCR5 risk region.

Figure 4.

(A-D) Radiolabeled electromobility shift assays (EMSA) were performed to assess the binding affinity of ribonucleoproteins isolated from EBV B or A253 cells to oligonucleotides containing the non-risk (NR) or risk (R) allele of (A-B) rs57494551 or (C-D) rs4938572. Probes incubated in the absence of nuclear lysate were used as negative control (Lanes 1, 2). Cold competitors were used to assess non-specific binding (Lanes 5, 6). Images shown in (A) and (C) are representative of n>6 biological replicates. (B, D) Bands indicated in (A, C) by the orange or green circles were quantified by densitometry and analyzed using paired t-test (n>6); p-values indicated. (E) Summary analysis of the allele-specific nuclear protein affinities of the five prioritized SNPs in EBV B, Daudi, Jurkat, THP1, and A253 cells shown in A-D and Supplemental Figures 4-9. Increases in binding relative to NR are shown in red; decreases relative to NR in blue; no change relative to NR in grey; no detected band in black; data not available in white.