Fig. 5: The SLE risk-associated SNP rs2431697 alters NF-κB binding and the chromatin state to modulate miR-146a expression. | Nature Communications

Fig. 5: The SLE risk-associated SNP rs2431697 alters NF-κB binding and the chromatin state to modulate miR-146a expression.

From: SLE non-coding genetic risk variant determines the epigenetic dysfunction of an immune cell specific enhancer that controls disease-critical microRNA expression

Fig. 5: The SLE risk-associated SNP rs2431697 alters NF-κB binding and the chromatin state to modulate miR-146a expression.The alt text for this image may have been generated using AI.

a Generation of homozygous clones harboring the major and minor alleles with CRISPR/Cas9 in U-937 cells. b RT-qPCR analysis demonstrates decreased miR-146a expression in T/T clones compared to C/C clones both at native and stimulatory conditions (*P = 0.0239, **P = 0.0095) (four biological samples replicates and three biological replicates). c NF-κB preferentially binds to the C non-risk allele of rs2431697, as predicted by bioinformatics analysis. d, e NF-κB favors binding to the C non-risk allele at rs2431697 as determined by EMSA (d) and ChIP followed by AS-qPCR (e) in rs2431697 heterozygous U-937 cell clones, **P = 0.0021 (n = 3, biological replicates). NE, nuclear extract. AS-ChIP-qPCR, allele-specific ChIP-qPCR. f The rs2431697 C allele has higher chromatin accessibility than the T allele. FAIRE signal is significantly higher at the rs2431697 region for the C allele compared to the T allele as examined by FAIRE followed by AS-qPCR, suggesting rs2431697 may alter chromatin accessibility of this locus, ***P = 0.0005 (n = 3, biological replicates). AS-FAIRE-qPCR, allele-specific FAIRE-qPCR. Data are represented as mean ± SEM, and P-values are calculated using unpaired two-tailed Student’s t-test. *P < 0.05; **P < 0.01; ***P < 0.001. See also Supplementary Fig. 10.

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