Fig. 4: A candidate causal variant in the MS4A locus disrupts an anchor CTCF binding site and is associated with reduced chromatin accessibility and increased MS4A6A gene expression in myeloid cells and in the brain. | Nature Communications

Fig. 4: A candidate causal variant in the MS4A locus disrupts an anchor CTCF binding site and is associated with reduced chromatin accessibility and increased MS4A6A gene expression in myeloid cells and in the brain.

From: Integration of Alzheimer’s disease genetics and myeloid genomics identifies disease risk regulatory elements and genes

Fig. 4: A candidate causal variant in the MS4A locus disrupts an anchor CTCF binding site and is associated with reduced chromatin accessibility and increased MS4A6A gene expression in myeloid cells and in the brain.

a (i) AD GWAS signal in the MS4A locus. (ii) H3K27ac peaks in microglia. (iii) H3K4me2 peaks in microglia. (iv) ATAC-seq peaks in microglia. (v) Genes that reside in the locus are plotted. Putative AD risk genes are highlighted in red. The arrow indicates the direction of transcription, while the bar indicates the gene body. (vi) Strongest promoter-capture Hi–C interactions between the MS4A6A promoter and distal regulatory elements contained within the CTCF loop in monocytes (blue) and macrophages (red). (vii) CTCF ChIP-Seq peaks in monocytes. The peaks highlighted in red are anchor CTCF binding sites for the chromatin loop. (viii) CTCF ChIA-PET interactions in GM12878. (ix) RAD21 ChiA-PET interaction in GM12878. b (i) AD GWAS signal in the MS4A locus. (ii) CTCF ChIP-Seq peaks in monocytes. The peak highlighted in red is an anchor CTCF binding site for a chromatin loop and contains the candidate causal variant (rs636317-T). (iii) A CTCF binding motif resides in the CTCF ChIP peak highlighted in red in (ii). The candidate causal variant (rs636317-T) resides in position 7 (boxed) of this motif and is predicted to disrupt CTCF binding. (iv) Genes that reside in the locus are plotted. Putative AD risk genes are highlighted in red. The arrow indicates the direction of transcription, while the bar indicates the gene body. c Immunofluorescent images of microglial markers (CX3CR1, TREM2, P2RY12 and PU.1) confirming differentiation of hiPSC-derived microglia. Scale bar = 100μm. d Allelic imbalance of chromatin accessibility at the rs636317 site is observed in hiPSC-derived microglia. Mean normalized ATAC-Seq read counts are plotted for the protective (C) and risk-increasing (T) alleles; the dots represent each individual, centers for the error bars represent mean normalized ATAC-seq read counts and error bars represent standard errors. The protective allele (C) shows significantly more ATAC-Seq read counts than the risk-increasing allele (T) (P-value = 0.007, paired one-sided t-test), which is consistent with the hypothesis that the presence of the rs636317 AD risk-increasing allele leads to disruption of CTCF binding. e Allelic imbalance of chromatin accessibility at the rs636317 site is observed in the brain. Each pair of dots connected by a grey line represent an individual. The protective allele (C) shows significantly more ATAC-Seq read counts than the risk-increasing allele (T) (P-value = 0.006, paired one-sided t-test, n = 32), which replicates our observations in hiPSC-derived microglia. f Allelic imbalance in normalized brain RNA-seq reads at rs12453 site. Each pair of dots connected by a grey line represent an individual. The protective allele (C) shows significantly less MS4A6A RNA-Seq read counts than the risk-increasing allele (T) (P-value = 0.002, paired one-sided t-test, n = 118), which is consistent with our hypothesis. g Relative expression of MS4A6A in macrophages increases in a rs636317-T allele dose-dependent manner. Each dot represents the relative expression level of MS4A6A in each individual, while the yellow dot represents the median. Horizontal lines in box plots depict 25%, 50%, and 75% quantiles; lower whisker = lower hinge - 1.5*IQR; upper whisker = upper hinge + 1.5*IQR.

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