Figure 2: Identification of allele-specific interactors for rs1800734 and its potential gene targets. | Nature Communications

Figure 2: Identification of allele-specific interactors for rs1800734 and its potential gene targets.

From: The non-coding variant rs1800734 enhances DCLK3 expression through long-range interaction and promotes colorectal cancer progression

Figure 2

(a) Motif analysis interpreted that A-allele of the loci perturbs E-box motif. (b) The specific binding of TFAP4 (P1=2.0 × 10−6, P2=3.1 × 10−5, P3=7.8 × 10−5, Student’s t-test) and ELF1 (P1=2.1 × 10−4, P2=0.011, P3=6.9 × 10−4, Student’s t-test) on G- and A-allele was observed in the three different cell lines (data are represented as mean and error bars indicate s.d., n=3 pulldowns per SNP). ZFP62 binding on A-allele, as shown in Fig. 1d, was not consistent in all the three cell lines and was hence not considered as the general TF regulator at this locus. (c) This allele-specific binding was validated by ChIP-seq of TFAP4. This SNP did not change (d) the local chromatin accessibility and the expression of two cis-regulated genes (MLH1 and EPM2AIP1) (G (G-allele) and A (A-allele) of rs1800734, wt (wild-type allele) and del (deletion allele) of rs35149869, P-values: Fisher’s exact test). (e) eQTL analysis revealed a novel gene targets DCLK3 of this SNP (P-values were calculated in FastQTL software based on linear regression model).

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