Common variants in signaling transcription-factor-binding sites drive phenotypic variability in red blood cell traits

Abstract

Genome-wide association studies (GWAS) reveal genomic variants associated with human traits and diseases. Most trait-associated variants are located within cell type-specific enhancers, but the molecular mechanism by which they cause phenotypic variation is understood in only a few instances. Here, we show that a striking proportion of enhancer-variants associated with red blood cell (RBC) traits map to enhancers that are co-bound by lineage-specific master transcription factors (MTFs) and signaling transcription factors (STFs) that modulate levels of gene expression in response to extracellular signals. We find that the majority of the enhancer variants alter STF and not MTF motifs. Consequently, they perturb DNA-binding by various signaling factors including BMP/TGF-directed SMADs, WNT-induced TCFs, Hedgehog-responsive GLIs, Notch-dependent HES and affect downstream gene expression. Analysis of activity of SNPs in human CD34+ cells and eQTL analysis from the Framingham Heart Study (FHS) verifies that human alleles with disrupted STF binding lead to altered expression of genes that are upregulated during human erythroid differentiation. Our results propose that, of the RBC trait-associated variants that reside on TF binding sequences, the majority fall on DNA sequences recognized by STFs. This suggests that, in many cases, the phenotypic variation of RBC traits could be due to disruptions in STF motifs that lead to altered responsiveness to extracellular stimuli.