Regulatory Variants and Disease: The E-Cadherin −160C/A SNP as an Example
Figure 1
rSNPs regulate gene transcription by affecting transcription factor (TF) binding. rSNPs in regulatory sequences such as gene promoters may affect gene expression at the transcriptional level and this regulation is mainly realized through affecting transcription factor binding. In the example of −160C/A SNP in E-cadherin promoter, the −160 location is the binding site of putative TFs. The C allele of this site allows for binding of the TFs, as evidenced by a protected footprint on DNA footprinting assay, leading to active transcription of E-cadherin gene (a), whereas the A allele prevents the TFs from binding likely due to steric hindrance, resulting in the loss of footprint of the TFs and attenuated transcription (b) [42].
