G-quadruplex structures at the promoter of HOXC10 regulate its expression

Abstract As a member of the homeobox gene family, HOXC10 plays an important role in cell differentiation and embryonic development of mammals. Increasing evidence also suggests a regulatory role of HOXC10 in oncogenesis, but the regulation of HOXC10 gene expression is relatively understudied. In this report, we revealed that the HOXC10 promoter contains multiple G-tracts in its negative strand and has high potential of forming G-quadruplex structures. In circular dichroism studies, synthesized oligonucleotides based on the G-rich region of 241–297 base pairs upstream of the HOXC10 transcription start site showed molar ellipticity at specific wavelengths characteristic of G-quadruplex structures. Analyses of these oligonucleotides by native polyacrylamide gel electrophoresis, gel-shift assay, immunostaining and replication stop assay revealed formation of multiple types of G-quadruplex structures in presence of potassium and lithium ions. In reporter assays, mutations or deletion of the G-tracts could differentially impact the expression of Gaussia luciferase downstream of the HOXC10 promoter. Additionally, CHD7, a chromatin remodeling protein with DNA helicase activity, could associate with the HOXC10 promoter and likely unwind the G-quadruplex structures to enhance its gene expression.