Methylation of a HTR3A promoter variant alters the binding of transcription factor CTCF

Genetic studies pertaining to effector molecules have been pivotal in schizophrenia research. The serotonin receptor HTR3A is an effector that plays a key role in schizophrenia development. Previously, we identified a promoter variant of HTR3A, rs1062613, to be associated with the disease in the Indian population. The present study was undertaken to dissect the possible functional role of rs1062613. Using in silico simulation and in vitro gel shift assays, the CCCTC-binding factor (CTCF) was found to bind at this variation site. A C/T polymorphism was found to affect the DNA binding of CTCF where CTCF binds less proficiently to the T-allele (alternate allele). Moreover, the binding was found to be dependent on methylation at the C-allele (reference allele). The CTCF was found to bind with a greater strength to methylated cytosine. A molecular dynamics simulation suggested the possible role of CTCF N-terminal in providing binding flexibility. Our results suggest the role of epigenetic mechanisms in the development of schizophrenia by modulating transcription factor binding.