PT - JOURNAL ARTICLE AU - Reafa A. Hossain AU - Nicholas R. Dunham AU - Megan E. Harris AU - Taylor L. Hutchinson AU - Justin M. Kidd AU - Lindsay R. Kohler AU - Gregory J. Salamon AU - Alexander L. Schmidt AU - Madison D. Thomas AU - Raymond A. Enke AU - Christopher E. Berndsen TI - Modeling of Epigenetic Modification-Induced Changes in CRX-dependent Genes <em>cis</em>-Regulatory Elements AID - 10.1101/179523 DP - 2017 Jan 01 TA - bioRxiv PG - 179523 4099 - http://biorxiv.org/content/early/2017/08/22/179523.short 4100 - http://biorxiv.org/content/early/2017/08/22/179523.full AB - Purpose DNA methylation is a well characterized epigenetic repressor of mRNA transcription in many plant and vertebrate systems. However, the mechanism of this repression is not fully understood. The process of synthesizing a strand of RNA from DNA, or transcription, is controlled by proteins that regulate RNA polymerase activity by binding to specific gene regulatory sequences. Cone-rod homeobox (CRX) is a well-characterized mammalian transcription factor that controls photoreceptor cell specific gene expression. While much is known about the functions and DNA binding specificity of CRX, less is known about how DNA methylation modulates CRX binding affinity to genomic cis-regulatory elements.Methods We used bisulfite pyrosequencing of human ocular tissues to measure DNA methylation levels of the regulatory regions of RHO, PDE6B, PAX6, and LINE. To describe the molecular mechanism of repression, we used molecular modeling to illustrate the effect of DNA methylation on human RHO regulatory sequences.Results In this study, we demonstrate an inverse correlation between DNA methylation in regulatory regions adjacent to the human RHO and PDE6B genes and their subsequent transcription in human ocular tissues. Docking of CRX to our DNA models shows that CRX interacts with the grooves of these sequences, suggesting changes in groove structure could regulate binding. Molecular dynamics simulations of the RHO promoter and enhancer regions show changes in the flexibility and groove width upon epigenetic modification. Models also demonstrate that changes to the local dynamics of CRX binding sites within RHO regulatory sequences which may account for the repression of CRX dependent transcription.Conclusion Collectively, these data demonstrate epigenetic regulation of CRX binding sites in human retinal tissue and provide insight into the mechanism of this mode of epigenetic regulation to be tested in future experiments.