Rhoenhancers play unexpectedly minor roles inRhodopsintranscription and rod cell integrity

Abstract

ABSTRACTEnhancers function with a basal promoter to control the transcription of target genes. Enhancer regulatory activity is often studied using reporter-based transgene assays. However, unmatched results have been reported when selected enhancers are silencedin situ. In this study, using genomic deletion analysis in mice, we investigated the roles of two previously identified enhancers and the promoter of theRhogene that codes for the visual pigment rhodopsin. TheRhogene is robustly expressed by rod photoreceptors of the retina, and essential for the subcellular structure and visual function of rod photoreceptors. Mutations inRHOcause severe vision loss in humans. We found that eachRhoregulatory region can independently mediate local epigenomic changes, but only the promoter is absolutely required for establishing activeRhochromatin configuration and transcription and maintaining the cell integrity and function of rod photoreceptors. To our surprise, twoRhoenhancers that enable strong promoter activation in reporter assays are largely dispensable forRhoexpressionin vivo. Only small and age-dependent impact is detectable when both enhancers are deleted. Our results demonstrate context-dependent roles of enhancers and highlight the importance of studying functions ofcis-regulatory regionsin the native genomic context.