The SNARE Regulator Complexin3 is a Target of the Cone Circadian Clock in the Mouse Retina

Purpose: The goals of this study are to evaluate the impact of the removal of the key circadian clock component BMAL1 on the transcriptome of cone photoreceptors Methods: Cone mRNA profiles of adult wild-type (WT, HRGPcre;Bmal1f/+) and cone-specific BMAL1 (HRGPcre;Bmal1f/f or cone-Bmal1-/-) mice were generated by deep sequencing, in triplicate, using Illumina GAIIx. The sequence reads that passed quality filters were analyzed at the transcript isoform level with two methods: Burrows–Wheeler Aligner (BWA) followed by ANOVA (ANOVA) and TopHat followed by Cufflinks. qRT–PCR validation was performed using TaqMan and SYBR Green assays Results: Comparison of the cone transcriptome between cone-Bmal1-/- and wild-type littermates at a single time point (middle of the light phase) revealed 88 genes differentially expressed (P < 0.05, fold change > 2). As expected, these 88 genes included known clock components but also genes known to be involved in a wide range of functions: gene regulation, neuron development and structure, protein binding, and transport. Conclusions: Our study represents the first detailed analysis of cone-BMAL1 transcriptomes, with biologic replicates, generated by RNA-seq technology. These data are consistent with the view that the cone clock controls many aspects of the development, maintenance, and function of the cones through its control of the transcriptome. Overall design: Retinal cone photoreceptor mRNA profiles of adult wild type (WT) and cone-specific BMAL1-/- mice