Transcriptional Profiling of Daily Patterns of mRNA Expression in the C57BL/6J Mouse Cornea

Purpose: The purpose of this study was to determine how the transcriptome of the murine cornea adapts to diurnal changes in physiology. Methods: C57BL/6J mice were maintained under a 12-h light/12-h dark (LD) cycle for two weeks. Corneas were collected from euthanized mice at Zeitgeber time (ZT) 0, 3, 6, 9, 12, 15, 18, and 21. Total RNA was extracted and subjected to RNA sequencing (RNA-Seq). A JTK_CYCLE algoithm and other software tools were used to analyze the transcriptional data to determine the periodicity, rhythmicity, and amplitude of the transcripts. Gene Ontology (GO) and the Kyoto Encyclopedia of Genes and Genomes (KEGG) were used to analyze the enrichment of cycling transcripts. Results: Approximately 24% of the total transcripts from the murine corneal genome were rhythmically expressed over an LD cycle. GO analysis showed that these cycling genes are primarily involved in cellular and metabolic processes. A KEGG pathway analysis identified 6 branches and 44 pathways that encode the gene outputs necessary for basic cellular functions and processes. More importantly, most of the rhythmic genes between the day and night are enriched in their own unique pathways in addition to some common pathways. Furthermore, most of the rhythmic gene expression was concentrated in the 12-h and 24-h periods. A comparative analysis of GO and KEGG showed large differences in metabolic processes, but not cellular processes. Finally, the murine cornea also rhythmically expressed 11 canonical components of circadian clock genes over an LD cycle at the transcriptional level. Conclusions: One fourth of the corneal transcriptome follows a rhythmic expression pattern involved in basic molecular and cellular mechanisms. This implies that the time of day contributes significantly to the overall temporal organization of the corneal transcriptome.