Transcriptomic Analysis Identifies Candidate Genes for Differential Expression duringXenopus laevisInner Ear Development

Abstract

ABSTRACTBackgroundThe genes involved in inner ear development and maintenance of the adult organ have yet to be fully characterized. Previous genetic analysis has emphasized the early development that gives rise to the otic vesicle. This study aimed to bridge the knowledge gap and identify candidate genes that are expressed as the auditory and vestibular sensory organs continue to grow and develop until the systems reach postmetamorphic maturity.MethodsAffymetrixmicroarrays were used to assess inner ear transcriptome profiles from threeXenopus laevisdevelopmental ages where all eight endorgans comprise mechanosensory hair cells: larval stages 50 and 56, and the post-metamorphic juvenile. Pairwise comparisons were made between the three developmental stages and the resulting differentially expressedX.laevisProbe Set IDs (Xl-PSIDs) were assigned to four groups based on differential expression patterns. DAVID analysis was undertaken to impart functional annotation to the differentially regulated Xl-PSIDs.ResultsAnalysis identified 1510 candidate genes for differential gene expression in one or more pairwise comparison. Annotated genes not previously associated with inner ear development emerged from this analysis, as well as annotated genes with established inner ear function, such asoncomodulin,neurod1,andsp7. Notably, 36% of differentially expressed Xl-PSIDs were unannotated.ConclusionsResults draw attention to the complex gene regulatory patterns that characterizeXenopusinner ear development, and underscore the need for improved annotation of theX. laevisgenome. Outcomes can be utilized to select candidate inner ear genes for functional analysis, and to promoteXenopusas a model organism for biomedical studies of hearing and balance.