Gene Expression Profiling of Granule Cells and Purkinje Cells in the Zebrafish Cerebellum

The structure of the neural circuitry of the cerebellum, which functions in some types of motor learning and coordination, is generally conserved among vertebrates. However, some cerebellar features are species-specific. It is not clear which genes are involved in forming these conserved and species-specific structures and functions. Here, using zebrafish transgenic larvae expressing fluorescent proteins in granule cells, Purkinje cells, or other cerebellar neurons and glial cells, we isolated each type of cerebellar cells by fluorescence-activated cell sorting and profiled their gene expressions by RNA sequencing and in situ hybridization. We identified genes that were upregulated in granule cells or Purkinje cells, including many genes that are also expressed in mammalian cerebella. A comparison of the transcriptomes in granule cells and Purkinje cells in zebrafish larvae revealed that more developmental genes are expressed in granule cells, whereas more neuronal-function genes are expressed in Purkinje cells. We further found that some genes that are upregulated in granule cells or Purkinje cells are also expressed in the cerebellum-like structures. Our data provide a platform for understanding the development and function of the cerebellar neural circuits in zebrafish, and the evolution of cerebellar circuits in vertebrates.