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. This study uses zebrafish transgenic larvae expressing fluorescent proteins in granule cells, Purkinje cells, or other cerebellar neurons and glial cells to isolate each type of cerebellar cells by fluorescence-activated cell sorting and to profile their gene expressions by RNA sequencing and in situ hybridization. We identify genes that are upregulated in granule cells or Purkinje cells, including many genes that are also expressed in mammalian cerebella. Comparison of the transcriptomes in granule cells and Purkinje cells in zebrafish larvae reveals that more developmental genes are expressed in granule cells, whereas more neuronal-function genes are expressed in Purkinje cells. We show 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. J. Comp. Neurol. 525:1558-1585, 2017. © 2016 Wiley Periodicals, Inc.
Laboratory of Organogenesis and Organ Function, Bioscience and Biotechnology, Nagoya University, Nagoya, Aichi, 464-8601, Japan.
Miki
M
Takeuchi
Division of Biological Science, Graduate School of Science, Nagoya University, Nagoya, Aichi, 464-8602, Japan.
Shingo
S
Yamaguchi
Division of Biological Science, Graduate School of Science, Nagoya University, Nagoya, Aichi, 464-8602, Japan.
Yoshimasa
Y
Sakakibara
Division of Biological Science, Graduate School of Science, Nagoya University, Nagoya, Aichi, 464-8602, Japan.
Takuto
T
Hayashi
Laboratory of Organogenesis and Organ Function, Bioscience and Biotechnology, Nagoya University, Nagoya, Aichi, 464-8601, Japan.|Division of Biological Science, Graduate School of Science, Nagoya University, Nagoya, Aichi, 464-8602, Japan.
Koji
K
Matsuda
Phyloinformatics Unit, RIKEN Center for Life Science Technologies, Kobe, Hyogo, 650-0047, Japan.
Yuichiro
Y
Hara
Phyloinformatics Unit, RIKEN Center for Life Science Technologies, Kobe, Hyogo, 650-0047, Japan.
Chiharu
C
Tanegashima
Laboratory of Organogenesis and Organ Function, Bioscience and Biotechnology, Nagoya University, Nagoya, Aichi, 464-8601, Japan.|Division of Biological Science, Graduate School of Science, Nagoya University, Nagoya, Aichi, 464-8602, Japan.
Takashi
T
Shimizu
Phyloinformatics Unit, RIKEN Center for Life Science Technologies, Kobe, Hyogo, 650-0047, Japan.
Shigehiro
S
Kuraku
Laboratory of Organogenesis and Organ Function, Bioscience and Biotechnology, Nagoya University, Nagoya, Aichi, 464-8601, Japan.|Division of Biological Science, Graduate School of Science, Nagoya University, Nagoya, Aichi, 464-8602, Japan.
Masahiko
M
Hibi
D000818:Animals; D030801:Animals, Genetically Modified; D002531:Cerebellum / Q000166:cytology* / Q000196:embryology / Q000254:growth & development; D005434:Flow Cytometry; D020869:Gene Expression Profiling; D007150:Immunohistochemistry; D017403:In Situ Hybridization; D046228:Microarray Analysis; D055495:Neurogenesis / Q000235:genetics*; D009474:Neurons / Q000166:cytology*; D016133:Polymerase Chain Reaction; D011689:Purkinje Cells / Q000166:cytology*; D059467:Transcriptome; D015027:Zebrafish / Q000196:embryology / Q000235:genetics / Q000254:growth & development
RNA-seq; RRID:AB_10013361; RRID:SCR_001120; RRID:SCR_001370; RRID:ZIRC_ZL1; cerebellar gene enrichment; cerebellum-like structures