Identification of novel cerebellar developmental transcriptional regulators with motif activity analysis
Thomas J. Ha,
Peter G. Y. Zhang,
Remi Robert,
Joanna Yeung,
Douglas J. Swanson,
Anthony Mathelier,
Wyeth W. Wasserman,
Sujin Im,
Masayoshi Itoh,
Hideya Kawaji,
Timo Lassmann,
Carsten O. Daub,
Erik Arner,
The FANTOM Consortium,
Piero Carninci,
Yoshihide Hayashizaki,
Alistair R. R. Forrest,
Daniel Goldowitz
Affiliations
Thomas J. Ha
Centre for Molecular Medicine and Therapeutics at the BC Children’s Hospital Research Institute, Department of Medical Genetics, University of British Columbia
Peter G. Y. Zhang
Centre for Molecular Medicine and Therapeutics at the BC Children’s Hospital Research Institute, Department of Medical Genetics, University of British Columbia
Remi Robert
Centre for Molecular Medicine and Therapeutics at the BC Children’s Hospital Research Institute, Department of Medical Genetics, University of British Columbia
Joanna Yeung
Centre for Molecular Medicine and Therapeutics at the BC Children’s Hospital Research Institute, Department of Medical Genetics, University of British Columbia
Douglas J. Swanson
Centre for Molecular Medicine and Therapeutics at the BC Children’s Hospital Research Institute, Department of Medical Genetics, University of British Columbia
Anthony Mathelier
Centre for Molecular Medicine and Therapeutics at the BC Children’s Hospital Research Institute, Department of Medical Genetics, University of British Columbia
Wyeth W. Wasserman
Centre for Molecular Medicine and Therapeutics at the BC Children’s Hospital Research Institute, Department of Medical Genetics, University of British Columbia
Sujin Im
Centre for Molecular Medicine and Therapeutics at the BC Children’s Hospital Research Institute, Department of Medical Genetics, University of British Columbia
Masayoshi Itoh
RIKEN Omics Science Center (OSC)
Hideya Kawaji
RIKEN Omics Science Center (OSC)
Timo Lassmann
RIKEN Omics Science Center (OSC)
Carsten O. Daub
RIKEN Omics Science Center (OSC)
Erik Arner
RIKEN Omics Science Center (OSC)
The FANTOM Consortium
RIKEN Omics Science Center (OSC)
Piero Carninci
RIKEN Omics Science Center (OSC)
Yoshihide Hayashizaki
RIKEN Omics Science Center (OSC)
Alistair R. R. Forrest
RIKEN Omics Science Center (OSC)
Daniel Goldowitz
Centre for Molecular Medicine and Therapeutics at the BC Children’s Hospital Research Institute, Department of Medical Genetics, University of British Columbia
Abstract Background The work of the FANTOM5 Consortium has brought forth a new level of understanding of the regulation of gene transcription and the cellular processes involved in creating diversity of cell types. In this study, we extended the analysis of the FANTOM5 Cap Analysis of Gene Expression (CAGE) transcriptome data to focus on understanding the genetic regulators involved in mouse cerebellar development. Results We used the HeliScopeCAGE library sequencing on cerebellar samples over 8 embryonic and 4 early postnatal times. This study showcases temporal expression pattern changes during cerebellar development. Through a bioinformatics analysis that focused on transcription factors, their promoters and binding sites, we identified genes that appear as strong candidates for involvement in cerebellar development. We selected several candidate transcriptional regulators for validation experiments including qRT-PCR and shRNA transcript knockdown. We observed marked and reproducible developmental defects in Atf4, Rfx3, and Scrt2 knockdown embryos, which support the role of these genes in cerebellar development. Conclusions The successful identification of these novel gene regulators in cerebellar development demonstrates that the FANTOM5 cerebellum time series is a high-quality transcriptome database for functional investigation of gene regulatory networks in cerebellar development.
