Identification of novel cerebellar developmental transcriptional regulators with motif activity analysis

• Published in: BMC genomics Vol. 20; no. 1; p. 718
• Main Authors: Ha, Thomas J, Zhang, Peter G Y, Robert, Remi, Yeung, Joanna, Swanson, Douglas J, Mathelier, Anthony, Wasserman, Wyeth W, Im, Sujin, Itoh, Masayoshi, Kawaji, Hideya, Lassmann, Timo, Daub, Carsten O, Arner, Erik, Carninci, Piero, Hayashizaki, Yoshihide, Forrest, Alistair R R, Goldowitz, Daniel
• Format: Journal Article
• Language: English
• Published: England BioMed Central Ltd 18.09.2019; BioMed Central; BMC
• Subjects: Activating Transcription Factor 4 - deficiency; Activating Transcription Factor 4 - genetics; Activating Transcription Factor 4 - metabolism; Animals; Binding sites; Biochemistry; Bioinformatics; Brain; Cerebellar development; Cerebellum; Cerebellum - embryology; Cerebellum - growth & development; Cerebellum - metabolism; Computational biology; Consortia; DNA binding proteins; Embryonic development; Embryos; Gene expression; Gene Expression Profiling; Gene Expression Regulation, Developmental; Gene Knockdown Techniques; Gene regulation; Genes; Genetic aspects; Genomics; HeliScopeCAGE; Laboratory rats; Libraries; Medicin och hälsovetenskap; Mice; Mice, Inbred C57BL; Motif activity; Novels; Nucleotide Motifs - genetics; Physiological aspects; Promoter Regions, Genetic - genetics; Regulatory Factor X Transcription Factors - deficiency; Regulatory Factor X Transcription Factors - genetics; Regulatory Factor X Transcription Factors - metabolism; RNA interference; Sequences; Transcription (Genetics); Transcription factors; Transcription Factors - deficiency; Transcription Factors - genetics; Transcription Factors - metabolism; Transcription, Genetic - genetics; Transcriptome; Transfactivity; Scrt2; RNAi; Transcription factors; HeliScopeCAGE; Transcriptome; Rfx3; Transfactivity; Atf4; Cerebellar development; Motif activity
• ISSN: 1471-2164; 1471-2164
• DOI: 10.1186/s12864-019-6063-9

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. 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. 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.