Prdm16 regulation of Shh-Gli1-Hoxc4 signaling is required for Granule Neuron Progenitor expansion and cerebellar related behavior

Purpose:To gain a deeper insight into how Prdm16 regulates cerebellar development, RNA-sequencing (RNA-seq) was performed to analyze the genome-wide changes by Prdm16 deletion at P3. Methods: Total RNA was extracted from P3 cerebellar tissue of Prdm16 cKO and Prdm16fl/fl mice. Then total RNA was quality controlled and quantified using an Agilent 2100 Bioanalyzer. After converting to cDNA and building library, high-throughput sequencing was performed using the Illumina HiSeq 2500 platform in Annoroad Genomics. Results: Approximately approximately one thousand transcripts showed differential expression between the Prdm16fl/fl and Prdm16 cKO cerebellum, with a fold change ≥1.5 and p value <0.05. Gene ontology (GO) analysis showed that the down-regulated genes were enriched in the terms related to regulation of glial cell differentiation and forebrain development, and cerebellum development. Up-regulated genes showed a significant enrichment of terms involved in negative regulation of cell differentiation. These results reflected the importance of Prdm16 in cerebellar development. Conclusions: We conclude that RNA-seq based transcriptome characterization would provide a framework for understanding how Prdm16 gene contribute to cerebellar development. Total RNA was extracted from P3 cerebellar tissue of Prdm16 cKO and Prdm16fl/fl mice and generated by deep sequencing, in triplicate, using Illumina HiSeq 2500.