Fig. 5: PRMT9 regulates pre-mRNA splicing of genes involved in synapse development and function. | Nature Communications

Fig. 5: PRMT9 regulates pre-mRNA splicing of genes involved in synapse development and function.

From: Loss-of-function mutation in PRMT9 causes abnormal synapse development by dysregulation of RNA alternative splicing

Fig. 5

a SF3B2 is the primary substrate of PRMT9 in mouse hippocampus and it is highly methylated in vivo. PRMT9 only produces 3H-labeled SF3B2 methylation signal in the KO, but not WT cells (black triangle). Samples were visualized by Ponceau staining (n = 3). b Violin plot demonstration of alternative splicing (AS) events identified in Prmt9 KO hippocampus. The middle line of the boxplot represents median value. The low and high ends of the box represent the 25% and 75% quantiles, respectively. The two whiskers extend to 1.5 times the interquartile range. The number of significant events within each category are indicated within parentheses along x-axis labels. WT: n = 3; KO: n = 3. c Scatter plot of gene expression levels in WT and Prmt9 KO hippocampus samples. Genes with significant changes in alternative splicing are depicted in yellow. Genes selected for RT-PCR validation of AS are highlighted in boxes. d Pathway enrichment analysis of alternatively spliced genes. Pathways were grouped by database resource origins (BioPlanet pathway or WikiPathway). The length of bars depicts the Benjamini-Hochberg adjusted p values calculated from a one-sided hypergeometric test. Odds ratio of the enrichment is indicated by bar opacity. e RT-PCR validation of alternatively spliced genes upon Prmt9 KO. RNA-seq read coverage across individual alternatively spliced exons in WT and Prmt9 KO samples is illustrated using the Sashimi plots. The number of reads mapped to each splice junction is shown. Percent Spliced In (PSI) values are indicated on the upper-right sides of the plots. RT-PCR was performed to validate selected alternative splicing events. Inclusion versus exclusion ratio was calculated. Data are presented as mean values ± SD. Error bars represent standard deviation calculated from three independent experiments. The splice site highlighted by a red triangle is a cryptic splice site that is not annotated in the reference genome (for the Celf5 gene). *, P < 0.05; **, P < 0.01; ***, P < 0.001. Source data are provided as a Source Data file.

Back to article page