Fig. 5: RBM15 controls m⁶A methylation on specific SWI/SNF mRNAs.

a Schematic of the m⁶A RNA methylation complex. Plot displays ranked p-values (permutation test using MAGeCK software, see Methods) of enriched genes in KO screen. Labeled genes are members of m⁶A RNA methylation pathway enriched in the screen. Created in BioRender https://BioRender.com/255etvx. b Plot shows fold change of ATPlite cell viability assay results following 48 h ABA treatment in ZF-DT-Nkx2-9 mESCs cultured with STM2457 m⁶A inhibitor (1 µM) or DMSO over EtOH treated controls for 96 hours, presented as mean ± SEM. Statistical significance calculated using two-sided t-test, replicates n = 6. c Schematic of RBM15 protein domains and western blot analysis of RBM15 levels in NT, KO and ΔRRM1 mESCs. GAPDH as loading control (n = 1). Created in BioRender https://BioRender.com/887opbj. d Volcano plot showing differentially expressed genes (DEGs) between NT and KO mESCs (n = 2, padj <0.05 and |FC | > 1.5). The downregulated genes are in blue and the upregulated genes are in red. Adjusted p-values were calculated using the Benjamini-Hochberg correction using DESeq2 software, see Methods. e MA plot showing differentially m⁶A modified mRNA sites between NT and KO mESCs (n = 2, padj <0.05 and |FC | > 1.5). The downregulated peaks are in cyan and the upregulated peaks are in magenta. Adjusted p-values were calculated using the Benjamini-Hochberg correction using DESeq2 software, see Methods. f Bar plot shows m⁶A peaks detected in control mESCs within indicated genomic regions. Peak frequency graph shows the distribution of m⁶A peaks across transcripts, with a strong enrichment at the 3’ end. Genome browser tracks showing m⁶A distribution at the Klf4 locus in mESCs. Red bars correspond to m⁶A-RIP-seq tracks. Gray bars correspond to input tracks. g Correlation plot showing the log2 fold change of gene expression in RBM15 KO compared to ΔRRM1 mESCs. The linear regression line was fitted using Pearson correlation and p-value calculated using a two-sided t-test. All significantly (padj < 0.05) changed genes that overlap in both datasets are colored in blue (downregulated) and red (upregulated). h Correlation plot showing the log2 fold change of m⁶A peaks in RBM15 KO compared to ΔRRM1 mESCs. The linear regression line was fitted using Pearson correlation and p-value calculated using a two-sided t-test. All significantly (padj <0.05) changed peaks that overlap in both datasets are colored in cyan (downregulated) and magenta (upregulated). i Venn diagrams displaying the overlap between RBM15 KO and ΔRRM1 differentially regulated genes (mRNA-seq) and m⁶A peaks (m⁶A-RIP-seq). Statistical significance calculated using a two-sided Fisher’s exact test. j Volcano plot showing differentially m⁶A modified mRNA sites in SWI/SNF genes between NT and Rbm15 KO mESCs (n = 2, padj <0.05 and |FC | > 1.5). The downregulated peaks are in cyan and the upregulated peaks are in magenta. Adjusted p-values were calculated using the Benjamini-Hochberg correction using DESeq2 software, see Methods. k Table summarizes changes in mRNA levels and m⁶A deposition for all SWI/SNF genes when comparing RBM15 KO to NT mESCs. l Genome browser tracks showing m⁶A distribution at selected SWI/SNF subunit mRNAs in RBM15 KO and NT mESCs. Significantly increased m⁶A peaks in RBM15 KO cells are highlighted by magenta boxes and decreased peaks by cyan boxes. Source data are provided as a Source Data file.