Fig. 3: MLF2 regulates a subset of SWI/SNF target genes in mESCs.

a Plot displays ranked p-values (permutation test using MAGeCK software, see Methods) of enriched genes in KO screen. Labeled genes are top hits Mlf2 and the HSP70 chaperone complex gene Hspa4. b Schematic of dTAG-degron system. The target protein is endogenously tagged with FKBPv-V5. Upon addition of dTAG-13, the proteasomal machinery is recruited to the FKBPv tag, the target protein is ubiquitylated and rapidly degraded via the proteasome. Created in BioRender https://BioRender.com/hatsa1bc. Western blot of SMARCA4 and MLF2 dTAG mESCs showing time course of dTAG-13 treatment vs DMSO control. Both SMARCA4 and MLF2 were detected using a V5 antibody (n = 1). d Volcano plots showing differentially expressed genes in SMARCA4-dTAG mESCs after 3 h, 8 h, and 24 h of dTAG-13 or DMSO treatment. Significantly downregulated genes are in blue and upregulated in red (sig. = padj. <0.05 & |FC | > 1.5; n = 3). Adjusted p-values were calculated using the Benjamini-Hochberg correction using DESeq2 software, see Methods. e Volcano plots showing differentially expressed genes in MLF2-dTAG mESCs after 3 h, 8 h, and 24 h of dTAG-13 or DMSO treatment. Significantly downregulated genes are in blue and upregulated in red (sig. = padj. <0.05 & |FC | > 1.5; n = 3). Adjusted p-values were calculated using the Benjamini-Hochberg correction using DESeq2 software, see Methods. f Venn diagrams showing the overlapping genes after 24 h dTAG-13 treatment in SMARCA4 and MLF2 dTAG mESCs. Statistical significance calculated using a two-sided Fisher’s exact test. g Dot plot of significantly (p < 0.05) changed genes, overlapping in the 24 h dTAG-13 datasets of SMARCA4 and MLF2 dTAG mESCs. The linear regression line was fitted using Pearson correlation, p-value was calculated using a two-sided t-test. h Confocal images of proximity ligation assay used to detect MLF2-V5 and SMARCA4 interactions in MLF2-dTAG mESCs treated with DMSO or dTAG-13 for 24 h. Nuclei stained with DAPI. Graph shows number of PLA dots detected in both conditions, as mean ± SEM. Statistical significance calculated using a two-sided t-test, replicates n = 9, scale bar = 15 µm. Source data are provided as a Source Data file.