Fig. 3: Global splicing analysis reveals increased intron retention of neural crest specifier genes and factors essential for EMT in embryos lacking DLC1, PHF5A, or SF3B1.

a List of genes involved in NC specification and EMT with intron retention (IR) observed in DLC1-, PHF5A-, and SF3B1-depleted cells. In contrast, the levels of IR for genes involved in neural plate border specification, NC induction, and NC lineage determinants were either low in all KO treatments or comparable to Ctrl gRNA. The levels of IR were quantified using percent intron retention scores assessed by VAST-TOOLs. b List of genes exhibiting varying degrees of exon skipping (ES), 5’ alternative splicing (5’ AS) and 3’ alternative splicing (3’ AS) in each gRNA treatment. ES events were quantified by percent spliced-in (PSI), while 5’ AS and 3’ AS events were evaluated using percent splice site usage (PSU). qPCR analysis revealed reduced expression levels of the indicated genes in DLC1 gRNA1 (c), PHF5A gRNA1 (d), and SF3B1 gRNA1 (e) compared to Ctrl gRNA. Other genes remained unaffected by these treatments (f–h). The exact p-values are listed in the Source data file. Mean ± SD. ns: no significant difference, **P < 0.01, ***P < 0.001, ****P < 0.0001.