Fig. 4: Presence of DLC1 binding motifs in a gene subset that determines the functional specificity of SF3B1-PHF5A in regulating NC specification. | Nature Communications

Fig. 4: Presence of DLC1 binding motifs in a gene subset that determines the functional specificity of SF3B1-PHF5A in regulating NC specification.

From: Determination of trunk neural crest cell fate and susceptibility to splicing perturbation by the DLC1-SF3B1-PHF5A splicing complex

Fig. 4

a DLC1 binding motif (CUCCGGKU), located either near or distant from BP-A, is found in introns of genes affected by DLC1 KO. The motif is ranked the highest among other motifs based on its statistically significant predominance in the affected gene introns compared to the unaffected ones. K represents A/G or U. Motif alignment is highlighted in green, and base pairs (bp) indicate the distance from the motif to BP-A. b, f Schematic diagram showing primer pairs flanking the motif (asterisk) and BP-A of SOX9 (a) and SNAI2 (b) introns for RNA-immunoprecipitation qPCR (RIP-qPCR). Graphs show the binding capacity of endogenous PHF5A (c, g), SF3B1 (d, h), and DLC1 (e, i) to the BP-A of SOX9 introns 1 and 2, as well as SNAI2 introns 1 and 3. n = 3 embryos per treatment. j IP shows that SF3B1 remained associated with PHF5A in the absence of DLC1. k–n RIP-qPCR analysis reveals reduced binding capacity of PHF5A-SF3B1 splicing complex to introns 1 and 2 of SOX9, as well as introns 1 and 3 of SNAI2 in embryos treated with DLC1 gRNA1 compared to Ctrl gRNA. n = 3 embryos per treatment. The exact p-values are listed in the Source data file. Mean ± SD. *P < 0.05, **P < 0.01, ***P < 0.001, ****P < 0.0001.

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