biostudies-literatureZheng ZResearch Grants Council, University Grants CommitteeResearch Grants Council, University Grants Committee (RGC, UGC)6718https://www.ebi.ac.uk/biostudies/studies/S-EPMC12280072biostudies-literatureUnknown16(1)How the ubiquitously expressed splicing factors specifically regulate neural crest (NC) development and enhance their vulnerability to splicing perturbations remain poorly understood. Here, we show that NC-specific DLC1, partnering with SF3B1-PHF5A splicing complex, are crucial for determining avian trunk NC cell fate by regulating the splicing of NC specifiers SOX9 and SNAI2 pre-mRNAs rather than their upstream regulators BMP4, WNT1, and PAX7. Mechanistically, SF3B1-PHF5A binds to the intronic branch site (BS) sequences of all factors, while DLC1 interacts with a specific motif near the BS sequences of SOX9 and SNAI2, thereby determining their functional specificity in NC specification. Moreover, DLC1 increases NC cells' vulnerability to splicing modulator pladienolide B (PB) by reducing Nature communicationsDetermination of trunk neural crest cell fate and susceptibility to splicing perturbation by the DLC1-SF3B1-PHF5A splicing complex.PMC122800721710162217102420Zheng ZTam HYCheung MPLWong KKWLiu JASharma RRao YHui MNGuo SLeung AWLWang JCheung MfalseDetermination of trunk neural crest cell fate and susceptibility to splicing perturbation by the DLC1-SF3B1-PHF5A splicing complex.How the ubiquitously expressed splicing factors specifically regulate neural crest (NC) development and enhance their vulnerability to splicing perturbations remain poorly understood. Here, we show that NC-specific DLC1, partnering with SF3B1-PHF5A splicing complex, are crucial for determining avian trunk NC cell fate by regulating the splicing of NC specifiers SOX9 and SNAI2 pre-mRNAs rather than their upstream regulators BMP4, WNT1, and PAX7. Mechanistically, SF3B1-PHF5A binds to the intronic branch site (BS) sequences of all factors, while DLC1 interacts with a specific motif near the BS sequences of SOX9 and SNAI2, thereby determining their functional specificity in NC specification. Moreover, DLC1 increases NC cells' vulnerability to splicing modulator pladienolide B (PB) by reducing 2025-01-01T00:00:00Z2025 Jul2026-03-31T10:42:35.574Z2025-08-24T03:08:47.559ZS-EPMC122800724069146410.1038/s41467-025-62003-6