Zheng Zhengfan, Guo Suisui, Tam Hoi Yau, Wang Jingkai, Rao Yanxia, Hui Man-Ning, Cheung May Pui Lai, Leung Alan Wai Lun, Wong Kelvin K W, Sharma Rakesh, Liu Jessica Aijia, Cheung Martin
School of Biomedical Sciences, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China.
Division of Life Science, The Hong Kong University of Science and Technology, Hong Kong, China.
Nat Commun. 2025 Jul 21;16(1):6718. doi: 10.1038/s41467-025-62003-6.
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 the binding capacity of the SF3B1-PHF5A splicing complex to the shorter length of both SOX9 intron 2 and SNAI2 intron 1, which possess weaker polypyrimidine tract 3' of the BS sequence, resulting in intron retention and loss of NC progenitors. Conversely, somite specific SLU7-SF3B1-PHF5A splicing complex regulates SOX9 and SNAI2 expression and imparts resistance to PB. Our data reveal the cell-type specific splicing complexes with distinct vulnerabilities to PB, highlighting the critical role of the DLC1-SF3B1-PHF5A in determining trunk NC cell fate and enhancing its susceptibility to splicing perturbation.
普遍表达的剪接因子如何特异性地调节神经嵴（NC）发育并增强其对剪接扰动的易感性，目前仍知之甚少。在这里，我们表明，与SF3B1-PHF5A剪接复合体合作的NC特异性DLC1，通过调节NC特异性因子SOX9和SNAI2前体mRNA的剪接，而不是其上游调节因子BMP4、WNT1和PAX7的剪接，对于决定禽类躯干NC细胞命运至关重要。从机制上讲，SF3B1-PHF5A与所有因子的内含子分支位点（BS）序列结合，而DLC1与SOX9和SNAI2的BS序列附近的特定基序相互作用，从而决定它们在NC特化中的功能特异性。此外，DLC1通过降低SF3B1-PHF5A剪接复合体与SOX9内含子2和SNAI2内含子1较短长度的结合能力，增加了NC细胞对剪接调节剂普拉地诺内酯B（PB）的易感性，这两个内含子在BS序列的3'端具有较弱的聚嘧啶序列，导致内含子保留和NC祖细胞的丧失。相反，体节特异性的SLU7-SF3B1-PHF5A剪接复合体调节SOX9和SNAI2的表达，并赋予对PB的抗性。我们的数据揭示了对PB具有不同易感性的细胞类型特异性剪接复合体，突出了DLC1-SF3B1-PHF5A在决定躯干NC细胞命运和增强其对剪接扰动的易感性方面的关键作用。
