The diversification of cell adhesion molecules by alternative splicing is proposed to underlie molecular codes for neuronal wiring. Transcriptomic approaches mapped detailed cell-type-specific mRNA splicing programs. However, it has been hard to probe the synapse-specific localization and function of the resulting protein splice isoforms, or “proteoforms,” in vivo. We here apply a proteoform-centric workflow in mice to test the synapse-specific functions of the splice isoforms of the synaptic adhesion molecule Neurexin-3 (NRXN3). We uncover a major proteoform, NRXN3 AS5, that is highly expressed in GABAergic interneurons and at dendrite-targeting GABAergic terminals. NRXN3 AS5 abundance significantly diverges from Nrxn3 mRNA distribution and is gated by translation-repressive elements. Nrxn3 AS5 isoform deletion results in a selective impairment of dendrite-targeting interneuron synapses in the dentate gyrus without affecting somatic inhibition or glutamatergic perforant-path synapses. This work establishes cell- and synapse-specific functions of a specific neurexin proteoform and highlights the importance of alternative splicing regulation for synapse specification.

建议通过选择性剪接使细胞粘附分子多样化，作为神经元布线的分子密码的基础。转录组学方法绘制了详细的细胞类型特异性 mRNA 剪接程序。然而，很难在体内探测所得蛋白质剪接同种型或“蛋白质型”的突触特异性定位和功能。我们在这里在小鼠中应用以蛋白质形式为中心的工作流程，以测试突触粘附分子 Neurexin-3 (NRXN3) 的剪接异构体的突触特异性功能。我们发现了一种主要的蛋白质形式 NRXN3 AS5，它在 GABA 能中间神经元和树突靶向 GABA 能末端中高度表达。NRXN3 AS5 丰度与Nrxn3显着不同mRNA 分布并由翻译抑制元件控制。Nrxn3 AS5亚型缺失导致齿状回中树突靶向中间神经元突触的选择性损伤，而不影响体细胞抑制或谷氨酸能穿孔通路突触。这项工作建立了特定神经突蛋白形式的细胞和突触特异性功能，并强调了选择性剪接调节对突触规范的重要性。