Moakley Daniel F, Campbell Melissa, Anglada-Girotto Miquel, Feng Huijuan, Califano Andrea, Au Edmund, Zhang Chaolin
Department of Systems Biology, Columbia University, New York, NY 10032, USA.
Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY 10032, USA.
bioRxiv. 2024 Jun 15:2024.06.13.597128. doi: 10.1101/2024.06.13.597128.
Cell type-specific alternative splicing (AS) enables differential gene isoform expression between diverse neuron types with distinct identities and functions. Current studies linking individual RNA-binding proteins (RBPs) to AS in a few neuron types underscore the need for holistic modeling. Here, we use network reverse engineering to derive a map of the neuron type-specific AS regulatory landscape from 133 mouse neocortical cell types defined by single-cell transcriptomes. This approach reliably inferred the regulons of 350 RBPs and their cell type-specific activities. Our analysis revealed driving factors delineating neuronal identities, among which we validated Elavl2 as a key RBP for MGE-specific splicing in GABAergic interneurons using an in vitro ESC differentiation system. We also identified a module of exons and candidate regulators specific for long- and short-projection neurons across multiple neuronal classes. This study provides a resource for elucidating splicing regulatory programs that drive neuronal molecular diversity, including those that do not align with gene expression-based classifications.
细胞类型特异性可变剪接（AS）能够使具有不同身份和功能的多种神经元类型之间的基因异构体表达产生差异。目前将单个RNA结合蛋白（RBP）与少数几种神经元类型中的AS联系起来的研究强调了整体建模的必要性。在这里，我们使用网络逆向工程从由单细胞转录组定义的133种小鼠新皮质细胞类型中推导神经元类型特异性AS调控景观图。这种方法可靠地推断出350个RBP的调控子及其细胞类型特异性活性。我们的分析揭示了界定神经元身份的驱动因素，其中我们使用体外胚胎干细胞分化系统验证了Elavl2是GABA能中间神经元中MGE特异性剪接的关键RBP。我们还鉴定了一个跨多个神经元类别的长投射和短投射神经元特有的外显子和候选调节因子模块。这项研究为阐明驱动神经元分子多样性的剪接调控程序提供了资源，包括那些与基于基因表达的分类不一致的程序。
