Choudhary Bikash, Napier-Jameson Rebekah, Norris Adam
Department of Biochemistry, University of California, Riverside, 3401 Watkins Drive, Boyce Hall, Riverside, CA, 92521, USA.
Department of Biological Sciences, Southern Methodist University, Dallas, TX, 75205, USA.
EMBO Rep. 2025 Jun 9. doi: 10.1038/s44319-025-00493-7.
Microexons are important components of the neuronal transcriptome. Though tiny, their splicing is essential for neuronal development and function. Microexons are typically included in the nervous system and skipped in other tissues, but less is known about whether they are alternatively spliced across neuron types, and if so what the regulatory mechanisms and functional consequences might be. We set out to globally address this question in C. elegans using deep single-cell transcriptomes and in vivo splicing reporters. We find widespread alternative microexon splicing across neuron types. Focusing on a broadly-conserved 9-nucleotide exon in the synaptic vesicle gene unc-13, we find that it is completely skipped in olfactory neurons, but completely included in motor neurons. This splicing pattern is established by two neuronal RNA binding proteins which recruit spliceosomal component PRP-40 to mediate microexon inclusion. Cell-specific microexon alternative splicing is functionally important, as forcing microexon inclusion causes olfactory defects, while forcing microexon skipping causes locomotory defects. These locomotory defects are caused by decreased inhibitory motor neuron synaptic transmission and altered synaptic vesicle distribution. Regulatory features of unc-13 microexon splicing are broadly conserved: related MUN-domain genes in worms, flies, and mice invariably encode microexons, and those we tested are subject to similar regulatory principles (e.g. included in motor neurons, skipped in olfactory neurons, and regulated by the same two RNA binding proteins). Thus, not only is microexon inclusion important for nervous system function, but microexon alternative splicing across neurons is important for tuning neuronal function in individual cell types.
微小外显子是神经元转录组的重要组成部分。尽管微小，但它们的剪接对于神经元的发育和功能至关重要。微小外显子通常在神经系统中被包含而在其他组织中被跳过，但对于它们是否在不同神经元类型中进行可变剪接，以及如果是这样其调控机制和功能后果是什么，人们了解得较少。我们着手利用深度单细胞转录组和体内剪接报告基因在秀丽隐杆线虫中全面解决这个问题。我们发现在不同神经元类型中广泛存在可变微小外显子剪接。聚焦于突触小泡基因unc-13中一个广泛保守的9核苷酸外显子，我们发现它在嗅觉神经元中完全被跳过，但在运动神经元中完全被包含。这种剪接模式由两种神经元RNA结合蛋白建立，它们招募剪接体成分PRP-40来介导微小外显子的包含。细胞特异性的微小外显子可变剪接在功能上很重要，因为强制包含微小外显子会导致嗅觉缺陷，而强制跳过微小外显子会导致运动缺陷。这些运动缺陷是由抑制性运动神经元突触传递减少和突触小泡分布改变引起的。unc-13微小外显子剪接的调控特征广泛保守：线虫、果蝇和小鼠中相关的MUN结构域基因总是编码微小外显子，并且我们测试的那些基因遵循相似的调控原则（例如在运动神经元中被包含，在嗅觉神经元中被跳过，并由相同的两种RNA结合蛋白调控）。因此，不仅微小外显子的包含对神经系统功能很重要，而且跨神经元的微小外显子可变剪接对于调节单个细胞类型中的神经元功能也很重要。
