Song Yan, Botvinnik Olga B, Lovci Michael T, Kakaradov Boyko, Liu Patrick, Xu Jia L, Yeo Gene W
Department of Cellular and Molecular Medicine, Stem Cell Program and Institute for Genomic Medicine, University of California, San Diego, La Jolla, CA 92093, USA.
Department of Cellular and Molecular Medicine, Stem Cell Program and Institute for Genomic Medicine, University of California, San Diego, La Jolla, CA 92093, USA; Bioinformatics and Systems Biology Graduate Program, University of California, San Diego, La Jolla, CA 92093, USA.
Mol Cell. 2017 Jul 6;67(1):148-161.e5. doi: 10.1016/j.molcel.2017.06.003. Epub 2017 Jun 29.
Alternative splicing (AS) generates isoform diversity for cellular identity and homeostasis in multicellular life. Although AS variation has been observed among single cells, little is known about the biological or evolutionary significance of such variation. We developed Expedition, a computational framework consisting of outrigger, a de novo splice graph transversal algorithm to detect AS; anchor, a Bayesian approach to assign modalities; and bonvoyage, a visualization tool using non-negative matrix factorization to display modality changes. Applying Expedition to single pluripotent stem cells undergoing neuronal differentiation, we discover that up to 20% of AS exons exhibit bimodality. Bimodal exons are flanked by more conserved intronic sequences harboring distinct cis-regulatory motifs, constitute much of cell-type-specific splicing, are highly dynamic during cellular transitions, preserve reading frame, and reveal intricacy of cell states invisible to conventional gene expression analysis. Systematic AS characterization in single cells redefines our understanding of AS complexity in cell biology.
可变剪接（Alternative splicing，AS）为多细胞生物中的细胞特性和内稳态产生了异构体多样性。尽管在单细胞中已观察到AS变异，但对于这种变异的生物学或进化意义却知之甚少。我们开发了Expedition，这是一个计算框架，由outrigger（一种用于检测AS的从头拼接图遍历算法）、anchor（一种用于分配模态的贝叶斯方法）和bonvoyage（一种使用非负矩阵分解来显示模态变化的可视化工具）组成。将Expedition应用于正在经历神经元分化的单能干细胞，我们发现高达20%的AS外显子呈现双峰性。双峰外显子两侧是含有不同顺式调控基序的更保守的内含子序列，构成了大部分细胞类型特异性剪接，在细胞转变过程中高度动态，保留阅读框，并揭示了传统基因表达分析无法察觉的细胞状态的复杂性。单细胞中的系统AS表征重新定义了我们对细胞生物学中AS复杂性的理解。
