预测人类选择性剪接的结构影响

IF 10.1 1区 生物学 Q1 BIOTECHNOLOGY & APPLIED MICROBIOLOGY
Yuxuan Song, Chengxin Zhang, Gilbert S. Omenn, Matthew J. O’Meara, Joshua D. Welch
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引用次数: 0

摘要

利用神经网络预测蛋白质结构是一种连接蛋白质序列、结构和功能的强有力的新方法,但通常只预测每个基因的单个同工异构体的结构,而忽略了剪接变体。为了研究选择性剪接的结构含义,我们使用AlphaFold2来预测超过11,000种人类同工异构体的结构。我们采用多种指标来识别拼接引起的结构改变,包括模板匹配评分、二级结构组成、表面电荷分布、旋转半径、翻译后修饰位点的可及性以及基于结构的功能预测。我们确定的例子如何选择性剪接诱导这些属性的明显变化。同种异构体之间的结构相似性在很大程度上与序列一致性有关,但我们发现了一个低结构相似性的亚型,尽管序列相似性很高。外显子跳跃和最后外显子的交替倾向于增加表面电荷和旋转半径。剪接也隐藏或暴露了许多翻译后修饰位点,尤其是在BAX的同工异构体中。功能预测识别了同一基因同种异构体之间的许多功能差异,与参考基因相比,功能损失占主导地位。最后,我们使用来自Tabula Sapiens的单细胞RNA-seq数据来确定每种结构表达的细胞类型。我们的工作为研究人体细胞类型剪接异构体的结构和功能提供了重要的资源。
本文章由计算机程序翻译,如有差异,请以英文原文为准。
Predicting the structural impact of human alternative splicing
Protein structure prediction with neural networks is a powerful new method for linking protein sequence, structure, and function, but structures have generally been predicted for only a single isoform of each gene, neglecting splice variants. To investigate the structural implications of alternative splicing, we use AlphaFold2 to predict the structures of more than 11,000 human isoforms. We employ multiple metrics to identify splicing-induced structural alterations, including template matching score, secondary structure composition, surface charge distribution, radius of gyration, accessibility of post-translational modification sites, and structure-based function prediction. We identify examples of how alternative splicing induces clear changes in each of these properties. Structural similarity between isoforms largely correlates with degree of sequence identity, but we identify a subset of isoforms with low structural similarity despite high sequence similarity. Exon skipping and alternative last exons tend to increase the surface charge and radius of gyration. Splicing also buries or exposes numerous post-translational modification sites, most notably among the isoforms of BAX. Functional prediction identifies numerous functional differences between isoforms of the same gene, with loss of function compared to the reference predominating. Finally, we use single-cell RNA-seq data from the Tabula Sapiens to determine the cell types in which each structure is expressed. Our work represents an important resource for studying the structure and function of splice isoforms across the cell types of the human body.
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来源期刊
Genome Biology
Genome Biology Biochemistry, Genetics and Molecular Biology-Genetics
CiteScore
21.00
自引率
3.30%
发文量
241
审稿时长
2 months
期刊介绍: Genome Biology stands as a premier platform for exceptional research across all domains of biology and biomedicine, explored through a genomic and post-genomic lens. With an impressive impact factor of 12.3 (2022),* the journal secures its position as the 3rd-ranked research journal in the Genetics and Heredity category and the 2nd-ranked research journal in the Biotechnology and Applied Microbiology category by Thomson Reuters. Notably, Genome Biology holds the distinction of being the highest-ranked open-access journal in this category. Our dedicated team of highly trained in-house Editors collaborates closely with our esteemed Editorial Board of international experts, ensuring the journal remains on the forefront of scientific advances and community standards. Regular engagement with researchers at conferences and institute visits underscores our commitment to staying abreast of the latest developments in the field.
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