Proteomics Can Rise to the Challenge of Pseudogenes' Coding Nature.

IF 3.8 2区 生物学 Q1 BIOCHEMICAL RESEARCH METHODS
Journal of Proteome Research Pub Date : 2024-12-06 Epub Date: 2024-11-01 DOI:10.1021/acs.jproteome.4c00116
Valeriia Vasylieva, Ihor Arefiev, Francis Bourassa, Félix-Antoine Trifiro, Marie A Brunet
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引用次数: 0

Abstract

Throughout the past decade, technological advances in genomics and transcriptomics have revealed pervasive translation throughout mammalian genomes. These putative proteins are usually excluded from proteomics analyses, as they are absent from common protein repositories. A sizable portion of these noncanonical proteins is translated from pseudogenes. Pseudogenes are commonly termed defective copies of coding genes unable to produce proteins. Here, we suggest that proteomics can help in their annotation. First, we define important terms and review specific examples underlining the caveats in pseudogene annotation and their coding potential. Then, we will discuss the challenges inherent to pseudogenes that have thus far rendered complex their confidence in omics data. Finally, we identify recent developments in experimental procedures, instrumentation, and computational methods in proteomics that put the field in a unique position to solve the pseudogene annotation conundrum.

蛋白质组学可以应对假基因编码性质的挑战。
过去十年间,基因组学和转录物组学的技术进步揭示了哺乳动物基因组中普遍存在的翻译现象。这些推定蛋白质通常被排除在蛋白质组学分析之外,因为它们不在常见的蛋白质库中。这些非规范蛋白质中有相当一部分是从假基因翻译而来的。假基因通常被称为无法产生蛋白质的编码基因缺陷拷贝。在此,我们建议蛋白质组学可以帮助对它们进行注释。首先,我们将定义重要术语并回顾具体实例,强调假基因注释中的注意事项及其编码潜力。然后,我们将讨论假基因固有的挑战,迄今为止,这些挑战使得假基因在 omics 数据中的可信度变得复杂。最后,我们将指出蛋白质组学在实验程序、仪器和计算方法方面的最新进展,这些进展使该领域处于解决伪基因注释难题的独特位置。
本文章由计算机程序翻译,如有差异,请以英文原文为准。
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来源期刊
Journal of Proteome Research
Journal of Proteome Research 生物-生化研究方法
CiteScore
9.00
自引率
4.50%
发文量
251
审稿时长
3 months
期刊介绍: Journal of Proteome Research publishes content encompassing all aspects of global protein analysis and function, including the dynamic aspects of genomics, spatio-temporal proteomics, metabonomics and metabolomics, clinical and agricultural proteomics, as well as advances in methodology including bioinformatics. The theme and emphasis is on a multidisciplinary approach to the life sciences through the synergy between the different types of "omics".
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