Resolving Chromosome-Centric Human Proteome with Translating mRNA Analysis: A Strategic Demonstration
Resolving Chromosome-Centric Human Proteome with Translating mRNA Analysis: A Strategic Demonstration
复制标题
通过翻译 mRNA 分析解析以染色体为中心的人类蛋白质组：战略演示。
DOI：
10.1021/pr4007409
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发表时间：
2014-01-01
影响因子：
4.4
通讯作者：
Wang, Tong
中科院分区：
文献类型：
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作者：
Zhong, Jiayong;Cui, Yizhi;Wang, Tong
以染色体为中心的人类蛋白质组计划（C-HPP）旨在从蛋白质表达、定量和修饰方面区分基于染色体的蛋白质组成和组织特异性蛋白质组成。我们以前发现，翻译mRNA（附着在核糖体新生链复合物上的mRNA，RNC-mRNA）的分析可以解释超过94%的mRNA-蛋白质丰度。因此，我们在这里建议使用全长RNC-mRNA信息来定性和定量地说明蛋白质表达。我们对RNC-mRNA（RNC-seq）进行了RNA-seq，并分别在人正常支气管上皮（HBE）细胞和人结直肠腺癌Caco-2细胞中检测到12，758和14，113个翻译基因。我们发现这些基因中的大多数以>80%的编码序列覆盖率被定位。在Caco-2细胞中，我们提供了4180个显著单核苷酸变异的翻译证据。虽然使用RNC-mRNA数据作为标准的蛋白质组学数据集成，翻译和蛋白质证据的7876个基因可以从四个实验室间的数据集与不同的MS平台。此外，我们检测到1397个附着在核糖体上的非编码mRNA，这表明了新蛋白质探索的潜在来源。通过比较这两种细胞系，共发现677个差异翻译基因在染色体上分布不均匀。此外，Caco-2中的2105个基因和HBE细胞中的750个基因以细胞特异性方式表达。这些基因显著且特异性地聚集在多条染色体上，例如19号染色体。我们的结论是，HPP/C-HPP调查可以大大提高整合RNC-mRNA分析与MS，生物信息学和抗体为基础的验证。
Chromosome-centric human proteome project (C-HPP) aims at differentiating chromosome-based and tissue-specific protein compositions in terms of protein expression, quantification, and modification. We previously found that the analysis of translating mRNA (mRNA attached to ribosome-nascent chain complex, RNC-mRNA) can explain over 94% of mRNA-protein abundance. Therefore, we propose here to use full-length RNC-mRNA information to illustrate protein expression both qualitatively and quantitatively. We performed RNA-seq on RNC-mRNA (RNC-seq) and detected 12,758 and 14,113 translating genes in human normal bronchial epithelial (HBE) cells and human colorectal adenocarcinoma Caco-2 cells, respectively. We found that most of these genes were mapped with >80% of coding sequence coverage. In Caco-2 cells, we provided translating evidence on 4180 significant single-nucleotide variations. While using RNC-mRNA data as a standard for proteomic data integration, both translating and protein evidence of 7876 genes can be acquired from four interlaboratory data sets with different MS platforms. In addition, we detected 1397 noncoding mRNAs that were attached to ribosomes, suggesting a potential source of new protein explorations. By comparing the two cell lines, a total of 677 differentially translated genes were found to be nonevenly distributed across chromosomes. In addition, 2105 genes in Caco-2 and 750 genes in HBE cells are expressed in a cell-specific manner. These genes are significantly and specifically clustered on multiple chromosomes, such as chromosome 19. We conclude that HPP/C-HPP investigations can be considerably improved by integrating RNC-mRNA analysis with MS, bioinformatics, and antibody-based verifications.