Profiling of biological relationships between different molecular layers dissects regulatory mechanisms that ultimately determine cellular function. To thoroughly assess the role of protein post-translational turnover, we devised a strategy combining pulse stable isotope-labeled amino acids in cells (pSILAC), data-independent acquisition mass spectrometry (DIA-MS), and a novel data analysis framework that resolves protein degradation rate on the level of mRNA alternative splicing isoforms and isoform groups. We demonstrated our approach by the genome-wide correlation analysis between mRNA amounts and protein degradation across different strains of HeLa cells that harbor a high grade of gene dosage variation. The dataset revealed that specific biological processes, cellular organelles, spatial compartments of organelles, and individual protein isoforms of the same genes could have distinctive degradation rate. The protein degradation diversity thus dissects the corresponding buffering or concerting protein turnover control across cancer cell lines. The data further indicate that specific mRNA splicing events such as intron retention significantly impact the protein abundance levels. Our findings support the tight association between transcriptome variability and proteostasis and provide a methodological foundation for studying functional protein degradation.

中文翻译：

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mRNA丰度调节与蛋白质水平降解之间的异构形式相关分析。

对不同分子层之间的生物学关系进行剖析会发现最终决定细胞功能的调控机制。为了彻底评估蛋白质翻译后转换的作用，我们设计了一种策略，该策略结合了脉冲稳定同位素标记的细胞内氨基酸（pSILAC），数据独立采集质谱（DIA-MS）和可解决以下问题的新颖数据分析框架蛋白降解率取决于mRNA水平的可变剪接异构体和异构体基团。我们通过全基因组相关分析证明了我们的方法，该分析在具有高水平基因剂量变异的不同HeLa细胞株之间的mRNA量和蛋白质降解之间进行。数据集显示特定的生物过程，细胞器，细胞器的空间区隔，相同基因的单个蛋白质同工型可能具有独特的降解率。因此，蛋白质降解多样性剖析了跨癌细胞系的相应缓冲或协同蛋白质转换控制。数据进一步表明特定的mRNA剪接事件（如内含子保留）显着影响蛋白质丰度水平。我们的发现支持转录组变异性与蛋白稳态之间的紧密联系，并为研究功能蛋白降解提供了方法学基础。数据进一步表明特定的mRNA剪接事件（如内含子保留）显着影响蛋白质丰度水平。我们的发现支持转录组变异性与蛋白稳态之间的紧密联系，并为研究功能蛋白降解提供了方法学基础。数据进一步表明，特定的mRNA剪接事件（例如内含子保留）会显着影响蛋白质丰度水平。我们的发现支持转录组变异性与蛋白稳态之间的紧密联系，并为研究功能蛋白降解提供了方法学基础。