mRNAs continually change their protein partners throughout their lifetimes, yet our understanding of mRNA-protein complex (mRNP) remodeling is limited by a lack of temporal data. Here, we present time-resolved mRNA interactome data by performing pulse metabolic labeling with photoactivatable ribonucleoside in human cells, UVA crosslinking, poly(A)+ RNA isolation, and mass spectrometry. This longitudinal approach allowed the quantification of over 700 RNA binding proteins (RBPs) across ten time points. Overall, the sequential order of mRNA binding aligns well with known functions, subcellular locations, and molecular interactions. However, we also observed RBPs with unexpected dynamics: the transcription-export (TREX) complex recruited posttranscriptionally after nuclear export factor 1 (NXF1) binding, challenging the current view of transcription-coupled mRNA export, and stress granule proteins prevalent in aged mRNPs, indicating roles in late stages of the mRNA life cycle. To systematically identify mRBPs with unknown functions, we employed machine learning to compare mRNA binding dynamics with Gene Ontology (GO) annotations. Our data can be explored at chronology.rna.snu.ac.kr.

mRNA 在其一生中不断改变其蛋白质伙伴，但我们对 mRNA-蛋白质复合物 (mRNP) 重塑的理解因缺乏时间数据而受到限制。在这里，我们通过在人体细胞中使用光活化核糖核苷进行脉冲代谢标记、UVA 交联、poly(A)+ RNA 分离和质谱分析来呈现时间分辨的 mRNA 相互作用组数据。这种纵向方法可以对 10 个时间点的 700 多种 RNA 结合蛋白 (RBP) 进行定量。总体而言，mRNA 结合的顺序与已知的功能、亚细胞位置和分子相互作用非常一致。然而，我们也观察到 RBP 具有意想不到的动态：转录-输出 (TREX) 复合物在核输出因子 1 (NXF1) 结合后在转录后募集，挑战了当前转录偶联 mRNA 输出的观点，以及老化 mRNP 中普遍存在的应激颗粒蛋白，表明在 mRNA 生命周期后期的作用。为了系统地识别具有未知功能的 mRBP，我们利用机器学习将 mRNA 结合动态与基因本体 (GO) 注释进行比较。我们的数据可以在chronology.rna.snu.ac.kr上探索。