Time-resolved profiling of mRNA-protein interaction through mRNA life cycle

From synthesis to decay, mRNA changes its protein partners, yet previous studies were limited in that they profiled only the mixed pools of RNA-binding proteins (RBPs) without temporal resolution. Here, we provide time-resolved profiles of human mRNA interactome by combining pulse metabolic labeling, photoactivatable ribonucleoside crosslinking, poly(A) RNA isolation, and mass spectrometry. We captured stage-specific RBPs across 10 time points and quantified over 700 RBPs. The chronological orders of mRNA binding are generally consistent with the known functions and localizations of RBPs: pre-mRNA processing factors are detected as “early binders” while decay factors appear as “late binders”. Notably, stress granule proteins are enriched in “aged” mRNPs, suggesting their roles in the final stage of mRNA life cycle. Many late binders also interact with viral transcripts, implying their regulatory activities on viruses. Furthermore, we built a computational model to systematically identify RBPs with unexpected binding dynamics, which indicates their unknown functions. Our study reveals a dynamic landscape of mRNP remodeling, offering new functional insights into RNA-protein interaction during mRNA life cycle.