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Ribosome dynamics orchestrate mRNA stability and translation across natural and synthetic systems

ABSTRACT: The dynamic interplay between ribosomes and mRNAs plays a central role in gene expression regulation, balancing protein synthesis and mRNA stability. However, traditional methods capturing static ribosome occupancy fail to resolve the temporal dynamics governing these processes. Here, we introduce Temporal Ribosome Density Profiling (TRiP), which combines metabolic RNA labeling and polysome sequencing to map ribosome density dynamics across the mRNA lifespan. TRiP reveals a striking temporal symmetry conserved across cell types: gene-specific ribosome loading rates are counterbalanced by coordinated unloading rates, creating a self-regulatory loop that, as demonstrated through biophysical modeling and experimental validation in diverse cellular contexts, directly couples ribosome dynamics to mRNA stability. We further uncover how mRNA structural motifs and m6A methylation fine-tune ribosome dynamics at the isoform level, simultaneously modulating protein output and transcript half-life. In macrophages, this dynamic control enables rapid immune responses by upregulating translation efficiency of pro-inflammatory genes. Remarkably, these principles extend to synthetic mRNAs, where machine learning-guided optimization of ribosome dynamics enhances protein production. Our work establishes ribosome density dynamics as a pervasive and tunable regulatory axis, with broad implications for adaptive immunity, RNA biology, and the design of therapeutic mRNAs.

INSTRUMENT(S):

ORGANISM(S): Homo Sapiens (human)

TISSUE(S): Kidney Epithelium, Permanent Cell Line Cell

SUBMITTER: Baoqiang Chen

LAB HEAD: Yihan Lin

PROVIDER: PXD070830 | Pride | 2025-12-10

REPOSITORIES: Pride

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	CBQ_20240412_HN123_LFQ.xlsx	Xlsx
	CBQ_20240412_HN1_1.raw	Raw
	CBQ_20240412_HN1_2.raw	Raw
	CBQ_20240412_HN1_3.raw	Raw
	CBQ_20240412_HN2_1.raw	Raw

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Project description:The dynamic interplay between ribosomes and mRNAs plays a central role in gene expression regulation, balancing protein synthesis and mRNA stability. However, traditional methods capturing static ribosome occupancy fail to resolve the temporal dynamics governing these processes. Here, we introduce Temporal Ribosome Density Profiling (TRiP), which combines metabolic RNA labeling and polysome sequencing to map ribosome density dynamics across the mRNA lifespan. TRiP reveals a striking temporal symmetry conserved across cell types: gene-specific ribosome loading rates are counterbalanced by coordinated unloading rates, creating a self-regulatory loop that, as demonstrated through biophysical modeling and experimental validation in diverse cellular contexts, directly couples ribosome dynamics to mRNA stability. We further uncover how mRNA structural motifs and m6A methylation fine-tune ribosome dynamics at the isoform level, simultaneously modulating protein output and transcript half-life. In macrophages, this dynamic control enables rapid immune responses by upregulating translation efficiency of pro-inflammatory genes. Remarkably, these principles extend to synthetic mRNAs, where machine learning-guided optimization of ribosome dynamics enhances protein production. Our work establishes ribosome density dynamics as a pervasive and tunable regulatory axis, with broad implications for adaptive immunity, RNA biology, and the design of therapeutic mRNAs.

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