PXD070845 is an
original dataset announced via ProteomeXchange.
Dataset Summary
| Title | THP-1 data for:Ribosome dynamics orchestrate mRNA stability and translation across natural and synthetic systems |
| 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. |
| HostingRepository | PRIDE |
| AnnounceDate | 2025-12-10 |
| AnnouncementXML | Submission_2025-12-10_03:51:56.617.xml |
| DigitalObjectIdentifier | https://dx.doi.org/10.6019/PXD070845 |
| ReviewLevel | Peer-reviewed dataset |
| DatasetOrigin | Original dataset |
| RepositorySupport | Supported dataset by repository |
| PrimarySubmitter | Baoqiang Chen |
| SpeciesList | scientific name: Homo sapiens (Human); NCBI TaxID: NEWT:9606; |
| ModificationList | No PTMs are included in the dataset |
| Instrument | Q Exactive |
Dataset History
| Revision | Datetime | Status | ChangeLog Entry |
|---|
| 0 | 2025-11-17 09:47:30 | ID requested | |
| ⏵ 1 | 2025-12-10 03:51:57 | announced | |
Publication List
Keyword List
| submitter keyword: Human, Activation, THP-1 |
Contact List
| Yihan Lin |
|---|
| contact affiliation | Peking University |
| contact email | yihan.lin@pku.edu.cn |
| lab head | |
| Baoqiang Chen |
|---|
| contact affiliation | Peking University |
| contact email | cbqcpu@163.com |
| dataset submitter | |
Full Dataset Link List
Dataset FTP location
NOTE: Most web browsers have now discontinued native support for FTP access within the browser window. But you can usually install another FTP app (we recommend FileZilla) and configure your browser to launch the external application when you click on this FTP link. Or otherwise, launch an app that supports FTP (like FileZilla) and use this address: ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2025/12/PXD070845 |
| PRIDE project URI |
Repository Record List
[ + ]
[ - ]
- PRIDE
- PXD070845
- Label: PRIDE project
- Name: THP-1 data for:Ribosome dynamics orchestrate mRNA stability and translation across natural and synthetic systems
