PXD041608 is an
original dataset announced via ProteomeXchange.
Dataset Summary
Title | Systematic Identification of Post-Transcriptional Regulatory Modules |
Description | In our cells, a limited number of RNA binding proteins (RBPs) are responsible for all aspects of RNA metabolism across the entire transcriptome. To accomplish this, RBPs form regulatory units that act on specific target regulons. However, the landscape of RBP combinatorial interactions remains poorly explored. Here, we performed a systematic annotation of RBP combinatorial interactions via multimodal data integration. We built a large-scale map of RBP protein neighborhoods by generating in vivo proximity-dependent biotinylation datasets of 50 human RBPs. In parallel, we used CRISPR interference with single-cell readout to capture transcriptomic changes upon RBP knockdowns. By combining these physical and functional interaction readouts, along with the atlas of RBP mRNA targets from eCLIP assays, we generated an integrated map of functional RBP interactions. We then used this map to match RBPs to their context-specific functions and validated the predicted functions biochemically for four RBPs. This study highlights the previously underappreciated scale of the inter-RBP interactions, be it genetic or physical, and is a first step towards a more comprehensive understanding of post-transcriptional regulatory processes and their underlying molecular grammar. |
HostingRepository | PRIDE |
AnnounceDate | 2024-08-09 |
AnnouncementXML | Submission_2024-08-09_05:25:35.159.xml |
DigitalObjectIdentifier | |
ReviewLevel | Peer-reviewed dataset |
DatasetOrigin | Original dataset |
RepositorySupport | Unsupported dataset by repository |
PrimarySubmitter | Vishvak Subramanyam |
SpeciesList | scientific name: Homo sapiens (Human); NCBI TaxID: 9606; |
ModificationList | biotinylated residue |
Instrument | LTQ Orbitrap |
Dataset History
Revision | Datetime | Status | ChangeLog Entry |
0 | 2023-04-17 21:52:24 | ID requested | |
⏵ 1 | 2024-08-09 05:25:35 | announced | |
2 | 2024-10-22 06:53:54 | announced | 2024-10-22: Updated project metadata. |
Publication List
Dataset with its publication pending |
Keyword List
submitter keyword: K562, RBP |
Contact List
Hani Goodarzi |
contact affiliation | Department of Biochemistry |
contact email | hani.goodarzi@ucsf.edu |
lab head | |
Vishvak Subramanyam |
contact affiliation | UCSF Goodarzi Lab |
contact email | vishvak.subramanyam@ucsf.edu |
dataset submitter | |
Full Dataset Link List
Dataset FTP location
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PRIDE project URI |
Repository Record List
[ + ]
[ - ]
- PRIDE
- PXD041608
- Label: PRIDE project
- Name: Systematic Identification of Post-Transcriptional Regulatory Modules