Nuclear and cytoplasmic specific RNA binding proteome enrichment and its changes upon ferroptosis induction
Abstract The key role of RNA-binding proteins (RBPs) in posttranscriptional regulation of gene expression is intimately tied to their subcellular localization. Here, we show a subcellular-specific RNA labeling method for efficient enrichment and deep profiling of nuclear and cytoplasmic RBPs. A tota...
| Main Authors: | , , , , |
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| Format: | Article |
| Language: | English |
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Nature Portfolio
2024-01-01
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| Series: | Nature Communications |
| Online Access: | https://doi.org/10.1038/s41467-024-44987-9 |
| _version_ | 1797274134817800192 |
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| author | Haofan Sun Bin Fu Xiaohong Qian Ping Xu Weijie Qin |
| author_facet | Haofan Sun Bin Fu Xiaohong Qian Ping Xu Weijie Qin |
| author_sort | Haofan Sun |
| collection | DOAJ |
| description | Abstract The key role of RNA-binding proteins (RBPs) in posttranscriptional regulation of gene expression is intimately tied to their subcellular localization. Here, we show a subcellular-specific RNA labeling method for efficient enrichment and deep profiling of nuclear and cytoplasmic RBPs. A total of 1221 nuclear RBPs and 1333 cytoplasmic RBPs were enriched and identified using nuclear/cytoplasm targeting enrichment probes, representing an increase of 54.4% and 85.7% compared with previous reports. The probes were further applied in the omics-level investigation of subcellular-specific RBP-RNA interactions upon ferroptosis induction. Interestingly, large-scale RBPs display enhanced interaction with RNAs in nucleus but reduced association with RNAs in cytoplasm during ferroptosis process. Furthermore, we discovered dozens of nucleoplasmic translocation candidate RBPs upon ferroptosis induction and validated representative ones by immunofluorescence imaging. The enrichment of Tricarboxylic acid cycle in the translocation candidate RBPs may provide insights for investigating their possible roles in ferroptosis induced metabolism dysregulation. |
| first_indexed | 2024-03-07T14:54:02Z |
| format | Article |
| id | doaj.art-f10b6e247fdb4672a24e7c998a01355a |
| institution | Directory Open Access Journal |
| issn | 2041-1723 |
| language | English |
| last_indexed | 2024-03-07T14:54:02Z |
| publishDate | 2024-01-01 |
| publisher | Nature Portfolio |
| record_format | Article |
| series | Nature Communications |
| spelling | doaj.art-f10b6e247fdb4672a24e7c998a01355a2024-03-05T19:34:55ZengNature PortfolioNature Communications2041-17232024-01-0115111610.1038/s41467-024-44987-9Nuclear and cytoplasmic specific RNA binding proteome enrichment and its changes upon ferroptosis inductionHaofan Sun0Bin Fu1Xiaohong Qian2Ping Xu3Weijie Qin4State Key Laboratory of Medical Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of LifeomicsState Key Laboratory of Medical Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of LifeomicsState Key Laboratory of Medical Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of LifeomicsState Key Laboratory of Medical Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of LifeomicsState Key Laboratory of Medical Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of LifeomicsAbstract The key role of RNA-binding proteins (RBPs) in posttranscriptional regulation of gene expression is intimately tied to their subcellular localization. Here, we show a subcellular-specific RNA labeling method for efficient enrichment and deep profiling of nuclear and cytoplasmic RBPs. A total of 1221 nuclear RBPs and 1333 cytoplasmic RBPs were enriched and identified using nuclear/cytoplasm targeting enrichment probes, representing an increase of 54.4% and 85.7% compared with previous reports. The probes were further applied in the omics-level investigation of subcellular-specific RBP-RNA interactions upon ferroptosis induction. Interestingly, large-scale RBPs display enhanced interaction with RNAs in nucleus but reduced association with RNAs in cytoplasm during ferroptosis process. Furthermore, we discovered dozens of nucleoplasmic translocation candidate RBPs upon ferroptosis induction and validated representative ones by immunofluorescence imaging. The enrichment of Tricarboxylic acid cycle in the translocation candidate RBPs may provide insights for investigating their possible roles in ferroptosis induced metabolism dysregulation.https://doi.org/10.1038/s41467-024-44987-9 |
| spellingShingle | Haofan Sun Bin Fu Xiaohong Qian Ping Xu Weijie Qin Nuclear and cytoplasmic specific RNA binding proteome enrichment and its changes upon ferroptosis induction Nature Communications |
| title | Nuclear and cytoplasmic specific RNA binding proteome enrichment and its changes upon ferroptosis induction |
| title_full | Nuclear and cytoplasmic specific RNA binding proteome enrichment and its changes upon ferroptosis induction |
| title_fullStr | Nuclear and cytoplasmic specific RNA binding proteome enrichment and its changes upon ferroptosis induction |
| title_full_unstemmed | Nuclear and cytoplasmic specific RNA binding proteome enrichment and its changes upon ferroptosis induction |
| title_short | Nuclear and cytoplasmic specific RNA binding proteome enrichment and its changes upon ferroptosis induction |
| title_sort | nuclear and cytoplasmic specific rna binding proteome enrichment and its changes upon ferroptosis induction |
| url | https://doi.org/10.1038/s41467-024-44987-9 |
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