Proximity labeling to detect RNA–protein interactions in live cells
RNA biology is orchestrated by the dynamic interactions of RNAs and RNA‐binding proteins (RBPs). In the present study, we describe a new method of proximity‐dependent protein labeling to detect RNA–protein interactions [RNA‐bound protein proximity labeling (RBPL)]. We selected the well‐studied RNA‐b...
| Main Authors: | , |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
Wiley
2019-11-01
|
| Series: | FEBS Open Bio |
| Subjects: | |
| Online Access: | https://doi.org/10.1002/2211-5463.12706 |
| _version_ | 1828792765132046336 |
|---|---|
| author | Mingxing Lu Wencheng Wei |
| author_facet | Mingxing Lu Wencheng Wei |
| author_sort | Mingxing Lu |
| collection | DOAJ |
| description | RNA biology is orchestrated by the dynamic interactions of RNAs and RNA‐binding proteins (RBPs). In the present study, we describe a new method of proximity‐dependent protein labeling to detect RNA–protein interactions [RNA‐bound protein proximity labeling (RBPL)]. We selected the well‐studied RNA‐binding protein PUF to examine the current proximity labeling enzymes birA* and APEX2. A new version of birA*, BASU, was used to validate that the PUF protein binds its RNA motif. We further optimized the RBPL labeling system using an inducible expression system. The RBPL (λN‐BASU) labeling experiments exhibited high signal‐to‐noise ratios. We subsequently determined that RBPL (λN‐BASU) is more suitable than RBPL (λN‐APEX2) for the detection of RNA–protein interactions in live cells. Interestingly, our results also reveal that proximity labeling is probably capable of biotinylating proximate nascent peptide. |
| first_indexed | 2024-12-12T03:15:20Z |
| format | Article |
| id | doaj.art-333233d67a2a473ea31fb415630251b2 |
| institution | Directory Open Access Journal |
| issn | 2211-5463 |
| language | English |
| last_indexed | 2024-12-12T03:15:20Z |
| publishDate | 2019-11-01 |
| publisher | Wiley |
| record_format | Article |
| series | FEBS Open Bio |
| spelling | doaj.art-333233d67a2a473ea31fb415630251b22022-12-22T00:40:18ZengWileyFEBS Open Bio2211-54632019-11-019111860186810.1002/2211-5463.12706Proximity labeling to detect RNA–protein interactions in live cellsMingxing Lu0Wencheng Wei1Department of Biomedical Sciences College of Veterinary Medicine and Life Sciences City University of Hong Kong Kowloon Tong Hong KongDepartment of Biology Southern University of Science and Technology Shenzhen ChinaRNA biology is orchestrated by the dynamic interactions of RNAs and RNA‐binding proteins (RBPs). In the present study, we describe a new method of proximity‐dependent protein labeling to detect RNA–protein interactions [RNA‐bound protein proximity labeling (RBPL)]. We selected the well‐studied RNA‐binding protein PUF to examine the current proximity labeling enzymes birA* and APEX2. A new version of birA*, BASU, was used to validate that the PUF protein binds its RNA motif. We further optimized the RBPL labeling system using an inducible expression system. The RBPL (λN‐BASU) labeling experiments exhibited high signal‐to‐noise ratios. We subsequently determined that RBPL (λN‐BASU) is more suitable than RBPL (λN‐APEX2) for the detection of RNA–protein interactions in live cells. Interestingly, our results also reveal that proximity labeling is probably capable of biotinylating proximate nascent peptide.https://doi.org/10.1002/2211-5463.12706APEX2birA*nascent peptideproximity labelingRNA binding proteinRNA–protein interactions |
| spellingShingle | Mingxing Lu Wencheng Wei Proximity labeling to detect RNA–protein interactions in live cells FEBS Open Bio APEX2 birA* nascent peptide proximity labeling RNA binding protein RNA–protein interactions |
| title | Proximity labeling to detect RNA–protein interactions in live cells |
| title_full | Proximity labeling to detect RNA–protein interactions in live cells |
| title_fullStr | Proximity labeling to detect RNA–protein interactions in live cells |
| title_full_unstemmed | Proximity labeling to detect RNA–protein interactions in live cells |
| title_short | Proximity labeling to detect RNA–protein interactions in live cells |
| title_sort | proximity labeling to detect rna protein interactions in live cells |
| topic | APEX2 birA* nascent peptide proximity labeling RNA binding protein RNA–protein interactions |
| url | https://doi.org/10.1002/2211-5463.12706 |
| work_keys_str_mv | AT mingxinglu proximitylabelingtodetectrnaproteininteractionsinlivecells AT wenchengwei proximitylabelingtodetectrnaproteininteractionsinlivecells |