The DOI matches its Crossref record; 42 of the 42 references it cites were found in a registry or an index.
RNA–protein interaction detection in living cells
Open accessAbstract
RNA–protein interactions play numerous roles in cellular function and disease. Here we describe RNA–protein interaction detection (RaPID), which uses proximity-dependent protein labeling, based on the BirA* biotin ligase, to rapidly identify the proteins that bind RNA sequences of interest in living cells. RaPID displays utility in multiple applications, including in evaluating protein binding to mutant RNA motifs in human genetic disorders, in uncovering potential post-transcriptional networks in breast cancer, and in discovering essential host proteins that interact with Zika virus RNA. To improve the BirA*-labeling component of RaPID, moreover, a new mutant BirA* was engineered from Bacillus subtilis, termed BASU, that enables >1,000-fold faster kinetics and >30-fold increased signal-to-noise ratio over the prior standard Escherichia coli BirA*, thereby enabling direct study of RNA–protein interactions in living cells on a timescale as short as 1 min.
Overview
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
Integrity signals
Registry
Cites
Statistics
Verification
Claims the paper makes
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
Self-check
Percentages, sums and reported differences re-computed from the paper’s own numbers.
The self-check needs the paper’s full text.
Citations
Cites
Cerami, E., Gao, J., Dogrusoz, U., Gross, B. E., Sumer, S. O., Aksoy, B. A., Jacobsen, A., Byrne, C. J., Heuer, M. L., Larsson, E., et al. (2012) · Cancer Discovery · doi:10.1158/2159-8290.cd-12-0095 · Cited by 17,455
Tissue-based map of the human proteome
Uhlén, M., Fagerberg, L., Hallström, B. M., Lindskog, C., Oksvold, P., Mardinoglu, A., Sivertsson, Å., Kampf, C., Sjöstedt, E., Asplund, A., et al. (2015) · Science · doi:10.1126/science.1260419 · Cited by 15,286
Integrative Analysis of Complex Cancer Genomics and Clinical Profiles Using the cBioPortal
Gao, J., Aksoy, B. A., Dogrusoz, U., Dresdner, G., Gross, B., Sumer, S. O., Sun, Y., Jacobsen, A., Sinha, R., Larsson, E., et al. (2013) · Science Signaling · doi:10.1126/scisignal.2004088 · Cited by 15,160
Zika Virus Associated with Microcephaly
Mlakar, J., Korva, M., Tul, N., Popović, M., Poljšak-Prijatelj, M., Mraz, J., Kolenc, M., Resman Rus, K., Vesnaver Vipotnik, T., Fabjan Vodušek, V., et al. (2016) · New England Journal of Medicine · doi:10.1056/nejmoa1600651 · Cited by 2,884
Rappsilber, J., Ishihama, Y., & Mann, M. (2003) · Analytical Chemistry · doi:10.1021/ac026117i · Cited by 2,644
Roux, K. J., Kim, D. I., Raida, M., & Burke, B. (2012) · Journal of Cell Biology · doi:10.1083/jcb.201112098 · Cited by 2,416
Keefe, A. D., Pai, S., & Ellington, A. (2010) · Nature Reviews Drug Discovery · doi:10.1038/nrd3141 · Cited by 2,289
Insights into RNA Biology from an Atlas of Mammalian mRNA-Binding Proteins
Castello, A., Fischer, B., Eichelbaum, K., Horos, R., Beckmann, B. M., Strein, C., Davey, N. E., Humphreys, D. T., Preiss, T., Steinmetz, L. M., et al. (2012) · Cell · doi:10.1016/j.cell.2012.04.031 · Cited by 2,132
A more efficient method to generate integration-free human iPS cells
Okita, K., Matsumura, Y., Sato, Y., Okada, A., Morizane, A., Okamoto, S., Hong, H., Nakagawa, M., Tanabe, K., Tezuka, K.-I., et al. (2011) · Nature Methods · doi:10.1038/nmeth.1591 · Cited by 2,061
The CRAPome: a contaminant repository for affinity purification–mass spectrometry data
Mellacheruvu, D., Wright, Z., Couzens, A. L., Lambert, J.-P., St-Denis, N. A., Li, T., Miteva, Y. V., Hauri, S., Sardiu, M. E., Low, T. Y., et al. (2013) · Nature Methods · doi:10.1038/nmeth.2557 · Cited by 1,686
Cited by
Efficient proximity labeling in living cells and organisms with TurboID
Branon, T. C., Bosch, J. A., Sanchez, A. D., Udeshi, N. D., Svinkina, T., Carr, S. A., Feldman, J. L., Perrimon, N., & Ting, A. Y. (2018) · Nature Biotechnology · doi:10.1038/nbt.4201 · Cited by 2,174
Deciphering molecular interactions by proximity labeling
Qin, W., Cho, K. F., Cavanagh, P. E., & Ting, A. Y. (2021) · Nature Methods · doi:10.1038/s41592-020-01010-5 · Cited by 671
Proximity labeling in mammalian cells with TurboID and split-TurboID
Cho, K. F., Branon, T. C., Udeshi, N. D., Myers, S. A., Carr, S. A., & Ting, A. Y. (2020) · Nature Protocols · doi:10.1038/s41596-020-0399-0 · Cited by 534
μMap-Red: Proximity Labeling by Red Light Photocatalysis
Buksh, B. F., Knutson, S. D., Oakley, J. V., Bissonnette, N. B., Oblinsky, D. G., Schwoerer, M. P., Seath, C. P., Geri, J. B., Rodriguez-Rivera, F. P., Parker, D. L., et al. (2022) · Journal of the American Chemical Society · doi:10.1021/jacs.2c01384 · Cited by 166
TREX reveals proteins that bind to specific RNA regions in living cells
(2024) · doi:10.1038/s41592-024-02181-1 · Cited by 36
Highly effective proximate labeling in Drosophila
Zhang, B., Zhang, Y., & Liu, J.-L. (2021) · G3 Genes|Genomes|Genetics · doi:10.1093/g3journal/jkab077 · Cited by 32
RNA stability enhancers for durable base-modified mRNA therapeutics
Jung, S.-J., Seo, J. J., Lee, S., Hyun, S.-I., Lee, J.-E., Lee, S., Lee, Y., Chang, H., Lee, H., Kim, J.-H., et al. (2025) · Nature Biotechnology · doi:10.1038/s41587-025-02891-7 · Cited by 26
SHIFTR enables the unbiased identification of proteins bound to specific RNA regions in live cells
Aydin, J., Gabel, A., Zielinski, S., Ganskih, S., Schmidt, N., Hartigan, C. R., Schenone, M., Carr, S. A., & Munschauer, M. (2024) · Nucleic Acids Research · doi:10.1093/nar/gkae038 · Cited by 12
Mapping RNA-Binding Proteins on the Ribosome by Tethered Micrococcal Nuclease
(2026) · doi:10.1021/acs.biochem.5c00660
Metadata
- Authors
- Ramanathan, M., Majzoub, K., Rao, D. S., Neela, P. H., Zarnegar, B. J., Mondal, S., Roth, J. G., Gai, H., Kovalski, J. R., Siprashvili, Z., Palmer, T. D., Carette, J. E., & Khavari, P. A.
- Venue
- Nature Methods
- Published
- 2018-02-05
- Volume
- 15
- Issue
- 3
- Pages
- 207-212
- ISSN
- 1548-7091 (ISSN-L)
- 1548-7105
- OpenAlex
- W2786230719
- Cited by
- 308
- References
- 42
- FWCI
- 15.80
- Type
- journal article
- Language
- en
- Open access
- green
About these checks
Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.
Statistics and arithmetic are recomputed, not judged.
Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.
What counts as a claim ›How we measure confidence ›How we check this ›
Are you an author, or do you see a problem with this page? Request a review
Data sources
Bibliographic data: Semantic Scholar, OpenAlex, Crossref.
Contains information from the Semantic Scholar Academic Graph Datasets, made available under the ODC Attribution License (ODC-BY 1.0).
Semantic Scholar’s data is described in: Kinney, R., et al. (2023). The Semantic Scholar Open Data Platform. arXiv:2301.10140.
