The DOI matches its Crossref record; 2 of the 2 references it cites were found in a registry or an index.
Photo-cross-linking and high-resolution mass spectrometry for assignment of RNA-binding sites in RNA-binding proteins
Open accessAbstract
RNA-protein complexes play pivotal roles in many central biological processes. Although methods based on high-throughput sequencing have advanced our ability to identify the specific RNAs bound by a particular protein, there is a need for precise and systematic ways to identify RNA interaction sites on proteins. We have developed an experimental and computational workflow combining photo-induced cross-linking, high-resolution mass spectrometry and automated analysis of the resulting mass spectra for the identification of cross-linked peptides, cross-linking sites and the cross-linked RNA oligonucleotide moieties of such RNA-binding proteins. The workflow can be applied to any RNA-protein complex of interest or to whole proteomes. We applied the approach to human and yeast mRNA-protein complexes in vitro and in vivo, demonstrating its powerful utility by identifying 257 cross-linking sites on 124 distinct RNA-binding proteins. The open-source software pipeline developed for this purpose, RNPxl, is available as part of the OpenMS project.
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
Cox, J., & Mann, M. (2008) · Nature Biotechnology · doi:10.1038/nbt.1511 · Cited by 14,855
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
Self-citation
Cited by
Mass-spectrometric exploration of proteome structure and function
Aebersold, R., & Mann, M. (2016) · Nature · doi:10.1038/nature19949 · Cited by 2,334
A brave new world of RNA-binding proteins
Hentze, M. W., Castello, A., Schwarzl, T., & Preiss, T. (2018) · Nature Reviews Molecular Cell Biology · doi:10.1038/nrm.2017.130 · Cited by 1,821
Self-citationSingle-nucleotide-resolution mapping of m6A and m6Am throughout the transcriptome
Linder, B., Grozhik, A. V., Olarerin-George, A. O., Meydan, C., Mason, C. E., & Jaffrey, S. R. (2015) · Nature Methods · doi:10.1038/nmeth.3453 · Cited by 1,569
Properties of Stress Granule and P-Body Proteomes
Youn, J.-Y., Dyakov, B. J. A., Zhang, J., Knight, J. D. R., Vernon, R. M., Forman-Kay, J. D., & Gingras, A.-C. (2019) · Molecular Cell · doi:10.1016/j.molcel.2019.09.014 · Cited by 445
CLIP and complementary methods
Hafner, M., Katsantoni, M., Köster, T., Marks, J., Mukherjee, J., Staiger, D., Ule, J., & Zavolan, M. (2021) · Nature Reviews Methods Primers · doi:10.1038/s43586-021-00018-1 · Cited by 365
Leitner, A., Faini, M., Stengel, F., & Aebersold, R. (2016) · Trends in Biochemical Sciences · doi:10.1016/j.tibs.2015.10.008 · Cited by 355
Grimm, M., Zimniak, T., Kahraman, A., & Herzog, F. (2015) · Nucleic Acids Research · doi:10.1093/nar/gkv463 · Cited by 121
Qin, W., Myers, S. A., Carey, D. K., Carr, S. A., & Ting, A. Y. (2021) · Nature Communications · doi:10.1038/s41467-021-25259-2 · Cited by 84
White, M. R., Khan, M. M., Deredge, D., Ross, C. R., Quintyn, R., Zucconi, B. E., Wysocki, V. H., Wintrode, P. L., Wilson, G. M., & Garcin, E. D. (2015) · Journal of Biological Chemistry · doi:10.1074/jbc.m114.618165 · Cited by 66
A viral ADP-ribosyltransferase attaches RNA chains to host proteins
Wolfram-Schauerte, M., Pozhydaieva, N., Grawenhoff, J., Welp, L. M., Silbern, I., Wulf, A., Billau, F. A., Glatter, T., Urlaub, H., Jäschke, A., et al. (2023) · Nature · doi:10.1038/s41586-023-06429-2 · Cited by 53
Self-citationJin, W., Brannan, K. W., Kapeli, K., Park, S. S., Tan, H. Q., Gosztyla, M. L., Mujumdar, M., Ahdout, J., Henroid, B., Rothamel, K., et al. (2023) · Molecular Cell · doi:10.1016/j.molcel.2023.06.019 · Cited by 52
Keil, P., Wulf, A., Kachariya, N., Reuscher, S., Hühn, K., Silbern, I., Altmüller, J., Keller, M., Stehle, R., Zarnack, K., et al. (2023) · Nucleic Acids Research · doi:10.1093/nar/gkac1206 · Cited by 17
Self-citationWelp, L. M., Wulf, A., Chernev, A., Horokhovskyi, Y., Moshkovskii, S., Dybkov, O., Neumann, P., Pašen, M., Siraj, A., Raabe, M., et al. (2025) · Nucleic Acids Research · doi:10.1093/nar/gkaf727 · Cited by 12
Self-citationFendler, N. L., Ly, J., Welp, L., Lu, D., Schulte, F., Urlaub, H., & Vos, S. M. (2025) · Nucleic Acids Research · doi:10.1093/nar/gkae1273 · Cited by 12
Self-citationTrendel, J., Prokofeva, P., Chen, Z. A., Horn, L., Trendel, S., Mema, M., Stuiver, M., Rappsilber, J., & Kuster, B. (2026) · Nucleic Acids Research · doi:10.1093/nar/gkag339 · Cited by 3
Keil, P., Wulf, A., Kachariya, N., Reuscher, S., Hühn, K., Silbern, I., Altmüller, J., Stehle, R., Zarnack, K., Sattler, M., et al. (2022) · doi:10.1101/2022.07.22.501171
Self-citation
Metadata
- Authors
- Kramer, K., Sachsenberg, T., Beckmann, B. M., Qamar, S., Boon, K.-L., Hentze, M. W., Kohlbacher, O., & Urlaub, H.
- Venue
- Nature Methods
- Published
- 2014-08-31
- Volume
- 11
- Issue
- 10
- Pages
- 1064-1070
- ISSN
- 1548-7091 (ISSN-L)
- 1548-7105
- OpenAlex
- W2077527436
- Cited by
- 259
- References
- 2
- FWCI
- 10.34
- Type
- journal article
- Language
- en
- Open access
- bronze
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.
