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.
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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
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
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- Kramer, K., Sachsenberg, T., Beckmann, B. M., Qamar, S., Boon, K.-L., Hentze, M. W., Kohlbacher, O., & Urlaub, H. (2014). Photo-cross-linking and high-resolution mass spectrometry for assignment of RNA-binding sites in RNA-binding proteins. Nature Methods. https://doi.org/10.1038/nmeth.3092
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