The DOI matches its Crossref record; 4 of the 4 references it cites were found in a registry or an index.
Grad-seq guides the discovery of ProQ as a major small RNA-binding protein
Open accessAbstract
Significance: Understanding the functions of cellular transcripts based on their sequence is challenging, in particular for noncoding RNAs, which tend to lack easily recognizable motifs. A more functionally relevant criterion is the association of RNAs with cognate RNA-binding proteins. Here, we describe the gradient profiling by sequencing (Grad-seq) approach to draft global RNA landscapes through partitioning all cellular transcripts into diverse coding and noncoding groups based on their shared RNA–protein interactions. Grad-seq has enabled us to define a large class of structured small RNAs that commonly associate with the conserved RNA-binding protein ProQ and appears to constitute a new branch of posttranscriptional control in bacteria. The generic nature of the Grad-seq approach will help to rapidly describe functional RNA landscapes in numerous understudied microbes.
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Cites
Genome-Wide Analysis in Vivo of Translation with Nucleotide Resolution Using Ribosome Profiling
Ingolia, N. T., Ghaemmaghami, S., Newman, J. R. S., & Weissman, J. S. (2009) · Science · doi:10.1126/science.1168978 · Cited by 3,853
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
Erickson, H. P. (2009) · Biological Procedures Online · doi:10.1007/s12575-009-9008-x · Cited by 1,571
Unusual biology across a group comprising more than 15% of domain Bacteria
Brown, C. T., Hug, L. A., Thomas, B. C., Sharon, I., Castelle, C. J., Singh, A., Wilkins, M. J., Wrighton, K. C., Williams, K. H., & Banfield, J. F. (2015) · Nature · doi:10.1038/nature14486 · Cited by 1,216 · cited 1×
“Conclusions The Grad-seq approach provides an experimental and analytical framework to rapidly visualize the major RNA collectives of an organism of interest, which will be particularly useful in drafting initial functional RNA landscapes for many understudied microbes with unexplored RNA biology (41, 42).”
Method
Cited by
Queiroz, R. M. L., Smith, T., Villanueva, E., Marti-Solano, M., Monti, M., Pizzinga, M., Mirea, D.-M., Ramakrishna, M., Harvey, R. F., Dezi, V., et al. (2019) · Nature Biotechnology · doi:10.1038/s41587-018-0001-2 · Cited by 365
Hfq CLASH uncovers sRNA-target interaction networks linked to nutrient availability adaptation
Iosub, I. A., van Nues, R. W., McKellar, S. W., Nieken, K. J., Marchioretto, M., Sy, B., Tree, J. J., Viero, G., & Granneman, S. (2020) · eLife · doi:10.7554/elife.54655 · Cited by 98
Gerovac, M., El Mouali, Y., Kuper, J., Kisker, C., Barquist, L., & Vogel, J. (2020) · RNA · doi:10.1261/rna.076992.120 · Cited by 47
Self-citationGerovac, M., Wicke, L., Chihara, K., Schneider, C., Lavigne, R., & Vogel, J. (2021) · mBio · doi:10.1128/mbio.03454-20 · Cited by 40
Self-citationInterrogation of RNA-protein interaction dynamics in bacterial growth
Monti, M., Herman, R., Mancini, L., Capitanchik, C., Davey, K., Dawson, C. S., Ule, J., Thomas, G. H., Willis, A. E., Lilley, K. S., et al. (2024) · Molecular Systems Biology · doi:10.1038/s44320-024-00031-y · Cited by 16
Metadata
- Authors
- Smirnov, A., Förstner, K. U., Holmqvist, E., Otto, A., Günster, R., Becher, D., Reinhardt, R., & Vogel, J.
- Venue
- Proceedings of the National Academy of Sciences
- Published
- 2016-09-26
- Volume
- 113
- Issue
- 41
- Pages
- 11591-11596
- ISSN
- 0027-8424 (ISSN-L)
- 1091-6490
- OpenAlex
- W2524503478
- Cited by
- 290
- References
- 4
- FWCI
- 28.38
- Type
- journal article
- Language
- en
- Open access
- bronze
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- Smirnov, A., Förstner, K. U., Holmqvist, E., Otto, A., Günster, R., Becher, D., Reinhardt, R., & Vogel, J. (2016). Grad-seq guides the discovery of ProQ as a major small RNA-binding protein. Proceedings of the National Academy of Sciences. https://doi.org/10.1073/pnas.1609981113
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