The DOI matches its Crossref record; 54 of the 54 references it cites were found in a registry or an index.
Global Mapping of Small RNA-Target Interactions in Bacteria
Open accessAbstract
Small RNAs (sRNAs) associated with the RNA chaperon protein Hfq are key posttranscriptional regulators of gene expression in bacteria. Deciphering the sRNA-target interactome is an essential step toward understanding the roles of sRNAs in the cellular networks. We developed a broadly applicable methodology termed RIL-seq (RNA interaction by ligation and sequencing), which integrates experimental and computational tools for in vivo transcriptome-wide identification of interactions involving Hfq-associated sRNAs. By applying this methodology to Escherichia coli we discovered an extensive network of interactions involving RNA pairs showing sequence complementarity. We expand the ensemble of targets for known sRNAs, uncover additional Hfq-bound sRNAs encoded in various genomic regions along with their trans encoded targets, and provide insights into binding and possible cycling of RNAs on Hfq. Comparison of the sRNA interactome under various conditions has revealed changes in the sRNA repertoire as well as substantial re-wiring of the network between conditions.
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
MEME SUITE: tools for motif discovery and searching
Bailey, T. L., Boden, M., Buske, F. A., Frith, M., Grant, C. E., Clementi, L., Ren, J., Li, W. W., & Noble, W. S. (2009) · Nucleic Acids Research · doi:10.1093/nar/gkp335 · Cited by 10,648
The Human Genome Browser at UCSC
Kent, W. J., Sugnet, C. W., Furey, T. S., Roskin, K. M., Pringle, T. H., Zahler, A. M., & Haussler, A. D. (2002) · Genome Research · doi:10.1101/gr.229102 · Cited by 10,400
Predicting effective microRNA target sites in mammalian mRNAs
Agarwal, V., Bell, G. W., Nam, J.-W., & Bartel, D. P. (2015) · eLife · doi:10.7554/elife.05005 · Cited by 7,318
Mapping the Human miRNA Interactome by CLASH Reveals Frequent Noncanonical Binding
Helwak, A., Kudla, G., Dudnakova, T., & Tollervey, D. (2013) · Cell · doi:10.1016/j.cell.2013.03.043 · Cited by 1,269
Regulation by Small RNAs in Bacteria: Expanding Frontiers
Storz, G., Vogel, J., & Wassarman, K. M. (2011) · Molecular Cell · doi:10.1016/j.molcel.2011.08.022 · Cited by 1,177
Novel small RNA-encoding genes in the intergenic regions of Escherichia coli
Argaman, L., Hershberg, R., Vogel, J., Bejerano, G., Wagner, E. G. H., Margalit, H., & Altuvia, S. (2001) · Current Biology · doi:10.1016/s0960-9822(01)00270-6 · Cited by 767
Self-citationIdentification of novel small RNAs using comparative genomics and microarrays
Wassarman, K. M., Repoila, F., Rosenow, C., Storz, G., & Gottesman, S. (2001) · Genes & Development · doi:10.1101/gad.901001 · Cited by 723
Sittka, A., Lucchini, S., Papenfort, K., Sharma, C. M., Rolle, K., Binnewies, T. T., Hinton, J. C. D., & Vogel, J. (2008) · PLoS Genetics · doi:10.1371/journal.pgen.1000163 · Cited by 565
Global analysis of small RNA and mRNA targets of Hfq
Zhang, A., Wassarman, K. M., Rosenow, C., Tjaden, B. C., Storz, G., & Gottesman, S. (2003) · Molecular Microbiology · doi:10.1046/j.1365-2958.2003.03734.x · Cited by 544
EcoCyc: fusing model organism databases with systems biology
Keseler, I. M., Mackie, A., Peralta-Gil, M., Santos-Zavaleta, A., Gama-Castro, S., Bonavides-Martínez, C., Fulcher, C., Huerta, A. M., Kothari, A., Krummenacker, M., et al. (2013) · Nucleic Acids Research · doi:10.1093/nar/gks1027 · Cited by 542
Cited by
Alternative ORFs and small ORFs: shedding light on the dark proteome
Orr, M. W., Mao, Y., Storz, G., & Qian, S.-B. (2020) · Nucleic Acids Research · doi:10.1093/nar/gkz734 · Cited by 319
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
Stein, E. M., Wang, S., Dailey, K. G., Gravel, C. M., Wang, S., Olejniczak, M., & Berry, K. E. (2023) · RNA · doi:10.1261/rna.079697.123 · Cited by 9
Metadata
- Authors
- Melamed, S., Peer, A., Faigenbaum-Romm, R., Gatt, Y. E., Reiss, N., Bar, A., Altuvia, Y., Argaman, L., & Margalit, H.
- Venue
- Molecular Cell
- Publisher
- Elsevier BV
- Published
- 2016-09
- Volume
- 63
- Issue
- 5
- Pages
- 884-897
- ISSN
- 1097-2765 (ISSN-L)
- OpenAlex
- W2516278741
- Cited by
- 396
- References
- 54
- FWCI
- 34.98
- Type
- journal article
- Language
- en
- Open access
- hybrid
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
How to cite
Cite CoChat for the checks on this page, and the paper for its own findings.
- This page
- CoChat. (2026). Citation check: Global Mapping of Small RNA-Target Interactions in Bacteria. https://app.cochat.ai/papers/10.1016/j.molcel.2016.07.026
- The paper
- Melamed, S., Peer, A., Faigenbaum-Romm, R., Gatt, Y. E., Reiss, N., Bar, A., Altuvia, Y., Argaman, L., & Margalit, H. (2016). Global Mapping of Small RNA-Target Interactions in Bacteria. Molecular Cell. https://doi.org/10.1016/j.molcel.2016.07.026
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.
