ArticleNature communications2018
High-throughput in vivo mapping of RNA accessible interfaces to identify functional sRNA binding sites.
Article in Nature communications, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 19 papers.
What it found
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
19 citing papers in PubMed, 32 citations in OpenAlex.
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- CsrA Shows Selective Regulation of sRNA-mRNA Networks.bioRxiv : the preprint server for biology · 2023Article
- CsrA selectively modulates sRNA-mRNA regulator outcomes.Frontiers in molecular biosciences · 2023Article
- Nucleic acid strand displacement - from DNA nanotechnology to translational regulation.RNA biology · 2023Article
- Engineering Toehold-Mediated Switches for Native RNA Detection and Regulation in Bacteria.Journal of molecular biology · 2022Review
- Coordination of gene expression with cell size enablesProceedings of the National Academy of Sciences of the United States of America · 2022Article
- sRNARFTarget: a fast machine-learning-based approach for transcriptome-wide sRNA target prediction.RNA biology · 2022Article
- Noncoding RNAs: biology and applications-a Keystone Symposia report.Annals of the New York Academy of Sciences · 2021Review
- The International Society of RNA Nanotechnology and Nanomedicine (ISRNN): The Present and Future of the Burgeoning Field.ACS nano · 2021Article
- Recent Research Advances in Small Regulatory RNAs in Streptococcus.Current microbiology · 2021Review
- Sequence-independent RNA sensing and DNA targeting by a split domain CRISPR-Cas12a gRNA switch.Nucleic acids research · 2021Article
- Translational control of enzyme scavenger expression with toxin-induced micro RNA switches.Scientific reports · 2021Article
- Divergently Transcribed ncRNAs inFrontiers in molecular biosciences · 2021Article
- Prediction of Novel Bacterial Small RNAs From RIL-Seq RNA-RNA Interaction Data.Frontiers in microbiology · 2021Article
- Uncovering Transcriptional Regulators and Targets of sRNAs Using an Integrative Data-Mining Approach: H-NS-Regulated RseX as a Case Study.Frontiers in cellular and infection microbiology · 2021Article
- RNA oxidation in chromatin modification and DNA-damage response following exposure to formaldehyde.Scientific reports · 2020Article
- Multiple Small RNAs Interact to Co-regulate Ethanol Tolerance inFrontiers in bioengineering and biotechnology · 2020Article
- RNA-Binding Proteins Driving the Regulatory Activity of Small Non-coding RNAs in Bacteria.Frontiers in molecular biosciences · 2020Review
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
9 authors at 3 institutions in 1 country.
Funding
Abstract
Herein we introduce a high-throughput method, INTERFACE, to reveal the capacity of contiguous RNA nucleotides to establish in vivo intermolecular RNA interactions for the purpose of functional characterization of intracellular RNA. INTERFACE enables simultaneous accessibility interrogation of an unlimited number of regions by coupling regional hybridization detection to transcription elongation outputs measurable by RNA-seq. We profile over 900 RNA interfaces in 71 validated, but largely mechanistically under-characterized, Escherichia coli sRNAs in the presence and absence of a global regulator, Hfq, and find that two-thirds of tested sRNAs feature Hfq-dependent regions. Further, we identify in vivo hybridization patterns that hallmark functional regions to uncover mRNA targets. In this way, we biochemically validate 25 mRNA targets, many of which are not captured by typically tested, top-ranked computational predictions. We additionally discover direct mRNA binding activity within the GlmY terminator, highlighting the information value of high-throughput RNA accessibility data.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.