ArticleBMC genomics2017
Detecting RNA-RNA interactions in E. coli using a modified CLASH method.
Article in BMC genomics, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 9 papers.
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Who cites it
9 citing papers in PubMed, 19 citations in OpenAlex.
- From environmental signals to adaptive phenotypes: signal-responsive regulation and network logic of bacterial small RNAs.FEMS microbiology reviews · 2026Review
- 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
- Thirty Years of sRNA-Mediated Regulation inInternational journal of molecular sciences · 2022Review
- Identification of an RNA sponge that controls the RoxS riboregulator of central metabolism in Bacillus subtilis.Nucleic acids research · 2021Article
- RNAnue: efficient data analysis for RNA-RNA interactomics.Nucleic acids research · 2021Article
- High-throughput in vivo mapping of RNA accessible interfaces to identify functional sRNA binding sites.Nature communications · 2018Article
- Synthetic Biology of Small RNAs and Riboswitches.Microbiology spectrum · 2018Review
- Discovering RNA-Based Regulatory Systems forFrontiers in cellular and infection microbiology · 2018Review
Corrections and comments
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Authors and funding
8 authors at 2 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundBacterial small regulatory RNAs (sRNAs) play important roles in sensing environment changes through sRNA-target mRNA interactions. However, the current strategy for detecting sRNA-mRNA interactions usually combines bioinformatics prediction and experimental verification, which is hampered by low prediction accuracy and low-throughput. Additionally, among the 4736 sequenced bacterial genomes, only about 2164 sRNAs from 319 strains have been described. Furthermore, target mRNAs of only 157 sRNAs have been uncovered. Obviously, highly efficient methods were required to detect sRNA-mRNA interactions in the sequenced genomes. This study aimed to apply a modified CLASH (cross-linking, ligation and sequencing hybrids) method to detect RNA-RNA interactions in E. coli, a model bacterial organism.
resultsStatistically significant interactions were detected in 29 transcript pairs. To the best of our knowledge, 24 pairs were reported for the first time and were novel RNA interactions, including tRNA-tRNA, tRNA-ncRNA (non-coding RNA), tRNA-rRNA, rRNA-mRNA, rRNA-ncRNA, rRNA-rRNA, rRNA-IGT (intergenic transcript), and tRNA-IGT interactions.
conclusionsDiscovery of novel RNA-RNA interactions in the present study demonstrates that RNA-RNA interactions might be far more complicated than ever expected. New methods may be required to help discover more novel RNA-RNA interactions. The present work describes a high-throughput protocol not only for discovering new RNA interactions, but also directly obtaining base-pairing sequences, which should be useful in assessing RNA structure and interactions.
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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.