ArticlePLoS genetics2013
Genome-wide identification of regulatory RNAs in the human pathogen Clostridium difficile.
Article in PLoS genetics, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 146 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.
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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.
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Who cites it
146 citing papers in PubMed, 237 citations in OpenAlex.
- Genomic and phenotypic insight intoEmerging microbes & infections · 2026Article
- Type IV pilin regulation: a transcriptional overview.Critical reviews in microbiology · 2026Review
- Role of Small Non-Coding RNA in Gram-Negative Bacteria: New Insights and Comprehensive Review of Mechanisms, Functions, and Potential Applications.Molecular biotechnology · 2025Review
- Deciphering the RNA-based regulation mechanism of the phage-encoded AbiF system in Clostridioides difficile.PLoS genetics · 2025Article
- An endoribonuclease of the YicC-like family delays sporulation via sRNA degradation in Clostridioides difficile.Nucleic acids research · 2025Article
- An antisense RNA regulates production of DnaA and affects sporulation in Bacillus subtilis.PLoS genetics · 2025Article
- Defense arsenal of the strict anaerobemBio · 2025Article
- Regulatory networks: Linking toxin production and sporulation in Clostridioides difficile.Anaerobe · 2025Review
- Bacteriophages: A Challenge for Antimicrobial Therapy.Microorganisms · 2025Review
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- The current riboswitch landscape inMicrobiology (Reading, England) · 2024Review
- Adaptation mechanisms of Clostridioides difficile to auranofin and its impact on human gut microbiota.NPJ biofilms and microbiomes · 2024Article
- Characterization of the dual regulation by a c-di-GMP riboswitch Bc1 with a long expression platform fromMicrobiology spectrum · 2024Article
- The multiplicity of thioredoxin systems meets the specific lifestyles of Clostridia.PLoS pathogens · 2024Article
- Methods for Bioinformatic Prediction of Genuine sRNAs from Outer Membrane Vesicles.Methods in molecular biology (Clifton, N.J.) · 2024Article
- Clostridioides difficile Biofilm.Advances in experimental medicine and biology · 2024Article
- Identification of an anti-CRISPR protein that inhibits the CRISPR-Cas type I-B system inmSphere · 2023Article
- A sporulation signature protease is required for assembly of the spore surface layers, germination and host colonization in Clostridioides difficile.PLoS pathogens · 2023Article
- Glycine fermentation byInfection and immunity · 2023Article
86 more citing papers are in PubMed but not listed here.
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
12 authors at 3 institutions in 4 countries.
Funding
Abstract
Clostridium difficile is an emergent pathogen, and the most common cause of nosocomial diarrhea. In an effort to understand the role of small noncoding RNAs (sRNAs) in C. difficile physiology and pathogenesis, we used an in silico approach to identify 511 sRNA candidates in both intergenic and coding regions. In parallel, RNA-seq and differential 5'-end RNA-seq were used for global identification of C. difficile sRNAs and their transcriptional start sites at three different growth conditions (exponential growth phase, stationary phase, and starvation). This global experimental approach identified 251 putative regulatory sRNAs including 94 potential trans riboregulators located in intergenic regions, 91 cis-antisense RNAs, and 66 riboswitches. Expression of 35 sRNAs was confirmed by gene-specific experimental approaches. Some sRNAs, including an antisense RNA that may be involved in control of C. difficile autolytic activity, showed growth phase-dependent expression profiles. Expression of each of 16 predicted c-di-GMP-responsive riboswitches was observed, and experimental evidence for their regulatory role in coordinated control of motility and biofilm formation was obtained. Finally, we detected abundant sRNAs encoded by multiple C. difficile CRISPR loci. These RNAs may be important for C. difficile survival in bacteriophage-rich gut communities. Altogether, this first experimental genome-wide identification of C. difficile sRNAs provides a firm basis for future RNome characterization and identification of molecular mechanisms of sRNA-based regulation of gene expression in this emergent enteropathogen.
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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.