ArticleJournal of bacteriology2015
Genome-wide analyses in bacteria show small-RNA enrichment for long and conserved intergenic regions.
Article in Journal of bacteriology, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 31 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
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
31 citing papers in PubMed, 57 citations in OpenAlex.
- Small RNA Transcriptome of the Oral Microbiome during Periodontitis Progression.Applied and environmental microbiology · 2015Trial
- Role of Small Non-Coding RNA in Gram-Negative Bacteria: New Insights and Comprehensive Review of Mechanisms, Functions, and Potential Applications.Molecular biotechnology · 2025Review
- Article
- Article
- Kastor: a reference-based comparative approach for assessment and correction of gene-fragmenting errors in long-read assemblies of small genomes.BMC genomics · 2025Article
- Advances in sRNA-mediated regulation ofFrontiers in cellular and infection microbiology · 2025Review
- Identification of Small RNAs inInternational journal of molecular sciences · 2024Article
- Quantitative morphological analysis ofApplied and environmental microbiology · 2024Article
- Article
- StORF-Reporter: finding genes between genes.Nucleic acids research · 2023Article
- Genome-wide high-resolution mapping of DNA methylation reveals epigenetic variation in the offspring of sexual and asexual propagation in Robinia pseudoacacia.Plant cell reports · 2021Article
- Article
- Pan-Genome of the GenusFrontiers in microbiology · 2021Article
- Divergently Transcribed ncRNAs inFrontiers in molecular biosciences · 2021Article
- Genome-wide identification of Azospirillum brasilense Sp245 small RNAs responsive to nitrogen starvation and likely involvement in plant-microbe interactions.BMC genomics · 2020Article
- The Transcriptomic Landscape ofGenes · 2020Article
- Prevalence of small base-pairing RNAs derived from diverse genomic loci.Biochimica et biophysica acta. Gene regulatory mechanisms · 2020Review
- Genome-wide identification of the context-dependent sRNA expression in Mycobacterium tuberculosis.BMC genomics · 2020Article
- Comparative Transcriptomic and Functional Assessments of Linezolid-Responsive Small RNA Genes in Staphylococcus aureus.mSystems · 2020Article
- Multiple Small RNAs Interact to Co-regulate Ethanol Tolerance inFrontiers in bioengineering and biotechnology · 2020Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
5 authors at 2 institutions in 1 country.
Funding
Abstract
Interest in finding small RNAs (sRNAs) in bacteria has significantly increased in recent years due to their regulatory functions. Development of high-throughput methods and more sophisticated computational algorithms has allowed rapid identification of sRNA candidates in different species. However, given their various sizes (50 to 500 nucleotides [nt]) and their potential genomic locations in the 5' and 3' untranslated regions as well as in intergenic regions, identification and validation of true sRNAs have been challenging. In addition, the evolution of bacterial sRNAs across different species continues to be puzzling, given that they can exert similar functions with various sequences and structures. In this study, we analyzed the enrichment patterns of sRNAs in 13 well-annotated bacterial species using existing transcriptome and experimental data. All intergenic regions were analyzed by WU-BLAST to examine conservation levels relative to species within or outside their genus. In total, more than 900 validated bacterial sRNAs and 23,000 intergenic regions were analyzed. The results indicate that sRNAs are enriched in intergenic regions, which are longer and more conserved than the average intergenic regions in the corresponding bacterial genome. We also found that sRNA-coding regions have different conservation levels relative to their flanking regions. This work provides a way to analyze how noncoding RNAs are distributed in bacterial genomes and also shows conserved features of intergenic regions that encode sRNAs. These results also provide insight into the functions of regions surrounding sRNAs and into optimization of RNA search algorithms.
Indexed as
Identifiers
What OpenQuestion holds
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.