ArticleNucleic acids research2015
Distinguishing between productive and abortive promoters using a random forest classifier in Mycoplasma pneumoniae.
Article in Nucleic acids research, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 18 papers.
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Who cites it
18 citing papers in PubMed, 31 citations in OpenAlex.
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- Quantitative essentiality in a reduced genome: a functional, regulatory and structural fitness map.Molecular systems biology · 2025Article
- Genomic evolution of ST228 SCCmec-I MRSA 10 years after a major nosocomial outbreak.Journal of clinical microbiology · 2024Article
- Developing a platform for secretion of biomolecules in Mycoplasma feriruminatoris.Microbial cell factories · 2024Article
- ProTInSeq: transposon insertion tracking by ultra-deep DNA sequencing to identify translated large and small ORFs.Nature communications · 2024Article
- Phenotypic and genetic insights into efflux pump mechanism inFrontiers in microbiology · 2023Article
- A genetic toolkit and gene switches to limit Mycoplasma growth for biosafety applications.Nature communications · 2022Article
- Characterization of promoters in archaeal genomes based on DNA structural parameters.MicrobiologyOpen · 2021Article
- Integrative characterization of the near-minimal bacterium Mesoplasma florum.Molecular systems biology · 2020Article
- Determination of the Gene Regulatory Network of a Genome-Reduced Bacterium Highlights Alternative Regulation Independent of Transcription Factors.Cell systems · 2019Article
- Predicting prognosis of endometrioid endometrial adenocarcinoma on the basis of gene expression and clinical features using Random Forest.Oncology letters · 2019Article
- SynMyco transposon: engineering transposon vectors for efficient transformation of minimal genomes.DNA research : an international journal for rapid publication of reports on genes and genomes · 2019Article
- Kinetic Modeling of the Genetic Information Processes in a Minimal Cell.Frontiers in molecular biosciences · 2019Article
- A reporter system coupled with high-throughput sequencing unveils key bacterial transcription and translation determinants.Nature communications · 2017Article
- Unveiling DNA structural features of promoters associated with various types of TSSs in prokaryotic transcriptomes and their role in gene expression.DNA research : an international journal for rapid publication of reports on genes and genomes · 2017Article
- Insights into the Mechanisms of Basal Coordination of Transcription Using a Genome-Reduced Bacterium.Cell systems · 2016Article
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Authors and funding
3 authors at 2 institutions in 1 country.
Funding
Abstract
Distinguishing between promoter-like sequences in bacteria that belong to true or abortive promoters, or to those that do not initiate transcription at all, is one of the important challenges in transcriptomics. To address this problem, we have studied the genome-reduced bacterium Mycoplasma pneumoniae, for which the RNAs associated with transcriptional start sites have been recently experimentally identified. We determined the contribution to transcription events of different genomic features: the -10, extended -10 and -35 boxes, the UP element, the bases surrounding the -10 box and the nearest-neighbor free energy of the promoter region. Using a random forest classifier and the aforementioned features transformed into scores, we could distinguish between true, abortive promoters and non-promoters with good -10 box sequences. The methods used in this characterization of promoters can be extended to other bacteria and have important applications for promoter design in bacterial genome engineering.
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Registered trials
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