ArticlePLoS genetics2015
A Conserved Pattern of Primer-Dependent Transcription Initiation in Escherichia coli and Vibrio cholerae Revealed by 5' RNA-seq.
Article in PLoS genetics, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 13 papers.
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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.
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Who cites it
13 citing papers in PubMed, 20 citations in OpenAlex.
- Diribonuclease activity eliminates toxic diribonucleotide accumulation.Cell reports · 2024Article
- Nano-RNases: oligo- or dinucleases?FEMS microbiology reviews · 2022Review
- Article
- Promoter-sequence determinants and structural basis of primer-dependent transcription initiation inProceedings of the National Academy of Sciences of the United States of America · 2021Article
- Regulation of mRNA Stability During Bacterial Stress Responses.Frontiers in microbiology · 2020Review
- Dinucleotide Degradation by REXO2 Maintains Promoter Specificity in Mammalian Mitochondria.Molecular cell · 2019Article
- A dedicated diribonucleotidase resolves a key bottleneck for the terminal step of RNA degradation.eLife · 2019Article
- Epitranscriptomics: RNA Modifications in Bacteria and Archaea.Microbiology spectrum · 2018Article
- Analysis of Bacterial Transcription by "Massively Systematic Transcript End Readout," MASTER.Methods in enzymology · 2018Article
- Structural Basis for the Bidirectional Activity of Bacillus nanoRNase NrnA.Scientific reports · 2017Article
- Mechanism of transcription initiation and promoter escape byProceedings of the National Academy of Sciences of the United States of America · 2017Article
- Open complex DNA scrunching: A key to transcription start site selection and promoter escape.BioEssays : news and reviews in molecular, cellular and developmental biology · 2017Review
- Interactions between RNA polymerase and the core recognition element are a determinant of transcription start site selection.Proceedings of the National Academy of Sciences of the United States of America · 2016Article
Corrections and comments
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Authors and funding
7 authors at 3 institutions in 1 country.
Funding
Abstract
Transcription initiation that involves the use of a 2- to ~4-nt oligoribonucleotide primer, "primer-dependent initiation," (PDI) has been shown to be widely prevalent at promoters of genes expressed during the stationary phase of growth in Escherichia coli. However, the extent to which PDI impacts E. coli physiology, and the extent to which PDI occurs in other bacteria is not known. Here we establish a physiological role for PDI in E. coli as a regulatory mechanism that modulates biofilm formation. We further demonstrate using high-throughput sequencing of RNA 5' ends (5' RNA-seq) that PDI occurs in the pathogenic bacterium Vibrio cholerae. A comparative global analysis of PDI in V. cholerae and E. coli reveals that the pattern of PDI is strikingly similar in the two organisms. In particular, PDI is detected in stationary phase, is not detected in exponential phase, and is preferentially apparent at promoters carrying the sequence T-1A+1 or G-1G+1 (where position +1 corresponds to the position of de novo initiation). Our findings demonstrate a physiological role for PDI and suggest PDI may be widespread among Gammaproteobacteria. We propose that PDI in both E. coli and V. cholerae occurs though a growth phase-dependent process that leads to the preferential generation of the linear dinucleotides 5´-UA-3´ and 5´-GG-3´.
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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.