ArticleNature communications2017
A reporter system coupled with high-throughput sequencing unveils key bacterial transcription and translation determinants.
Article in Nature communications, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 21 papers.
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Who cites it
21 citing papers in PubMed, 42 citations in OpenAlex.
- Unraveling the start element and regulatory divergence of core promoters across the domain bacteria.Nucleic acids research · 2025Article
- Emerging methylation-based approaches in microbiome engineering.Biotechnology for biofuels and bioproducts · 2024Review
- 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
- Improved transformation efficiency inMicrobiology spectrum · 2023Article
- Comprehensive quantitative modeling of translation efficiency in a genome-reduced bacterium.Molecular systems biology · 2023Article
- Ultradeep characterisation of translational sequence determinants refutes rare-codon hypothesis and unveils quadruplet base pairing of initiator tRNA and transcript.Nucleic acids research · 2023Article
- Bacterial expression of a designed single-chain IL-10 prevents severe lung inflammation.Molecular systems biology · 2023Article
- Accuracy and data efficiency in deep learning models of protein expression.Nature communications · 2022Article
- SURE editing: combining oligo-recombineering and programmable insertion/deletion of selection markers to efficiently edit the Mycoplasma pneumoniae genome.Nucleic acids research · 2022Article
- A genetic toolkit and gene switches to limit Mycoplasma growth for biosafety applications.Nature communications · 2022Article
- Engineering a genome-reduced bacterium to eliminate Staphylococcus aureus biofilms in vivo.Molecular systems biology · 2021Article
- Programmable cross-ribosome-binding sites to fine-tune the dynamic range of transcription factor-based biosensor.Nucleic acids research · 2020Article
- So close, no matter how far: multiple paths connecting transcription to mRNA translation in eukaryotes.EMBO reports · 2020Review
- Genome and sequence determinants governing the expression of horizontally acquired DNA in bacteria.The ISME journal · 2020Article
- Large-scale DNA-based phenotypic recording and deep learning enable highly accurate sequence-function mapping.Nature communications · 2020Article
- Impact of C-terminal amino acid composition on protein expression in bacteria.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
- 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
- Multiplex transcriptional characterizations across diverse bacterial species using cell-free systems.Molecular systems biology · 2019Article
Corrections and comments
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Authors and funding
4 authors at 3 institutions in 2 countries.
Funding
Abstract
Quantitative analysis of the sequence determinants of transcription and translation regulation is relevant for systems and synthetic biology. To identify these determinants, researchers have developed different methods of screening random libraries using fluorescent reporters or antibiotic resistance genes. Here, we have implemented a generic approach called ELM-seq (expression level monitoring by DNA methylation) that overcomes the technical limitations of such classic reporters. ELM-seq uses DamID (Escherichia coli DNA adenine methylase as a reporter coupled with methylation-sensitive restriction enzyme digestion and high-throughput sequencing) to enable in vivo quantitative analyses of upstream regulatory sequences. Using the genome-reduced bacterium Mycoplasma pneumoniae, we show that ELM-seq has a large dynamic range and causes minimal toxicity. We use ELM-seq to determine key sequences (known and putatively novel) of promoter and untranslated regions that influence transcription and translation efficiency. Applying ELM-seq to other organisms will help us to further understand gene expression and guide synthetic biology.Quantitative analysis of how DNA sequence determines transcription and translation regulation is of interest to systems and synthetic biologists. Here the authors present ELM-seq, which uses Dam activity as reporter for high-throughput analysis of promoter and 5'-UTR regions.
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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.