ArticleBMC genomics2021
Massively parallel gene expression variation measurement of a synonymous codon library.
Article in BMC genomics, 2021. 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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Who cites it
13 citing papers in PubMed, 19 citations in OpenAlex.
- Advancing codon language modeling with synonymous codon constrained masking.Nucleic acids research · 2026Article
- Regulatory time-kill sequencing maps antibiotic-specific transcriptional control ofFrontiers in microbiology · 2026Article
- Hurdles to horizontal gene transfer: species-specific effects of synonymous variation and plasmid copy number determine antibiotic resistance phenotype.Microbiology (Reading, England) · 2026Article
- Automated characterization and analysis of expression compatibility between regulatory sequences and metabolic genes inSynthetic and systems biotechnology · 2024Article
- Specific codons control cellular resources and fitness.Science advances · 2024Article
- Deep-learning-assisted Sort-Seq enables high-throughput profiling of gene expression characteristics with high precision.Science advances · 2023Article
- Genome-wide promoter responses to CRISPR perturbations of regulators reveal regulatory networks in Escherichia coli.Nature communications · 2023Article
- Deep Mutational Scanning of an Oxygen-Independent Fluorescent Protein CreiLOV for Comprehensive Profiling of Mutational and Epistatic Effects.ACS synthetic biology · 2023Article
- Effective design and inference for cell sorting and sequencing based massively parallel reporter assays.Bioinformatics (Oxford, England) · 2023Article
- Diverse mechanisms of bioproduction heterogeneity in fermentation and their control strategies.Journal of industrial microbiology & biotechnology · 2023Review
- Performance upgrade of a microbial explosives' sensor strain by screening a high throughput saturation library of a transcriptional regulator.Computational and structural biotechnology journal · 2023Article
- Intelligent host engineering for metabolic flux optimisation in biotechnology.The Biochemical journal · 2021Review
- Linking genome variants to disease: scalable approaches to test the functional impact of human mutations.Human molecular genetics · 2021Review
Corrections and comments
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Authors and funding
2 authors at 1 institution in 1 country.
Funding
Abstract
backgroundCell-to-cell variation in gene expression strongly affects population behavior and is key to multiple biological processes. While codon usage is known to affect ensemble gene expression, how codon usage influences variation in gene expression between single cells is not well understood.
resultsHere, we used a Sort-seq based massively parallel strategy to quantify gene expression variation from a green fluorescent protein (GFP) library containing synonymous codons in Escherichia coli. We found that sequences containing codons with higher tRNA Adaptation Index (TAI) scores, and higher codon adaptation index (CAI) scores, have higher GFP variance. This trend is not observed for codons with high Normalized Translation Efficiency Index (nTE) scores nor from the free energy of folding of the mRNA secondary structure. GFP noise, or squared coefficient of variance (CV
conclusionsOur results suggest that the main source of noise for high-abundance proteins is likely not originating at translation elongation. Additionally, the drastic change in mean protein abundance with small changes in protein noise seen from our library implies that codon optimization can be performed without concerning gene expression noise for biotechnology applications.
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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.