ArticleNucleic acids research2015
Increased functional protein expression using nucleotide sequence features enriched in highly expressed genes in zebrafish.
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 67 papers.
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Who cites it
67 citing papers in PubMed.
- Article
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- Universal conditional knockout approach to multiple species, from fish to human induced pluripotent stem cells.Nucleic acids research · 2026Article
- Functional interrogation of neuronal connections by chemoptogenetic presynaptic ablation.Science advances · 2026Article
- Molecular and functional dissection using CaMPARI-seq reveals the neuronal organization for dissociating optic flow-dependent behaviors.Nature communications · 2026Article
- Versatile CRISPR-Cas Tools for Gene Regulation in Zebrafish via an Enhanced Q Binary System.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026Article
- CaBLAM: a high-contrast bioluminescent CaNature methods · 2026Article
- MultiSite Assembly of Gateway Induced Clones (MAGIC): a flexible cloning toolbox for use in vertebrate model systems.Development (Cambridge, England) · 2025Article
- Codon Composition in Human Oocytes Reveals Age-Associated Defects in mRNA Decay.International journal of molecular sciences · 2025Article
- Imaging cellular activity simultaneously across all organs of a vertebrate reveals body-wide circuits.bioRxiv : the preprint server for biology · 2025Article
- CaBLAM! A high-contrast bioluminescent CabioRxiv : the preprint server for biology · 2025Article
- Rhabdomyosarcoma fusion oncoprotein initially pioneers a neural signature in vivo.Cell reports · 2025Article
- Macrophage vacuolar ATPase (v-ATPase) function controlsbioRxiv : the preprint server for biology · 2025Article
- In vivo profiling of the endothelium using 'AngioTag' zebrafish.Angiogenesis · 2025Article
- HMGCS1 variants cause rigid spine syndrome amenable to mevalonic acid treatment in an animal model.Brain : a journal of neurology · 2025Article
- Rapid and robust generation of cardiomyocyte-specific crispants in zebrafish using the cardiodeleter system.Cell reports methods · 2025Article
- CutIn: a ready-to-use construct for rapid generation of urgently needed transgenic cell lines in emerging infection research.Functional & integrative genomics · 2025Article
- Effective Gene Expression Prediction and Optimization from Protein Sequences.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2025Article
7 more citing papers are in PubMed but not listed here.
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7 authors.
Funding
Abstract
Many genetic manipulations are limited by difficulty in obtaining adequate levels of protein expression. Bioinformatic and experimental studies have identified nucleotide sequence features that may increase expression, however it is difficult to assess the relative influence of these features. Zebrafish embryos are rapidly injected with calibrated doses of mRNA, enabling the effects of multiple sequence changes to be compared in vivo. Using RNAseq and microarray data, we identified a set of genes that are highly expressed in zebrafish embryos and systematically analyzed for enrichment of sequence features correlated with levels of protein expression. We then tested enriched features by embryo microinjection and functional tests of multiple protein reporters. Codon selection, releasing factor recognition sequence and specific introns and 3' untranslated regions each increased protein expression between 1.5- and 3-fold. These results suggested principles for increasing protein yield in zebrafish through biomolecular engineering. We implemented these principles for rational gene design in software for codon selection (CodonZ) and plasmid vectors incorporating the most active non-coding elements. Rational gene design thus significantly boosts expression in zebrafish, and a similar approach will likely elevate expression in other animal models.
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