Distinct responses to rare codons in select Drosophila tissues

SR Allen, RK Stewart, M Rogers, IJ Ruiz, E Cohen… - Elife, 2022 - elifesciences.org
Codon usage bias has long been appreciated to influence protein production. Yet, relatively
few studies have analyzed the impacts of codon usage on tissue-specific mRNA and protein …

Codon Usage Differences among Genes Expressed in Different Tissues of Drosophila melanogaster

BL Payne, D Alvarez-Ponce - Genome Biology and Evolution, 2019 - academic.oup.com
Codon usage patterns are affected by both mutational biases and translational selection.
The frequency at which each codon is used in the genome is directly linked to the cellular …

Genes enriched in A/T-ending codons are co-regulated and conserved across mammals

H Benisty, X Hernandez-Alias, M Weber… - Cell Systems, 2023 - cell.com
Codon usage influences gene expression distinctly depending on the cell context. Yet, the
importance of codon bias in the simultaneous turnover of specific groups of protein-coding …

Ribo-seq enlightens codon usage bias

D Paulet, A David, E Rivals - DNA Research, 2017 - academic.oup.com
Codon usage is biased between lowly and highly expressed genes in a genome-specific
manner. This universal bias has been well assessed in some unicellular species, but …

Codon usage bias in animals: disentangling the effects of natural selection, effective population size, and GC-biased gene conversion

N Galtier, C Roux, M Rousselle… - Molecular biology …, 2018 - academic.oup.com
Selection on codon usage bias is well documented in a number of microorganisms. Whether
codon usage is also generally shaped by natural selection in large organisms, despite their …

Codon usage biases co-evolve with transcription termination machinery to suppress premature cleavage and polyadenylation

Z Zhou, Y Dang, M Zhou, H Yuan, Y Liu - Elife, 2018 - elifesciences.org
Codon usage biases are found in all genomes and influence protein expression levels. The
codon usage effect on protein expression was thought to be mainly due to its impact on …

[HTML][HTML] Minor shift in background substitutional patterns in the Drosophila saltans and willistoni lineages is insufficient to explain GC content of coding sequences

ND Singh, PF Arndt, DA Petrov - BMC biology, 2006 - Springer
Background Several lines of evidence suggest that codon usage in the Drosophila saltans
and D. willistoni lineages has shifted towards a less frequent use of GC-ending codons …

Effects of codon usage on gene expression are promoter context dependent

Q Yang, X Lyu, F Zhao, Y Liu - Nucleic Acids Research, 2021 - academic.oup.com
Codon usage bias is a universal feature of all genomes. Although codon usage has been
shown to regulate mRNA and protein levels by influencing mRNA decay and transcription in …

[HTML][HTML] Positive selection for unpreferred codon usage in eukaryotic genomes

DE Neafsey, JE Galagan - BMC Evolutionary Biology, 2007 - Springer
Background Natural selection has traditionally been understood as a force responsible for
pushing genes to states of higher translational efficiency, whereas lower translational …

Patterns of Synonymous Codon Usage in Drosophila melanogaster Genes With Sex-Biased Expression

TM Hambuch, J Parsch - Genetics, 2005 - academic.oup.com
The nonrandom use of synonymous codons (codon bias) is a well-established phenomenon
in Drosophila. Recent reports suggest that levels of codon bias differ among genes that are …