Codon optimality, bias and usage in translation and mRNA decay

G Hanson, J Coller - Nature reviews Molecular cell biology, 2018 - nature.com
The advent of ribosome profiling and other tools to probe mRNA translation has revealed
that codon bias—the uneven use of synonymous codons in the transcriptome—serves as a …

On the dependency of cellular protein levels on mRNA abundance

Y Liu, A Beyer, R Aebersold - Cell, 2016 - cell.com
The question of how genomic information is expressed to determine phenotypes is of central
importance for basic and translational life science research and has been studied by …

Combinatorial optimization of mRNA structure, stability, and translation for RNA-based therapeutics

K Leppek, GW Byeon, W Kladwang… - Nature …, 2022 - nature.com
Therapeutic mRNAs and vaccines are being developed for a broad range of human
diseases, including COVID-19. However, their optimization is hindered by mRNA instability …

mRNA structure regulates protein expression through changes in functional half-life

DM Mauger, BJ Cabral, V Presnyak… - Proceedings of the …, 2019 - National Acad Sciences
Messenger RNAs (mRNAs) encode information in both their primary sequence and their
higher order structure. The independent contributions of factors like codon usage and …

Ribosomopathies: There's strength in numbers

EW Mills, R Green - Science, 2017 - science.org
BACKGROUND Ribosomopathies are a heterogeneous group of human disorders that are
in some cases known, and in other cases suspected, to result from ribosome dysfunction …

Ribosome levels selectively regulate translation and lineage commitment in human hematopoiesis

RK Khajuria, M Munschauer, JC Ulirsch, C Fiorini… - Cell, 2018 - cell.com
Blood cell formation is classically thought to occur through a hierarchical differentiation
process, although recent studies have shown that lineage commitment may occur earlier in …

Codon bias as a means to fine-tune gene expression

TEF Quax, NJ Claassens, D Söll, J van der Oost - Molecular cell, 2015 - cell.com
The redundancy of the genetic code implies that most amino acids are encoded by multiple
synonymous codons. In all domains of life, a biased frequency of synonymous codons is …

Pseudouridine profiling reveals regulated mRNA pseudouridylation in yeast and human cells

TM Carlile, MF Rojas-Duran, B Zinshteyn, H Shin… - Nature, 2014 - nature.com
Post-transcriptional modification of RNA nucleosides occurs in all living organisms.
Pseudouridine, the most abundant modified nucleoside in non-coding RNAs, enhances the …

Synonymous but not silent: the codon usage code for gene expression and protein folding

Y Liu, Q Yang, F Zhao - Annual review of biochemistry, 2021 - annualreviews.org
Codon usage bias, the preference for certain synonymous codons, is found in all genomes.
Although synonymous mutations were previously thought to be silent, a large body of …

The organizing principles of eukaryotic ribosome recruitment

J Pelletier, N Sonenberg - Annual review of biochemistry, 2019 - annualreviews.org
The stage at which ribosomes are recruited to messenger RNAs (mRNAs) is an elaborate
and highly regulated phase of protein synthesis. Upon completion of this step, a ribosome is …