Sequence modeling and design from molecular to genome scale with Evo

E Nguyen, M Poli, MG Durrant, B Kang, D Katrekar… - Science, 2024 - science.org
The genome is a sequence that encodes the DNA, RNA, and proteins that orchestrate an
organism's function. We present Evo, a long-context genomic foundation model with a …

Sense codon reassignment enables viral resistance and encoded polymer synthesis

WE Robertson, LFH Funke, D de la Torre, J Fredens… - Science, 2021 - science.org
It is widely hypothesized that removing cellular transfer RNAs (tRNAs)—making their
cognate codons unreadable—might create a genetic firewall to viral infection and enable …

Augmented genetic decoding: global, local and temporal alterations of decoding processes and codon meaning

PV Baranov, JF Atkins, MM Yordanova - Nature Reviews Genetics, 2015 - nature.com
The non-universality of the genetic code is now widely appreciated. Codes differ between
organisms, and certain genes are known to alter the decoding rules in a site-specific …

[PDF][PDF] Read between the lines: diversity of nontranslational selection pressures on local codon usage

M Callens, L Pradier, M Finnegan… - Genome Biology and …, 2021 - academic.oup.com
Protein coding genes can contain specific motifs within their nucleotide sequence that
function as a signal for various biological pathways. The presence of such sequence motifs …

Gene autoregulation by 3'UTR-derived bacterial small RNAs

M Hoyos, M Huber, KU Förstner, K Papenfort - Elife, 2020 - elifesciences.org
Negative feedback regulation, that is the ability of a gene to repress its own synthesis, is the
most abundant regulatory motif known to biology. Frequently reported for transcriptional …

Evolution of termination codons of proteins and the TAG-TGA paradox

M Trexler, L Bányai, K Kerekes, L Patthy - Scientific Reports, 2023 - nature.com
In most eukaryotes and prokaryotes TGA is used at a significantly higher frequency than
TAG as termination codon of protein-coding genes. Although this phenomenon has been …

Transient disome complex formation in native polysomes during ongoing protein synthesis captured by cryo-EM

T Flügel, M Schacherl, A Unbehaun, B Schroeer… - Nature …, 2024 - nature.com
Structural studies of translating ribosomes traditionally rely on in vitro assembly and stalling
of ribosomes in defined states. To comprehensively visualize bacterial translation, we …

Laboratory evolution, transcriptomics, and modeling reveal mechanisms of paraquat tolerance

K Rychel, J Tan, A Patel, C Lamoureux, Y Hefner… - Cell reports, 2023 - cell.com
Relationships between the genome, transcriptome, and metabolome underlie all evolved
phenotypes. However, it has proved difficult to elucidate these relationships because of the …

Epistasis between promoter activity and coding mutations shapes gene evolvability

AF Cisneros, I Gagnon-Arsenault, AK Dubé… - Science …, 2023 - science.org
The evolution of protein-coding genes proceeds as mutations act on two main dimensions:
regulation of transcription level and the coding sequence. The extent and impact of the …

Intergenic ORFs as elementary structural modules of de novo gene birth and protein evolution

C Papadopoulos, I Callebaut, JC Gelly, I Hatin… - Genome …, 2021 - genome.cshlp.org
The noncoding genome plays an important role in de novo gene birth and in the emergence
of genetic novelty. Nevertheless, how noncoding sequences' properties could promote the …