Sequence modeling and design from molecular to genome scale with Evo
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 …
organism's function. We present Evo, a long-context genomic foundation model with a …
Sense codon reassignment enables viral resistance and encoded polymer synthesis
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 …
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
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 …
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
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 …
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 …
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 …
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 …
of ribosomes in defined states. To comprehensively visualize bacterial translation, we …
Laboratory evolution, transcriptomics, and modeling reveal mechanisms of paraquat tolerance
Relationships between the genome, transcriptome, and metabolome underlie all evolved
phenotypes. However, it has proved difficult to elucidate these relationships because of the …
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 …
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
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 …
of genetic novelty. Nevertheless, how noncoding sequences' properties could promote the …