Publications

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A major scientific drive is to characterize the protein-coding genome, which is a primary basis for studying human health. But the fundamental question remains of what has been missed in previous analyses. Over the past decade, the translation of non-canonical open reading frames (ncORFs) has been observed across human cell types and disease states, –,...

Non-canonical (i.e. unannotated) open reading frames (ncORFs) have until recently been omitted from reference genome annotations, despite evidence of their translation, limiting their incorporation into biomedical research. To address this, in 2022, we initiated the TransCODE consortium and built the first community-driven consensus catalog of human ncORFs, which was openly distributed to the research community...

New protein-coding genes can arise de novo from ancestrally noncoding regions when open reading frames (ORFs) outside existing genes are exposed to selection via pervasive translation. These ORFs are usually born short, and their elongation is considered a key step in de novo gene birth. However, mechanisms of de novo gene elongation remain understudied. Here,...

Thousands of short open reading frames (sORFs) are translated outside of annotated coding sequences. Recent studies have pioneered searching for sORF-encoded microproteins in mass spectrometry (MS)-based proteomics and peptidomics datasets. Here, we assessed literature-reported MS-based identifications of unannotated human proteins. We find that studies vary by three orders of magnitude in the number of unannotated...

Recent evidence demonstrates that eukaryotic genomes encode thousands of evolutionarily novel proteins that originate de novo from non-coding DNA and can contribute to species-specific adaptations. Yet, it remains unclear how these incipient proteins—whose sequences are entirely new to nature—navigate the cellular environment to bring about phenotypic change. Here, we conduct a systematic in vivo investigation...

RNA molecules as templates. All cellular proteins are products of translation, and the identification of protein-coding regions is the primary goal of genome annotation. Beyond protein synthesis, translation has long been known to have regulatory functions independent of its products 1, 2. However, only with the advent of ribosome profiling was the broad scale and...

A major scientific drive is to characterize the protein-coding genome as it provides the primary basis for the study of human health. But the fundamental question remains: what has been missed in prior genomic analyses? Over the past decade, the translation of non-canonical open reading frames (ncORFs) has been observed across human cell types and...

Integration by parts Network biologists today have access to a rich assortment of interaction networks produced by assays such as affinity purification-mass spectrometry (AP-MS), yeast two-hybrid (Y2H) screening, co-fractionation mass spectrometry (CF-MS), or thermal proximity co-aggregation (TPCA), to name just a few. But high-throughput interaction data are notoriously noisy, such that similar experiments performed in...

Thousands of short open reading frames (sORFs) are translated outside of annotated coding sequences. Recent studies have pioneered searching for sORF-encoded microproteins in mass spectrometry (MS)- based proteomics and peptidomics datasets. Here, we assessed literature-reported MS-based identifications of unannotated human proteins. We find that studies vary by three orders of magnitude in the number of...

Complexification of macrobiomolecules, such as homodimer to heterodimer transitions, are common during evolution. Is such complexification always adaptive? Using large-scale experiments and in-depth biochemical analyses, Després et al. recently demonstrated that an obligate heterodimer can evolve from a homodimer through neutral, nonadaptive events, and quantified key parameters required for such transitions.

New protein-coding genes can evolve from previously noncoding genomic regions through a process known as de novo gene emergence. Evidence suggests that this process has likely occurred throughout evolution and across the tree of life. Yet, confidently identifying de novo emerged genes remains challenging. Ancestral sequence reconstruction is a promising approach for inferring whether a...

Ribosome profiling is a sequencing technique that provides a global picture of translation across a genome. Here, we present iRibo, a software program for integrating any number of ribosome profiling samples to obtain sensitive inference of annotated or unannotated translated open reading frames. We describe the process of using iRibo to generate a species' translatome...

By demonstrating that the conditions for homodimer-to-heterodimer transition by CNE are achieved fairly readily following gene duplication, the experimental results from Després et al. indicate that adaptive explanations are not necessary to explain the prevalence of this transition in evolution. There are possible adaptive explanations for why a heterodimer might be superior. Yet, given Després...

BackgroundRecent studies uncovered pervasive transcription and translation of thousands of noncanonical open reading frames (nORFs) outside of annotated genes. The contribution of nORFs to cellular phenotypes is difficult to infer using conventional approaches because nORFs tend to be short, of recent de novo origins, and lowly expressed. Here we develop a dedicated coexpression analysis framework...

Ribosome profiling experiments indicate pervasive translation of short open reading frames (ORFs) outside of annotated protein-coding genes. However, shotgun mass spectrometry (MS) experiments typically detect only a small fraction of the predicted protein products of this noncanonical translation. The rarity of detection could indicate that most predicted noncanonical proteins are rapidly degraded and not present...

There are thousands of unannotated translated open reading frames (ORFs) in the Saccharomyces cerevisiae genome. Previous investigation into one such unannotated ORF, which was systemically labeled YGR016C-A based on its genomic coordinates, showed that replacing the ORF’s ATG start codon with AAG led to a change in cellular fitness under different stress conditions (Wacholder et...

Translation is the process by which ribosomes synthesize proteins. Ribosome profiling recently revealed that many short sequences previously thought to be noncoding are pervasively translated. To identify protein-coding genes in this noncanonical translatome, we combine an integrative framework for extremely sensitive ribosome profiling analysis, iRibo, with high-powered selection inferences tailored for short sequences. We construct...

Comparative analysis of human and macaque brain transcripts together with experiments in mice and in a cortical organoid model show the de novo emergence of a hominoid-specific protein-coding gene implicated in brain development. The evolution of RNA nuclear export signals enabled a new protein to become translated from an ancestral long-noncoding RNA locus.

Organisms must either synthesize or assimilate essential organic compounds to survive. The homocysteine synthase Met15 has been considered essential for inorganic sulfur assimilation in yeast since its discovery in the 1970s. As a result, MET15 has served as a genetic marker for hundreds of experiments that play a foundational role in eukaryote genetics and systems...

De novo gene birth is the process by which new genes emerge in sequences that were previously noncoding. Over the past decade, researchers have taken advantage of the power of yeast as a model and a tool to study the evolutionary mechanisms and physiological implications of de novo gene birth. We summarize the mechanisms that...

To the Editor—Ribosome profiling (Ribo-seq) has extended our understanding of the translational ‘vocabulary’of the human genome, uncovering thousands of open reading frames (ORFs) within long noncoding RNAs (lncRNAs) and presumed untranslated regions (UTRs) of protein-coding genes. However, reference gene annotation projects have been circumspect in their incorporation of these ORFs because of uncertainties about their...

Post-transcriptional regulatory mechanisms play a role in many biological contexts through the control of mRNA degradation, translation and localization. Here, we show that the RING finger protein RNF219 co-purifies with the CCR4-NOT complex, the major mRNA deadenylase in eukaryotes, which mediates translational repression in both a deadenylase activity-dependent and -independent manner. Strikingly, RNF219 both inhibits...

The high-level organization of the cell is embedded in indirect relationships that connect distinct cellular processes. Existing computational approaches for detecting indirect relationships between genes typically consist of propagating abstract information through network representations of the cell. However, the selection of genes to serve as the source of propagation is inherently biased by prior knowledge....

CAREER: Investigation Of How Proto-Gene Expression Impacts Growth In Budding Yeast - ADS Now on home page ads icon ads Enable full ADS view ADS CAREER: Investigation Of How Proto-Gene Expression Impacts Growth In Budding Yeast Carvunis, Anne-Ruxandra Abstract This award is funded in whole or in part under the American Rescue Plan Act of...

Microproteins (

The vast phenotypic diversity of life is in part a consequence of a continual process of genetic innovation. New genes, with distinct structures and capabilities, emerge regularly throughout evolutionary history. Making use of genomics technologies, researchers are beginning to form an understanding of the details of the processes by which new genes arise. On page...

Microbial growth characteristics have long been used to investigate fundamental questions of biology. Colony-based high-throughput screens enable parallel fitness estimation of thousands of individual strains using colony growth as a proxy for fitness. However, fitness estimation is complicated by spatial biases affecting colony growth, including uneven nutrient distribution, agar surface irregularities, and batch effects. Analytical...

Ribosome profiling experiments demonstrate widespread translation of eukaryotic genomes outside of annotated protein-coding genes. However, it is unclear how much of this “noncanonical” translation contributes biologically relevant microproteins rather than insignificant translational noise. Here, we developed an integrative computational framework (iRibo) that leverages hundreds of ribosome profiling experiments to detect signatures of translation with high...

Microproteins (< 100 amino acids) are receiving increasing recognition as important participants in numerous biological processes, but their evolutionary dynamics are poorly understood. SPAAR is a recently discovered microprotein that regulates muscle regeneration and angiogenesis through interactions with conserved signaling pathways. Interestingly, SPAAR does not belong to any known protein family and has known homologs...

All mammals progress through similar physiological stages throughout life, from early development to puberty, aging, and death. Yet, the extent to which this conserved physiology reflects underlying genomic events is unclear. Here, we map the common methylation changes experienced by mammalian genomes as they age, focusing on comparison of humans with dogs, an emerging model...

The origin of ‘orphan’ genes, species-specific sequences that lack detectable homologues, has remained mysterious since the dawn of the genomic era. There are two dominant explanations for orphan genes: complete sequence divergence from ancestral genes, such that homologues are not readily detectable; and de novo emergence from ancestral non-genic sequences, such that homologues genuinely do...

Recent evidence demonstrates that novel protein-coding genes can arise de novo from non-genic loci. This evolutionary innovation is thought to be facilitated by the pervasive translation of non-genic transcripts, which exposes a reservoir of variable polypeptides to natural selection. Here, we systematically characterize how these de novo emerging coding sequences impact fitness in budding yeast....

In this essay, we demonstrate how rhetorical analyses of style can maintain their focus on linguistic patterns while simultaneously attending to material ones. Focusing on the trope of metonymy and the figures of incrementum and epistrophe, we show how these devices represent different modes of material-semiotic addressivity, resiliently turning and reconfiguring the rhetorical ecologies they...

“Function” is a vitally important concept in the scientific community. Scientists use it to describe and address a wide variety of research problems. In publications, however, scientists within and across disciplines interpret function differently. For example, intense debate surrounds what percentage of the human genome should be deemed “functional” rather than “junk DNA.” In this...

The word function has many different meanings in molecular biology. Here we explore the use of this word (and derivatives like functional) in research papers about de novo gene birth. Based on an analysis of 20 abstracts we propose a simple lexicon that, we believe, will help scientists and philosophers discuss the meaning of function...

De novo gene birth is the process by which new genes evolve from DNA sequences that were ancestrally non-genic. De novo genes represent a subset of novel genes, and may be proteincoding or instead act as RNA genes [1]. The processes that govern de novo gene birth (Fig 1A) are not well understood, though several...

Animal models have been tremendously useful to translational research, but there is a need to maximize their predictive value to human disease. This Comment proposes novel strategies that consider evolutionary history and the presence, absence or modification of molecular networks in one species that are being studied in the other.

Phylostratigraphy is a computational framework for dating the emergence of DNA and protein sequences in a phylogeny. It has been extensively applied to make inferences on patterns of genome evolution, including patterns of disease gene evolution, ontogeny and de novo gene origination. Phylostratigraphy typically relies on BLAST searches along a species tree, but new simulation studies have...

Protein microarrays enable investigation of diverse biochemical properties for thousands of proteins in a single experiment, an unparalleled capacity. Using a high-density system called HaloTag nucleic acid programmable protein array (HaloTag-NAPPA), we created high-density protein arrays comprising 12,000 Arabidopsis ORFs. We used these arrays to query protein–protein interactions for a set of 38 transcription factors...

Genome sequences diverge more rapidly in mammals than in other animal lineages, such as birds or insects. However, the effect of this rapid divergence on transcriptional evolution remains unclear. Recent reports have indicated a faster divergence of transcription factor binding in mammals than in insects, but others found the reverse for mRNA expression. Here, we...

Just as reference genome sequences revolutionized human genetics, reference maps of interactome networks will be critical to fully understand genotype-phenotype relationships. Here, we describe a systematic map of ∼14,000 high-quality human binary protein-protein interactions. At equal quality, this map is ∼30% larger than what is available from small-scale studies published in the literature in the...

Modern genomics is very efficient at mapping genes and gene networks, but how to transform these maps into predictive models of the cell remains unclear. Recent progress in computer science, embodied by intelligent agents such as Siri, inspires an approach for moving from networks to multiscale models able to predict a range of cellular phenotypes...

Efficient repair of UV-induced DNA damage requires the precise coordination of nucleotide excision repair (NER) with numerous other biological processes. To map this crosstalk, we generated a differential genetic interaction map centered on quantitative growth measurements of >45,000 double mutants before and after different doses of UV radiation. Integration of genetic data with physical interaction networks...

A central goal of systems biology is to elucidate the structural and functional architecture of the cell. To this end, large and complex networks of molecular interactions are being rapidly generated for humans and model organisms. A recent focus of bioinformatics research has been to integrate these networks with each other and with diverse molecular...

A central hypothesis of systems biology is that genotype–phenotype relationships are, at least in part, mediated by complex macromolecular networks, referred to as’ interactome’networks, which are formed by large numbers of physical and functional interactions between genes and gene products. Proteins, in particular, physically interact with one another to form molecular machines, interconnected signaling pathways...

Pseudomonas aeruginosa strain PA14 is an opportunistic human pathogen capable of infecting a wide range of organisms including the nematode Caenorhabditis elegans. We used a non-redundant transposon mutant library consisting of 5,850 clones corresponding to 75% of the total and approximately 80% of the non-essential PA14 ORFs to carry out a genome-wide screen for attenuation...

Genotypic differences greatly influence susceptibility and resistance to disease. Understanding genotype–phenotype relationships requires that phenotypes be viewed as manifestations of network properties, rather than simply as the result of individual genomic variations. Genome sequencing efforts have identified numerous germline mutations, and large numbers of somatic genomic alterations, associated with a predisposition to cancer. However, it...

Novel protein-coding genes can arise either through re-organization of pre-existing genes or de novo,. Processes involving re-organization of pre-existing genes, notably after gene duplication, have been extensively described,. In contrast, de novo gene birth remains poorly understood, mainly because translation of sequences devoid of genes, or ‘non-genic’ sequences, is expected to produce insignificant polypeptides rather...

NOUVELLE m/sn 3, vol. 28, mars 2012 238 possible. Selon ce second modèle, les récepteurs intracellulaires devraient interagir directement avec les protéines effectrices, alors que selon l’hypothèse des défenses gardées, ces interactions seraient indirectes. Les interactions entre protéines effectrices et récepteurs intracellulaires que nous avons expérimentalement détectées se sont avérées majoritairement indirectes, donc en accord...

Plants generate effective responses to infection by recognizing both conserved and variable pathogen-encoded molecules. Pathogens deploy virulence effector proteins into host cells, where they interact physically with host proteins to modulate defense. We generated an interaction network of plant-pathogen effectors from two pathogens spanning the eukaryote-eubacteria divergence, three classes of Arabidopsis immune system proteins, and...

Plants have unique features that evolved in response to their environments and ecosystems. A full account of the complex cellular networks that underlie plant-specific functions is still missing. We describe a proteome-wide binary protein-protein interaction map for the interactome network of the plant Arabidopsis thaliana containing about 6200 highly reliable interactions between about 2700 proteins....

Darwin a révélé au monde que les espèces vivantes ne cessent jamais d’évoluer, mais les mécanismes moléculaires de cette évolution restent le sujet de recherches intenses. La biologie systémique propose que les relations entre génotype, environnement et phénotype soient sous-tendues par un ensemble de réseaux moléculaires dynamiques au sein de la cellule, mais l’organisation de...

L’idée selon laquelle les gènes et leurs produits sont les unités fondamentales de la biologie a profondément marqué la pensée scientifique de la seconde moitié du xxe siècle. Aujourd’hui, cette approche réductionniste est remise en cause par la renaissance de la biologie systémique, qui a pour objets d’étude les systèmes formés par les produits de...

High-quality datasets are needed to understand how global and local properties of protein-protein interaction, or 'interactome', networks relate to biological mechanisms, and to guide research on individual proteins. In an evaluation of existing curation of protein interaction experiments reported in the literature, we found that curation can be error-prone and possibly of lower quality than...

To provide accurate biological hypotheses and elucidate global properties of cellular networks, systematic identification of protein-protein interactions must meet high quality standards. We present an expanded C. elegans protein-protein interaction network, or 'interactome' map, derived from testing a matrix of ∼10,000 × ∼10,000 proteins using a highly specific, high-throughput yeast two-hybrid system. Through a new...

Accurately defining the coding potential of an organism, i.e., all protein-encoding open reading frames (ORFs) or “ORFeome,” is a prerequisite to fully understand its biology. ORFeome annotation involves iterative computational predictions from genome sequences combined with experimental verifications. Here we reexamine a set of Saccharomyces cerevisiae “orphan” ORFs recently removed from the original ORFeome annotation...

Differential regulation of gene expression is essential for cell fate specification in metazoans. Characterizing the transcriptional activity of gene promoters, in time and in space, is therefore a critical step toward understanding complex biological systems. Here we present an in vivo spatiotemporal analysis for ∼900 predicted C. elegans promoters (∼5% of the predicted protein-coding genes),...

The influence of the network topology on the dynamics of systems of coupled excitable units is studied numerically and demonstrates a lower dynamical variability for power-law networks than for Poisson ones. This effect which reflects a robust collective excitable behavior is however lower than that observed for diffusion processes or network robustness. Instead, the presence...

De novo gene birth is the process by which new genes evolve from DNA sequences that were ancestrally non-genic. De novo genes represent a subset of novel genes, and may be protein-coding or instead act as RNA genes.[1] The processes that govern de novo gene birth (Figure 1A) are not well understood, though several models...