Endothelial cells (ECs) are key regulators in vascular homeostasis, and their physiological state depends on hemodynamic forces produced by the blood flow. Laminar shear stress (LSS) maintains endothelial integrity, whereas oscillatory shear stress (OSS) leads to endothelial dysfunction and subsequently to cardiovascular disease. Here, we delineated the proteomic signatures of human umbilical vein endothelial cells (HUVECs) exposed to a protective flow (LSS) or a disturbed flow (OSS) in comparison to static conditions, using trapped ion mobility spectrometry coupled with parallel accumulation-serial fragmentation. OSS induced limited changes in cell morphology and the proteomic profile, whereas LSS triggered major modifications in cell shape and a proteomic signature related to the cell surface and extracellular matrix. Membrane subproteomic profiling confirmed the identification of membrane effectors involved in flow-mediated responses and in silico integrating promoter analysis suggested Krüppel-like Factor 4 (KLF4) as an important transcriptional regulator of this effector cluster. Using a novel EC model, TeloHAECs, we demonstrated that KLF4 likely contributes to LSS-induced alignment and elongation by increasing the expression of CD34, HEG1, PI16, and ITGB4 and that KLF4 is involved in PI16 and ITGB4 expression. Collectively, these findings provide a robust discovery data set on EC proteomic profiles related to flow and a refined view of KLF4-associated regulatory signatures at the level of membrane protein-coding genes in response to LSS.

Horizontal gene transfer is the movement of genetic material across species. In Saccharomyces cerevisiae, a DNA segment known as Region B was acquired horizontally from a distant yeast species. This region (∼17 Kb) encodes five genes and is present in the genomes of yeast strains from different phylogenetic clades. Interestingly, the presence of Region B is not restricted to yeast strains isolated from fermentative environments, leaving its contribution to yeast niche-specific adaptation unclear. In this work, the genomic structure of Region B was analyzed in yeast strains from the ScRAP (S. cerevisiae Reference Assembly Panel) collection, identifying ten structural variants that maintain a circular continuity. To assess the role of Region B in yeast adaptation, we performed a high-throughput phenotyping of the ScRAP collection under different growth conditions, identifying that Region B is associated with higher tolerance to oxidative stress. Then, we characterized the transcriptional activity of each gene within Region B using a fluorescent reporter. The results revealed that gene expression depends on the host's genetic background and transcription factors encoded within Region B. To identify the genetic determinants involved in Region B expression within different genetic backgrounds, three expression quantitative trait loci were mapped and validated. Finally, by performing the deletion of Region B in two different strains, we determined a background-dependent contribution of this region to various fermentative phenotypes. Altogether, our results suggest a complex regulatory interaction between the horizontally acquired genes and the host genome that contributes to yeast adaptation under fermentation conditions.

Endothelial cells (ECs) are key regulators in vascular homeostasis, and their physiological state depends on hemodynamic forces produced by the blood flow. Laminar shear stress (LSS) maintains endothelial integrity, whereas oscillatory shear stress (OSS) leads to endothelial dysfunction and subsequently to cardiovascular disease. Here, we delineated the proteomic signatures of human umbilical vein endothelial cells (HUVECs) exposed to a protective flow (LSS) or a disturbed flow (OSS) in comparison to static conditions, using trapped ion mobility spectrometry coupled with parallel accumulation-serial fragmentation. OSS induced limited changes in cell morphology and the proteomic profile, whereas LSS triggered major modifications in cell shape and a proteomic signature related to the cell surface and extracellular matrix. Membrane subproteomic profiling confirmed the identification of membrane effectors involved in flow-mediated responses and in silico integrating promoter analysis suggested Kruppel-like Factor 4 (KLF4) as an important transcriptional regulator of this effector cluster. Using a novel EC model, TeloHAECs, we demonstrated that KLF4 likely contributes to LSS-induced alignment and elongation by increasing the expression of CD34, HEG1, PI16, and ITGB4 and that KLF4 is involved in PI16 and ITGB4 expression. Collectively, these findings provide a robust discovery data set on EC proteomic profiles related to flow and a refined view of KLF4-associated regulatory signatures at the level of membrane protein-coding genes in response to LSS.

Endothelial cells (EC) play a pivotal role in vascular homeostasis. By sensing shear stress generated by blood flow, EC endorse vasculoprotection through mechanotransduction signaling pathways. Various ion channels are involved in mechanosignaling, and here, we investigated the endothelial voltage-gated Na+ channels (NaV channels), since their mechanosensitivity has been previously demonstrated in cardiomyocytes. First, we showed that EC from aorta (TeloHAEC) behave as EC from umbilical vein (HUVEC) under laminar shear stress (LSS). For both EC models, cell alignment and elongation occurred with the activation of the KLF2/KLF4 atheroprotective signaling pathways. We found that LSS decreased the expression of SCN5A, encoding NaV1.5, while LSS increased that of SCN3B, encoding NaVβ3. We demonstrated that the KLF4 transcription factor is involved in SCN3B expression under both static and LSS conditions. Interestingly, SCN3B silencing impaired EC alignment induced by LSS. The characterization of NaVβ3 interactome by coimmunoprecipitation and proteomic analysis revealed that mTOR, implicated in autophagy, binds to NaVβ3. This result was evidenced by the colocalization between NaVβ3 and mTOR inside cells. Moreover, we showed that SCN3B silencing led to the decrease in LC3B expression and the number of LC3B positive autophagosomes. Furthermore, we showed that NaVβ3 is retained within the cell and colocalized with LAMP1 and LC3B. Finally, we found that resveratrol, a stimulating-autophagy and vasculoprotective molecule, induced KLF4 together with NaVβ3 expression. Altogether, our findings highlight a novel role of NaVβ3 in endothelial function and cell alignment as an actor in shear stress vasculoprotective intracellular pathway through autophagy modulation.

Horizontal Gene Transfer (HGT) is the movement of genetic material across species. In Saccharomyces cerevisiae , a DNA segment known as Region B was acquired horizontally from a distant yeast species. This region (∼17 Kb) encodes 5 genes and is present in the genomes of yeast strains from different phylogenetic clades, with its contribution to yeast niche-specific adaptation remaining unclear. In this work, the genomic structure of Region B was analyzed in yeast strains from the ScRAP ( Saccharomyces cerevisiae Reference Assembly Panel) collection, identifying 10 variants that maintain a circular continuity. To assess the role of Region B in yeast adaptation, we performed a high-throughput phenotyping of the ScRAP collection under different growth conditions, identifying that Region B is potentially associated with higher tolerance to oxidative stress. Then, we selected a single yeast strain from the ScRAP collection for characterization of the transcriptional activity of each gene within Region B using a fluorescent reporter. The results revealed that gene expression depends on the host’s genetic background and transcription factors encoded within Region B. To identify the genetic determinants involved in Region B expression within different genetic backgrounds, three expression Quantitative Trait Loci (eQTLs) were mapped and validated. Finally, by performing Region B deletion, we determine the contribution of this region to different fermentative phenotypes, including fermentation rate and amino acid consumption. Altogether, our results suggest a complex regulatory interaction between the horizontally acquired genes and the host genome that contributes to yeast adaptation under fermentation conditions. ### Competing Interest Statement The authors have declared no competing interest. ANID-FONDECYT, 1210955, 1220026, 1250815 ANID-Millennium Science Initiative Program, ICN17_22 ANID-Subdirección de Investigación Apicada, ID24I10027 ANID-PhD scholarships, 21210525

To gain insight into how researchers of aging perceive the process they study, we conducted a survey among experts in the field. While highlighting some common features of aging, the survey exposed broad disagreement on the foundational issues. What is aging? What causes it? When does it begin? What constitutes rejuvenation? Not only was there no consensus on these and other core questions, but none of the questions received a majority opinion-even regarding the need for consensus itself. Despite many researchers believing they understand aging, their understanding diverges considerably. Importantly, as different processes are labeled as "aging" by researchers, different experimental approaches are prioritized. The survey shed light on the need to better define which aging processes this field should target and what its goals are. It also allowed us to categorize contemporary views on aging and rejuvenation, revealing critical, yet largely unanswered, questions that appear disconnected from the current research focus. Finally, we discuss ways to address the disagreement, which we hope will ultimately aid progress in the field.

Most organisms' traits result from the complex interplay of many genetic and environmental factors, making their prediction from genotypes difficult. Here, we used machine learning models to explore genotype-phenotype connections for 223 life history traits measured across 1011 genome-sequenced Saccharomyces cerevisiae strains. Firstly, we used genome-wide association studies to connect genetic variants with the phenotypes. Next, we benchmarked an automated machine learning pipeline that includes preprocessing, feature selection, and hyperparameters optimization in combination with multiple linear and complex machine learning methods. We determined gradient boosting machines as best performing in 65% of predictions and pangenome as best predictor, suggesting a considerable contribution of the accessory genome in controlling phenotypes. The accuracy broadly varied among the phenotypes (r = 0.2-0.9), consistent with varying levels of complexity, with stress resistance being easier to predict compared to growth across carbon and nitrogen nutrients. While no specific genomic features could be linked to the predictions for most phenotypes, machine learning identifies high-impact variants with established relationships to phenotypes despite being rare in the population. Near-perfect accuracies (r>0.95) were achieved when other phenomics data were used to aid predictions, suggesting shared useful information can be conveyed across phenotypes. Overall, our study underscores the power of machine learning to interpret the functional outcome of genetic variants. ### Competing Interest Statement The developed computational pipeline and scripts are available at: https://github.com/SakshiKhaiwal/Genotype-to-phenotype-mapping-in-yeast/tree/main. This software is provided solely for the purpose of scientific reproduction of the research described in the associated article and general academic research. Any other use, including commercial use, is prohibited without prior written consent from the authors. All rights reserved.

Supplementary Figure 1 from Regulation of Cyclin D1 RNA Stability by SNIP1

Supplementary Figure Legends 1-2 from Regulation of Cyclin D1 RNA Stability by SNIP1

Telomeres are ribonucleoproteins that cap chromosome-ends and their DNA length is controlled by counteracting elongation and shortening processes. The budding yeast Saccharomyces cerevisiae has been a leading model to study telomere DNA length control and dynamics. Its telomeric DNA is maintained at a length that slightly varies between laboratory strains, but little is known about its variation at the species level. The recent publication of the genomes of over 1,000 S. cerevisiae strains enabled us to explore telomere DNA length variation at an unprecedented scale. Here, we developed a bioinformatic pipeline (YeaISTY) to estimate telomere DNA length from whole-genome sequences and applied it to the sequenced S. cerevisiae collection. Our results revealed broad natural telomere DNA length variation among the isolates. Notably, telomere DNA length is shorter in those derived from wild rather than domesticated environments. Moreover, telomere DNA length variation is associated with mitochondrial metabolism, and this association is driven by wild strains. Overall, these findings reveal broad variation in budding yeast's telomere DNA length regulation, which might be shaped by its different ecological life-styles.

Domestication of plants and animals is the foundation for feeding the world human population but can profoundly alter the biology of the domesticated species. Here we investigated the effect of domestication on one of our prime model organisms, the yeast Saccharomyces cerevisiae, at a species-wide level. We tracked the capacity for sexual and asexual reproduction and the chronological life span across a global collection of 1,011 genome-sequenced yeast isolates and found a remarkable dichotomy between domesticated and wild strains. Domestication had systematically enhanced fermentative and reduced respiratory asexual growth, altered the tolerance to many stresses and abolished or impaired the sexual life cycle. The chronological life span remained largely unaffected by domestication and was instead dictated by clade-specific evolution. We traced the genetic origins of the yeast domestication syndrome using genome-wide association analysis and genetic engineering and disclosed causative effects of aneuploidy, gene presence/absence variations, copy number variations and single-nucleotide polymorphisms. Overall, we propose domestication to be the most dramatic event in budding yeast evolution, raising questions about how much domestication has distorted our understanding of the natural biology of this key model species.

Recent studies suggest the existence of a natural rejuvenation event during early embryonic development of mice, followed by epigenetic aging. Here, by profiling embryonic DNA methylation in the African clawed frog, Xenopus laevis , we found that the epigenetic entropy basepoint maps to the gastrulation stage of embryogenesis and corresponds to a rapid increase in embryo transcript abundance. We further developed a frog aging clock, revealing that this species epigenetically ages. Application of this clock to developmental stages identified a decrease in epigenetic age during early embryogenesis, with the minimal age reached around gastrulation. By examining individual developmental trajectories of 6,457 embryos, we found that this stage is also accompanied by a higher incidence of disrupted development. Taken together, our data point to gastrulation as a critical stage for aging and natural rejuvenation, characterized by the lowest epigenetic age, increased mortality, nadir of DNA methylation entropy and rapid increase in embryo transcript abundance, defining aging ground zero as the basepoint where rejuvenation ends and the aging process begins.

Hybrids between diverged lineages contain novel genetic combinations but an impaired meiosis often makes them evolutionary dead ends. Here, we explore to what extent an aborted meiosis followed by a return-to-growth (RTG) promotes recombination across a panel of 20 Saccharomyces cerevisiae and S. paradoxus diploid hybrids with different genomic structures and levels of sterility. Genome analyses of 275 clones reveal that RTG promotes recombination and generates extensive regions of loss-of-heterozygosity in sterile hybrids with either a defective meiosis or a heavily rearranged karyotype, whereas RTG recombination is reduced by high sequence divergence between parental subgenomes. The RTG recombination preferentially arises in regions with low local heterozygosity and near meiotic recombination hotspots. The loss-of-heterozygosity has a profound impact on sexual and asexual fitness, and enables genetic mapping of phenotypic differences in sterile lineages where linkage analysis would fail. We propose that RTG gives sterile yeast hybrids access to a natural route for genome recombination and adaptation.

La coupole de Montebras est un petit massif de granite à métaux rares (Sn, W, Li, Nb-Ta) situé au nord du Massif Central Français qui se met en place au Carbonifère supérieur dans un encaissant plus ancien, le granite de Chanon (357,2 ± 2,1 Ma). Deux épisodes magmatiques, un microgranite (316,1 ± 4,3 Ma) et un leucogranite albitique (309,8 ± 3,9 Ma), sont distingués. Le second développe à son toit des formations de contact, notamment une puissante pegmatite stockscheider (309,7 ± 4,5 Ma), passant vers l’est à des greisens à lithium et des filons plats de quartz stannifères anciennement exploités (303,8 ± 4,8 Ma). Le dépôt de cassitérite (associée à la manganocolumbite) s’étale depuis la phase magmatique avec des cristaux disséminés dans le leucogranite, jusqu’à la fin de la phase pneumatolytique marquée par des filons de quartz stannifères. Cet étalement se traduit par une baisse progressive des concentrations en éléments-traces (Nb, Ta, Fe, Mn, Mg, Ti) dans la cassitérite mais sans que soit atteint le domaine des compositions typiquement hydrothermales. Lors de la phase pneumatolytique, la cassitérite est accompagnée de rare scheelite, de la rarissime qitianlingite et d’une wolframite fréquente dont la composition (hübnérite) indique une origine magmatique pour le métal et les fluides impliqués dans le dépôt du tungstène. La paragenèse à sulfures riches en Cu, As et Sn (löllingite, chalcopyrite, tennantite, stannoïdite, mawsonite…) marque le passage à la phase hydrothermale et suggère une origine dans les roches encaissantes pour le cuivre et l’arsenic. L’événement fluo-barytique liasique se manifeste par l’apparition locale de fissures à fluorine violette, barytine et manganapatite. La coupole de Montebras fournit un exemple représentatif des granites à métaux rares de la chaîne varisque. Elle est contemporaine des autres magmas granitiques à éléments rares du nord Massif central avec lesquels elle présente des points de similitude mais aussi des différences. Sa mise en place pourrait relever d’un mécanisme de type cauldron subsidence.

Genome introgressions drive evolution across the animal 1 , plant 2 and fungal 3 kingdoms. Introgressions initiate from archaic admixtures followed by repeated backcrossing to one parental species. However, how introgressions arise in reproductively isolated species, such as yeast 4 , has remained unclear. Here we identify a clonal descendant of the ancestral yeast hybrid that founded the extant Saccharomyces cerevisiae Alpechin lineage 5 , which carries abundant Saccharomyces paradoxus introgressions. We show that this clonal descendant, hereafter defined as a ‘living ancestor’, retained the ancestral genome structure of the first-generation hybrid with contiguous S. cerevisiae and S. paradoxus subgenomes. The ancestral first-generation hybrid underwent catastrophic genomic instability through more than a hundred mitotic recombination events, mainly manifesting as homozygous genome blocks generated by loss of heterozygosity. These homozygous sequence blocks rescue hybrid fertility by restoring meiotic recombination and are the direct origins of the introgressions present in the Alpechin lineage. We suggest a plausible route for introgression evolution through the reconstruction of extinct stages and propose that genome instability allows hybrids to overcome reproductive isolation and enables introgressions to emerge.

Hybrids between species or diverged lineages contain fundamentally novel genetic combinations but an impaired meiosis often makes them evolutionary dead ends. Here, we explored to what extent and how an aborted meiosis followed by a return-to-growth (RTG) promotes recombination across a panel of 20 yeast diploid backgrounds with different genomic structures and levels of sterility. Genome analyses of 284 clones revealed that RTG promoted recombination and generated extensive regions of loss-of-heterozygosity in sterile hybrids with either a defective meiosis or a heavily rearranged karyotype, whereas RTG recombination was reduced by high sequence divergence between parental subgenomes. The RTG recombination preferentially occurred in regions with local sequence homology and in meiotic recombination hotspots. The loss-of-heterozygosity had a profound impact on sexual and asexual fitness, and enabled genetic mapping of phenotypic differences in sterile lineages where linkage or association analyses failed. We propose that RTG gives sterile hybrids access to a natural route for genome recombination and adaptation. One sentence summary Aborting meiosis followed by a return to mitotic growth promotes evolution by genome wide-recombination in sterile yeast hybrids.

Aging varies among individuals due to both genetics and environment, but the underlying molecular mechanisms remain largely unknown. Using a highly recombined Saccharomyces cerevisiae population, we found 30 distinct quantitative trait loci (QTLs) that control chronological life span (CLS) in calorie-rich and calorie-restricted environments and under rapamycin exposure. Calorie restriction and rapamycin extended life span in virtually all genotypes but through different genetic variants. We tracked the two major QTLs to the cell wall glycoprotein genes FLO11 and HPF1. We found that massive expansion of intragenic tandem repeats within the N-terminal domain of HPF1 was sufficient to cause pronounced life span shortening. Life span impairment by HPF1 was buffered by rapamycin but not by calorie restriction. The HPF1 repeat expansion shifted yeast cells from a sedentary to a buoyant state, thereby increasing their exposure to surrounding oxygen. The higher oxygenation altered methionine, lipid, and purine metabolism, and inhibited quiescence, which explains the life span shortening. We conclude that fast-evolving intragenic repeat expansions can fundamentally change the relationship between cells and their environment with profound effects on cellular lifestyle and longevity.

Background Mitochondria are essential organelles partially regulated by their own genomes. The mitochondrial genome maintenance and inheritance differ from the nuclear genome, potentially uncoupling their evolutionary trajectories. Here, we analysed mitochondrial sequences obtained from the 1011 Saccharomyces cerevisiae strain collection and identified pronounced differences with their nuclear genome counterparts. Results In contrast with pre-whole genome duplication fungal species, S. cerevisiae mitochondrial genomes show higher genetic diversity compared to the nuclear genomes. Strikingly, mitochondrial genomes appear to be highly admixed, resulting in a complex interconnected phylogeny with a weak grouping of isolates, whereas interspecies introgressions are very rare. Complete genome assemblies revealed that structural rearrangements are nearly absent with rare inversions detected. We tracked intron variation in COX1 and COB to infer gain and loss events throughout the species evolutionary history. Mitochondrial genome copy number is connected with the nuclear genome and linearly scale up with ploidy. We observed rare cases of naturally occurring mitochondrial DNA loss, petite, with a subset of them that do not suffer the expected growth defect in fermentable rich media. Conclusions Overall, our results illustrate how differences in the biology of two genomes coexisting in the same cells can lead to discordant evolutionary histories.

Pre-existing and de novo genetic variants can both drive adaptation to environmental changes, but their relative contributions and interplay remain poorly understood. Here we investigated the evolutionary dynamics in drug-treated yeast populations with different levels of pre-existing variation by experimental evolution coupled with time-resolved sequencing and phenotyping. We found a doubling of pre-existing variation alone boosts the adaptation by 64.1% and 51.5% in hydroxyurea and rapamycin, respectively. The causative pre-existing and de novo variants were selected on shared targets: RNR4 in hydroxyurea and TOR1, TOR2 in rapamycin. Interestingly, the pre-existing and de novo TOR variants map to different functional domains and act via distinct mechanisms. The pre-existing TOR variants from two domesticated strains exhibited opposite rapamycin resistance effects, reflecting lineage-specific functional divergence. This study provides a dynamic view on how pre-existing and de novo variants interactively drive adaptation and deepens our understanding of clonally evolving populations.

Aging varies among individuals due to both genetics and environment but the underlying molecular mechanisms remain largely unknown. Using a highly recombined Saccharomyces cerevisiae population, we found 30 distinct Quantitative Trait Loci (QTLs) that control chronological life span (CLS) in calorie rich and calorie restricted environments, and under rapamycin exposure. Calorie restriction and rapamycin extended life span in virtually all genotypes, but through different genetic variants. We tracked the two major QTLs to massive expansions of intragenic tandem repeats in the cell wall glycoproteins FLO11 and HPF1 , which caused a dramatic life span shortening. Life span impairment by N-terminal HPF1 repeat expansion was partially buffered by rapamycin but not by calorie restriction. The HPF1 repeat expansion shifted yeast cells from a sedentary to a buoyant state, thereby increasing their exposure to surrounding oxygen. The higher oxygenation perturbed methionine, lipid, and purine metabolism, which likely explains the life span shortening. We conclude that fast evolving intragenic repeat expansions can fundamentally change the relationship between cells and their environment with profound effects on cellular life style and longevity.