Nucleosomes at the Dawn of Eukaryotes

Genome regulation in eukaryotes revolves around the nucleosome, the fundamental building block of eukaryotic chromatin. Its constituent parts, the four core histones (H3, H4, H2A, H2B), are universal to eukaryotes. Yet despite its exceptional conservation and central role in orchestrating transcription, repair, and other DNA-templated processes, the origins and early evolution of the nucleosome remain opaque. Histone-fold proteins are also found in archaea, but the nucleosome we know—a hetero-octameric complex composed of histones with long, disordered tails—is a hallmark of eukaryotes. What were the properties of the earliest nucleosomes? Did ancestral histones inevitably assemble into nucleosomes? When and why did the four core histones evolve? This review will look at the evolution of the eukaryotic nucleosome from the vantage point of archaea, focusing on the key evolutionary transitions required to build a modern nucleosome. We will highlight recent work on the closest archaeal relatives of eukaryotes, the Asgardarchaea, and discuss what their histones can and cannot tell us about the early evolution of eukaryotic chromatin. We will also discuss how viruses have become an unexpected source of information about the evolutionary path toward the nucleosome. Finally, we highlight the properties of early nucleosomes as an area where new tools and data promise tangible progress in the not-too-distant future

Polyextremophile engineering: a review of organisms that push the limits of life

Nature exhibits an enormous diversity of organisms that thrive in extreme environments. From snow algae that reproduce at sub-zero temperatures to radiotrophic fungi that thrive in nuclear radiation at Chernobyl, extreme organisms raise many questions about the limits of life. Is there any environment where life could not “find a way”? Although many individual extremophilic organisms have been identified and studied, there remain outstanding questions about the limits of life and the extent to which extreme properties can be enhanced, combined or transferred to new organisms. In this review, we compile the current knowledge on the bioengineering of extremophile microbes. We summarize what is known about the basic mechanisms of extreme adaptations, compile synthetic biology’s efforts to engineer extremophile organisms beyond what is found in nature, and highlight which adaptations can be combined. The basic science of extremophiles can be applied to engineered organisms tailored to specific biomanufacturing needs, such as growth in high temperatures or in the presence of unusual solvents

Maternal and fetal genetic effects on birth weight and their relevance to cardio-metabolic risk factors.

Birth weight variation is influenced by fetal and maternal genetic and non-genetic factors, and has been reproducibly associated with future cardio-metabolic health outcomes. In expanded genome-wide association analyses of own birth weight (n = 321,223) and offspring birth weight (n = 230,069 mothers), we identified 190 independent association signals (129 of which are novel). We used structural equation modeling to decompose the contributions of direct fetal and indirect maternal genetic effects, then applied Mendelian randomization to illuminate causal pathways. For example, both indirect maternal and direct fetal genetic effects drive the observational relationship between lower birth weight and higher later blood pressure: maternal blood pressure-raising alleles reduce offspring birth weight, but only direct fetal effects of these alleles, once inherited, increase later offspring blood pressure. Using maternal birth weight-lowering genotypes to proxy for an adverse intrauterine environment provided no evidence that it causally raises offspring blood pressure, indicating that the inverse birth weight-blood pressure association is attributable to genetic effects, and not to intrauterine programming.The Fenland Study is funded by the Medical Research Council (MC_U106179471) and Wellcome Trust

Exploration de la plasticité de domaines chromosomiques sur la surexpression de facteurs silencieux dans Saccharomyces cerevisiae

La présence de domaines chromosomiques heterochromatiniens associé à des effets de position est une propriété communes à de nombreux génomes eukaryotes. L'intensité et l'étendue de la variégation liée aux effets de position sont généralement sensibles à la dose des protéines effectrices de l'hétérochromatine. Les propriétés d'auto-propagation des complexes d'hétérochromatine a un cout, qui est la nécessité d'établir des mécanismes stoppant la propagation de la répression transcriptionelle. Cette thèse explore la dose-dépendance de l'effet de position télomérique en étudiant le complexe SIR de la levure du boulanger. La caractérisation du groupement des télomères en foyers, de la localisation de Sir3 et de la transcription dans des souches sur-exprimant Sir3 a permis d'établir l'étendue maximale des domaines silencieux présent aux subtelomeres. L'étude de jeux de données publiés a révélé que ces domaines terminent généralement au niveau de zones correspondant où les propriétés de la chromatine montrent une transition importante. Ces transitions chromatiniennes sont requises pour survivre en présence d'un excès de protéines Sir3 puisque nous avons démontré que les mutants dot1 ne survivent pas un tel excès. En outre nous avons conduit un crible génétique qui a révélé de nombreux gènes requis pour la survie en présence d'une surdose de Sir3. Ce travail caractérise la réponse du génome à une surdose d'hétérochromatine et a permis de révéler des domaines subtélomeriques associés à des propriétés chromatiniennes particulières. En conséquence nous démontrons comment l'effet de position télomerique est efficacement restreint au subtelomere chez la levure.A shared property of several eukaryotic genomes is the presence of heterochromatic chromosomal domains experiencing transcriptional variegation. The intensity and the extent of position effect variegation are sensitive to the dosage of silencing effectors in many systems. The self-propagating properties of heterochromatin machineries come with a cost, which is the requirement for mechanisms preventing ectopic spreading of silencing. This thesis explores the dose-dependency of telomere position effect, using the budding yeast SIR system as a model for chromatin based heterochromatic silencing. To assess the dose-dependency of telomere position effect in budding yeast, we systematically characterized the impact of Sir3 overexpression by quantifying the clustering of telomeres, the genome wide binding of Sir3 and its impact on coding and non coding transcription. Analysis of published data sets enabled to uncover candidates potentially responsible for the limitation of subtelomeric silent domains. Our study reveals that extension of silent domains can reach saturation, associated with the anti-silencing properties of histone marks deposited by the conserved enzyme Dot1. In addition we discovered genes required for viability upon SIR3 overexpression by conducting a genetic screen. Our work describes the dynamics of the dose dependency of heterochromatin propagation in budding yeast. It uncovers previously uncharacterized discrete chromosomal domains associated with specific chromatin features and demonstrates how telomere position effect is efficiently restricted to subtelomeres by the preexisting chromatin landscape

exploration de la plasticité de domaines chromosomiques par la surexpression de facteurs de silencing chez Saccharomyces cerevisiae

Background: A shared property of several eukaryotic genomes is the presence of heterochromatic chromosomal domains experiencing transcriptional variegation. The intensity and the extent ofposition effect variegation are sensitive to the dosage of silencing effectors in many systems. Mechanistically, the self-propagating properties of heterochromatin machineries come with a cost, which is the requirement for mechanisms preventing ectopic spreading of silencing. This work explores the dose-dependency of telomere position effect, using the budding yeast SIR system as a model for chromatin based heterochromatic silencing.Results: To assess the dose-dependency of telomere position effect in budding yeast, we built a set of strains in which SIR2 and SIR3 endogenous promoters are changed. We systematically characterized the impact of Sir3 overexpression by quantifying the clustering of telomeres, the genome wide binding of Sir3 and its impact on coding and non coding transcription. Analysis of published data sets enabled to uncover candidates potentially responsible for the limitation of subtelomeric silent domains that were confirmed by genetic assay. Our study reveals that extension of silent domains can reach saturation, associated with the anti-silencing properties of histone marks deposited by the conserved enzyme Dot1. An outcome of this work is the determination of the maximal extends of subtelomeric domains, which offer a new point of view on subtelomeric properties.Conclusions: Our work uncovers the dynamics of the dose dependency of heterochromatin propagation in budding yeast. It uncovers previously uncharacterized discrete chromosomal domains associated with specific chromatin features and demonstrates how telomere position effect is efficiently restricted to subtelomeres by the preexisting chromatin landscape.La présence de domaines chromosomiques heterochromatiniens associés à des effets de position est une propriété commune à de nombreux génomes eukaryotes. L'intensité et l'étendue de la variégation liée aux effets de position sont généralement sensibles à la dose des protéines effectrices de l'hétérochromatine. Les propriétés d'auto-propagation des complexes d'hétérochromatine nécessitent d'établir des mécanismes stoppant la propagation de la répression transcriptionelle. Cette thèse explore la dose-dépendance de l'effet de position télomérique en étudiant le complexe SIR (silencing information regulator) de la levure du boulanger. La caractérisation du groupement des télomères en foyers, de la localisation de Sir3 et de la transcription dans des souches sur-exprimant Sir3 a permis d'établir l'étendue maximale des domaines silencieux présents aux subtelomeres. L'étude de jeux de données publiés a révélé que ces domaines terminent généralement au niveau de zones correspondant à des zones de transition des marques chromatiniennes. Ces transitions chromatiniennes sont requises pour survivre en présence d'un excès de protéines Sir3 puisque nous avons démontré que les mutants dot1 ne survivent pas un tel excès. En outre nous avons conduit un crible génétique qui a révélé de nombreux gènes requis pour la survie en présence d'une surdose de Sir3. Ce travail caractérise la réponse du génome à une surdose d'hétérochromatine et a permis de révéler des domaines subtélomeriques associés à des propriétés chromatiniennes particulières. En conséquence nous démontrons comment l'effet de position télomerique est efficacement restreint au subtelomere chez la levure

Growth temperature and chromatinization in archaea

International audienceAbstract DNA in cells is associated with proteins that constrain its structure and affect DNA-templated processes including transcription and replication. HU and histones are the main constituents of chromatin in bacteria and eukaryotes, respectively, with few exceptions. Archaea, in contrast, have diverse repertoires of nucleoid-associated proteins (NAPs). To analyse the evolutionary and ecological drivers of this diversity, we combined a phylogenomic survey of known and predicted NAPs with quantitative proteomic data. We identify the Diaforarchaea as a hotbed of NAP gain and loss, and experimentally validate candidate NAPs in two members of this clade, Thermoplasma volcanium and Methanomassiliicoccus luminyensis . Proteomic analysis across a diverse sample of 19 archaea revealed that NAP investment varies from 5% of total protein. This variation is predicted by growth temperature. We propose that high levels of chromatinization have evolved as a mechanism to prevent uncontrolled helix denaturation at higher temperatures, with implications for the origin of chromatin in both archaea and eukaryotes

Growth temperature and chromatinization in archaea

International audienceAbstract DNA in cells is associated with proteins that constrain its structure and affect DNA-templated processes including transcription and replication. HU and histones are the main constituents of chromatin in bacteria and eukaryotes, respectively, with few exceptions. Archaea, in contrast, have diverse repertoires of nucleoid-associated proteins (NAPs). To analyse the evolutionary and ecological drivers of this diversity, we combined a phylogenomic survey of known and predicted NAPs with quantitative proteomic data. We identify the Diaforarchaea as a hotbed of NAP gain and loss, and experimentally validate candidate NAPs in two members of this clade, Thermoplasma volcanium and Methanomassiliicoccus luminyensis . Proteomic analysis across a diverse sample of 19 archaea revealed that NAP investment varies from 5% of total protein. This variation is predicted by growth temperature. We propose that high levels of chromatinization have evolved as a mechanism to prevent uncontrolled helix denaturation at higher temperatures, with implications for the origin of chromatin in both archaea and eukaryotes

Sir3 mediates long-range chromosome interactions in budding yeast

International audiencePhysical contacts between distant loci contribute to regulate genome function. However, the molecular mechanisms responsible for settling and maintaining such interactions remain poorly understood. Here, we investigate the well-conserved interactions between heterochromatin loci. In budding yeast, the 32 telomeres cluster in 3-5 foci in exponentially growing cells. This clustering is functionally linked to the formation of heterochromatin in subtelomeric regions through the recruitment of the silencing SIR complex composed of Sir2/3/4. Combining microscopy and Hi-C on strains expressing different alleles of SIR3, we show that the binding of Sir3 directly promotes long-range contacts between distant regions, including the rDNA, telomeres, and internal Sir3-bound sites. Furthermore, we unveil a new property of Sir3 in promoting rDNA compaction. Finally, using a synthetic approach, we demonstrate that Sir3 can bond loci belonging to different chromosomes together, when targeted to these loci, independently of its interaction with its known partners (Rap1, Sir4), Sir2 activity, or chromosome context. Altogether, these data suggest that Sir3 acts as a molecular bridge that stabilizes long-range interactions

Expanding heterochromatin reveals discrete subtelomeric domains delimited by chromatin landscape transitions

International audienc