18 research outputs found
Role of the antagonistic histone methylation marks H3K4me3 and H3K27me3 in the cold stress response of Arabidopsis thaliana
As sessile organisms, plants need to adapt to their changing environment, including temperature fluctuations. As low temperatures can have major noxious consequences on their development and survival, plants need to establish the proper defences in order to endure the stress. This requires a massive and very fast transcriptome reprogramming involving, among others, the induction of hundreds of cold-responsive (COR) genes. Following the immediate response to chilling stress, plants are also able to memorize cold spells, leading to an improved survival during a second stress episode. This process is associated with a revised transcriptomic response also called transcriptional memory. Overall, both the response to cold and the memory of this stress rely on the tight transcriptional regulation of the COR genes. While numerous transcription factors necessary for their induction were already identified, the role of chromatin modifications in this process remains largely undiscovered. As the combination of chromatin modifications (the âchromatin stateâ) is a key determinant of gene expression, this study aimed at uncovering the potential role of histone modifications in the transcriptional regulation of COR genes before, during and after a cold episode. First, a comprehensive in silico analysis of the chromatin state of COR genes prior to any cold occurrence revealed that a majority of those genes carry both the activating mark H3K4me3 and the silencing mark H3K27me3, forming a specific chromatin state called bivalency. The in vivo characterization of bivalent genes revealed that this chromatin state decorates not only cold-inducible genes but numerous reversibly silenced stress-responsive genes and might poise them for expression by maintaining them in an open chromatin conformation. Furthermore, the putative bivalency reader DEK2 was shown to prevent the over-induction of bivalent COR genes during a cold episode, suggesting that bivalency can also participate in transcriptional regulation in trans through the action of specific readers. In a second stage, the dynamics of H3K4me3 and H3K27me3 during a cold stress were analysed using genome-wide approaches, revealing that both marks underwent intensive redistribution already after three hours of low temperature. Those changes partially correlated with expression changes: in particular, the induction of COR genes was associated with a loss of the repressive mark H3K27me3 or a gain of the activating mark H3K4me3. However, each mark displayed different targets and dynamics, suggesting that they hold distinct roles in the cold response: H3K4me3 associated with immediate stress responses while H3K27me3 rather correlated with longer-term adaptation. Upon return to ambient temperature, the cold-induced variations reverted at a different pace depending on the gene and some changes were maintained for up to seven days. Both the maintenance of H3K4me3 and H3K27me3 changes were linked to transcriptional memory: higher levels of H3K4me3 were associated with sustained induction while lower levels of H3K27me3 were correlated with a faster re-induction during a second stress exposure. Finally, the H3K27me3 demethylase ELF6 was shown to be essential for cold stress memory. This led to the hypothesis that cold stress memory might rely on the maintained loss of H3K27me3 on specific COR genes, allowing a faster re-establishment of defences during a second stress episode. In conclusion, this study demonstrates that the antagonistic marks H3K4me3 and H3K27me3 jointly participate to the transcriptional regulation of COR genes and reveals a new role of bivalency in the plant cold stress response and memory.Da Pflanzen an ihren Standort gebunden sind, mĂŒssen sie sich stĂ€ndig an verĂ€nderte Umweltbedingungen anpassen. KĂ€lte kann schĂ€dliche Folgen fĂŒr die Pflanzenentwicklung und sogar zum Absterben von Pflanzen fĂŒhren. Daher mĂŒssen Pflanzen auf diesen Stress reagieren, indem sie eine geeignete Abwehr zum Ăberleben aufbauen. Dies erfordert eine erhebliche Umprogrammierung des Transkriptoms, welche die Induktion von zahlreichen kĂ€lteempfindlichen (COR) Genen enthĂ€lt. Nach einer direkten Stressantwort sind Pflanzen in der Lage ein KĂ€ltegedĂ€chtnis aufzubauen, wodurch sie eine zweite KĂ€lteepisode besser ĂŒberstehen. Dieser Prozess ist mit massiven Ănderungen auf Genexpressionsebene verbunden, die auch âtranskriptionelles GedĂ€chtnisâ genannt wird. Sowohl die unmittelbare Reaktion auf, als auch das Bilden eines lĂ€ngerfristigen GedĂ€chtnisses an KĂ€lte, sind auf eine prĂ€zise Transkriptionsregulation von COR Genen angewiesen. Obwohl der Chromatinzustand ein bestimmender Faktor fĂŒr Genexpression ist, ist die Rolle von Chromatinmodifikationen in der Induktion von COR Genen noch weitgehend unbekannt. Deshalb war es das Ziel dieser Arbeit, die Rolle von Histonmodifikationen in der Transkriptionsregulation von COR Genen vor, wĂ€hrend, und nach KĂ€ltestress zu analysieren. ZunĂ€chst offenbarte eine umfassende in silico Analyse des Chromatinzustands von COR Genen vor einem KĂ€lteereignis, dass die Mehrheit dieser Gene sowohl die aktivierende Modifikation H3K4me3 als auch die repressive Modifikation H3K27me3 tragen. Dieser Chromatinzustand wird auch als bivalent bezeichnet. Die in vivo Charakterisierung bivalenter Gene zeigte, dass besonders stillgelegte, induzierbare Gene durch einen bivalenten Chromatinzustand markiert sind. Diese könnten dadurch fĂŒr eine eventuelle Expression vorbereitet sein, indem diese Genbereiche in einer offenen Chromatin-Konformation verbleiben. Der vermeintliche Bivalenz-Leser DEK2 verhinderte die Ăberinduktion von bivalenten Genen wĂ€hrend einer KĂ€lteepisode. Dies weist darauf hin, dass Bivalenz auch an der Transkriptionsregulation in trans durch die Aktion von bestimmten Reader-Proteinen Anteil nehmen kann. Die Analyse der H3K4me3 und H3K27me3 Dynamik mittels genomweiter Methoden zeigte, dass bei niedrigen Temperaturen eine intensive Neuverteilung beider Modifikationen stattfindet, die teilweise mit Expressionsvariationen korrelierte. Insbesondere war die Induktion von COR Genen mit einem Verlust der repressiven Modifikation H3K27me3 oder einer Zunahme der aktivierenden Modifikation H3K4me3 assoziiert. Die Modifikationen haben jedoch distinkte Rollen in der KĂ€lteantwort. H3K4me3 war mit der unmittelbaren Stressantwort assoziiert, wĂ€hrend H3K27me3 eher mit Langzeitadaptation korreliert war. Nach der RĂŒckkehr zu ambienter Umgebungstemperatur kehrte das Chromatin zu seinem Ausgangzustand in unterschiedlichem Tempo abhĂ€ngig vom Gen zurĂŒck, wobei manche VerĂ€nderungen bis zu sieben Tage beibehalten wurden. Die Aufrechterhaltung von sowohl H3K4me3 als auch H3K27me3 Variationen waren mit transkriptionellem GedĂ€chtnis assoziiert: höhere H3K4me3 Mengen korrelierten mit bestĂ€ndiger Induktion und niedrigere H3K27me3 Mengen waren mit einer schnelleren Re-Induktion wĂ€hrend einer zweiten KĂ€lteepisode assoziiert. SchlieĂlich wurde gezeigt, dass die H3K27me3 Demethylase ELF6 unabdingbar fĂŒr das KĂ€ltestressgedĂ€chtnis ist. Der fortbestehende Verlust von H3K27me3 auf spezifischen Genen könnte daher die molekulare Basis fĂŒr das KĂ€ltestressgedĂ€chtnis sein, indem ein schnellerer Wiederaufbau der Abwehr wĂ€hrend einer zweiten Stressepisode ermöglicht wird. Insgesamt zeigt diese Studie, dass die antagonistischen Modifikationen H3K4me3 und H3K27me3 gemeinsam an der Transkriptionsregulation von COR Genen teilhaben, und offenbart eine neue Rolle der Bivalenz bei der KĂ€ltestressreaktion von Pflanzen
Transcriptional and Post-Transcriptional Regulation and Transcriptional Memory of Chromatin Regulators in Response to Low Temperature
Chromatin regulation ensures stable repression of stress-inducible genes under non-stress conditions and transcriptional activation and memory of stress-related genes after stress exposure. However, there is only limited knowledge on how chromatin genes are regulated at the transcriptional and post-transcriptional level upon stress exposure and relief from stress. We reveal that the repressive modification histone H3 lysine 27 trimethylation (H3K27me3) targets genes which are quickly activated upon cold exposure, however, H3K27me3 is not necessarily lost during a longer time in the cold. In addition, we have set-up a quantitative reverse transcription polymerase chain reaction-based platform for high-throughput transcriptional profiling of a large set of chromatin genes. We find that the expression of many of these genes is regulated by cold. In addition, we reveal an induction of several DNA and histone demethylase genes and certain histone variants after plants have been shifted back to ambient temperature (deacclimation), suggesting a role in the memory of cold acclimation. We also re-analyze large scale transcriptomic datasets for transcriptional regulation and alternative splicing (AS) of chromatin genes, uncovering an unexpected level of regulation of these genes, particularly at the splicing level. This includes several vernalization regulating genes whose AS may result in cold-regulated protein diversity. Overall, we provide a profiling platform for the analysis of chromatin regulatory genes and integrative analyses of their regulation, suggesting a dynamic regulation of key chromatin genes in response to low temperature stress
Polycomb proteins control floral determinacy by H3K27me3-mediated repression of pluripotency genes in arabidopsis thaliana
Vuorovaikutteisen suunnittelun haasteet ja mahdollisuudet metsÀtalouden vesiensuojelussa
Rapport de l'expertise scientifique collectiveLes animaux peuvent-ils Ă©prouver des Ă©motions, peuvent-ils penser, ont-ils une histoire de vie ? Depuis lâAntiquitĂ©, les philosophes ont proposĂ© des rĂ©ponses contrastĂ©es Ă ces questions. Du XIXĂšme siĂšcle Ă nos jours, la rĂ©flexion sur ce que sont les animaux sâest enrichie dâapports scientifiques : thĂ©orie de lâĂ©volution, Ă©thologie, neurophysiologie, sciences cognitives. Mais la conscience animale reste toujours lâobjet de dĂ©bats importants dans la communautĂ© scientifique. Ainsi en 2012 un groupe de scientifiques de premier plan a Ă©prouvĂ© la nĂ©cessitĂ© de publier un manifeste intitulĂ© « DĂ©claration de Cambridge sur la Conscience », qui Ă©nonce quâ«âŠune convergence de preuves indique que les animaux non humains disposent des substrats neuro-anatomiques, neurochimiques et neurophysiologiques des Ă©tats conscients ainsi que la capacitĂ© dâexprimer des comportements intentionnels...».Les connaissances actuelles, dont cette expertise collective propose une synthĂšse, montrent que les animaux possĂšdent un large Ă©ventail de capacitĂ©s cognitives associĂ©es Ă des comportements plus ou moins complexes. Les formes de conscience Ă©tudiĂ©es chez les humains supposent des capacitĂ©s cognitives distinctes que lâon retrouve chez certains animaux. Peut-on en postuler que ceux-ci ont des formes de consciences Ă©quivalentes Ă celles de lâhomme, sans ĂȘtre forcĂ©ment identiques ?LâĂ©tude des niveaux et des contenus de la conscience chez les animaux est en passe de devenir un enjeu scientifique important en raison de la complexitĂ© du sujet et des controverses quâil ne manquera pas de susciter. Enfin, les acquis scientifiques dans ce domaine invitent Ă reprendre les rĂ©flexions morales concernant les relations que les hommes entretiennent avec les animaux (et particuliĂšrement avec les animaux domestiques
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The extruded non-template strand determines the architecture of R-loops.
Three-stranded R-loop structures have been associated with genomic instability phenotypes. What underlies their wide-ranging effects on genome stability remains poorly understood. Here we combined biochemical and atomic force microscopy approaches with single molecule R-loop footprinting to demonstrate that R-loops formed at the model Airn locus in vitro adopt a defined set of three-dimensional conformations characterized by distinct shapes and volumes, which we call R-loop objects. Interestingly, we show that these R-loop objects impose specific physical constraints on the DNA, as revealed by the presence of stereotypical angles in the surrounding DNA. Biochemical probing and mutagenesis experiments revealed that the formation of R-loop objects at Airn is dictated by the extruded non-template strand, suggesting that R-loops possess intrinsic sequence-driven properties. Consistent with this, we show that R-loops formed at the fission yeast gene sum3 do not form detectable R-loop objects. Our results reveal that R-loops differ by their architectures and that the organization of the non-template strand is a fundamental characteristic of R-loops, which could explain that only a subset of R-loops is associated with replication-dependent DNA breaks
La conscience animale. Résumé de l'expertise scientifique collective
Les animaux peuvent-ils Ă©prouver des Ă©motions ? Ont-ils une histoire de vie ? LâInra (DĂ©lĂ©gation Ă l'Expertise scientifique collective, Ă la Prospective et aux Etudes) sâest saisi de ces questions en rĂ©alisant une expertise scientifique collective sur la conscience animale, Ă la demande de lâAutoritĂ© europĂ©enne de sĂ©curitĂ© alimentaire (EFSA). Les rĂ©sultats ont Ă©tĂ© prĂ©sentĂ©s aux reprĂ©sentants des pays membres du rĂ©seau europĂ©en sur le Bien-Etre animal et de lâEFSA le 11 mai 2017 Ă Parme (Italie)
Animal consciousness. Summary of the multidisciplinary assesment: Summary
Summary of the multidisciplinary assesmentDo animals experience emotions? Think? Have a life story? Since antiquity, philosophers have contrasting answers to those questions. From the Nineteenth century onwards, thoughts on the nature of animals were enriched by scientific insights from evolutionary theory, ethology, neurophysiology and cognitive sciences. Meanwhile, animal consciousness remains controversial within the scientific community. In 2012, a group of leading scientists felt the need to publish a manifesto entitled the âCambridge Declaration on Consciousnessâ it states that âconvergent evidence indicates that nonhuman animals have the neuroanatomical, neurochemical, and neurophysiological substrates of conscious states along with the capacity to exhibit intentional behavioursâ.Current knowledge, including the outcome of this multidisciplinary scientific assessment, shows that animals possess a wide range of cognitive abilities associated with behaviours of varying complexity. The forms of consciousness observed in humans presuppose distinct cognitive abilities which are found in certain animals. Could it be concluded that animals possess some sort of consciousness similar, albeit not identical, to that of humans?Research on levels and contents of consciousness in animals is emerging as a scientific topic of major interest due to its high level of complexity and associated controversies. Current scientific advances invite us to revisit ethical considerations regarding the relationships between humans and animals (domestic animals in particular)
Animal consciousness. Summary of the multidisciplinary assesment: Summary
Summary of the multidisciplinary assesmentDo animals experience emotions? Think? Have a life story? Since antiquity, philosophers have contrasting answers to those questions. From the Nineteenth century onwards, thoughts on the nature of animals were enriched by scientific insights from evolutionary theory, ethology, neurophysiology and cognitive sciences. Meanwhile, animal consciousness remains controversial within the scientific community. In 2012, a group of leading scientists felt the need to publish a manifesto entitled the âCambridge Declaration on Consciousnessâ it states that âconvergent evidence indicates that nonhuman animals have the neuroanatomical, neurochemical, and neurophysiological substrates of conscious states along with the capacity to exhibit intentional behavioursâ.Current knowledge, including the outcome of this multidisciplinary scientific assessment, shows that animals possess a wide range of cognitive abilities associated with behaviours of varying complexity. The forms of consciousness observed in humans presuppose distinct cognitive abilities which are found in certain animals. Could it be concluded that animals possess some sort of consciousness similar, albeit not identical, to that of humans?Research on levels and contents of consciousness in animals is emerging as a scientific topic of major interest due to its high level of complexity and associated controversies. Current scientific advances invite us to revisit ethical considerations regarding the relationships between humans and animals (domestic animals in particular)
La conscience animale: Une expertise scientifique collective de lâInra
Ce dossier a prĂ©alablement Ă©tĂ© publiĂ© par lâInra sur son site : http://institut.Inra.fr/Missions/Eclairer-les-decisions/Expertises/Toutes-les-actualites/Conscience-animaleThis paper presents the outcome of a scientific multidisciplinary assessment on animal consciousness carried out by Inra from 2015 to 2017. The experts, produced in a 169 pages report in English, an exhaustive analysis of the scientific and philosophical knowledge available in the international literature. It first describes the knowledge about humans in which the concepts and tools describing consciousness have been developed. The available data on animals are much less numerous, but they make it possible to draw firm conclusions, even if they still require more data. Most of the reported results were obtained on laboratory and wild vertebrates and little on livestock species. Consciousness is defined as the subjective experience that the animal has of its environment and of its own knowledge. The overall view of the behavioral, cognitive and neurobiological studies analyzed in the report tends to show the existence of elaborate consciousness contents in the species studied. The consequences for animals of the presence of consciousness on pain and on ethical behavior towards them are presented. Additional researches should complement existing ones, particularly on farmed species.Ce dossier prĂ©sente les rĂ©sultats dâune expertise scientifique collective sur la conscience animale rĂ©alisĂ©e par lâInra en 2015-2017. Les experts ont produit dans un rapport de 169 pages en anglais une analyse exhaustive des connaissances scientifiques et philosophiques disponibles dans la littĂ©rature internationale. Il dĂ©crit tout dâabord les connaissances sur les humains oĂč ont Ă©tĂ© Ă©laborĂ©s les concepts et les outils dĂ©crivant la conscience. Les donnĂ©es disponibles sur les animaux sont beaucoup moins nombreuses mais elles permettent cependant de tirer des conclusions solides, mĂȘme si elles demandent Ă ĂȘtre confortĂ©es. La plupart des rĂ©sultats rapportĂ©s ont Ă©tĂ© obtenus sur des vertĂ©brĂ©s de laboratoire ou sauvages et peu sur les espĂšces de rente. La conscience est dĂ©finie comme lâexpĂ©rience subjective que lâanimal a de son environnement et de ses propres connaissances. La vision dâensemble des Ă©tudes comportementales, cognitives et neurobiologiques analysĂ©es dans le rapport tend Ă montrer lâexistence de contenus Ă©laborĂ©s de conscience chez les espĂšces Ă©tudiĂ©es. Les consĂ©quences pour les animaux de la prĂ©sence dâune conscience sur la douleur et sur les conduites Ă©thiques vis-Ă -vis dâeux sont prĂ©sentĂ©es. Des recherches supplĂ©mentaires devront complĂ©ter celles existantes, particuliĂšrement sur les espĂšces dâĂ©levage