@phdthesis{Siebler2024, author = {Siebler, Lara}, title = {Identifying novel regulators of heat stress memory in Arabidopsis thaliana}, doi = {10.25932/publishup-63447}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-634477}, school = {Universit{\"a}t Potsdam}, pages = {135}, year = {2024}, abstract = {Heat stress (HS) is a major abiotic stress that negatively affects plant growth and productivity. However, plants have developed various adaptive mechanisms to cope with HS, including the acquisition and maintenance of thermotolerance, which allows them to respond more effectively to subsequent stress episodes. HS memory includes type II transcriptional memory which is characterized by enhanced re-induction of a subset of HS memory genes upon recurrent HS. In this study, new regulators of HS memory in A. thaliana were identified through the characterization of rein mutants. The rein1 mutant carries a premature stop in CYCLIN-DEPENDENT-KINASE 8 (CDK8) which is part of the cyclin kinase module of the Mediator complex. Rein1 seedlings show impaired type II transcriptional memory in multiple heat-responsive genes upon re-exposure to HS. Additionally, the mutants exhibit a significant deficiency in HS memory at the physiological level. Interaction studies conducted in this work indicate that CDK8 associates with the memory HEAT SHOCK FACTORs HSAF2 and HSFA3. The results suggest that CDK8 plays a crucial role in HS memory in plants together with other memory HSFs, which may be potential targets of the CDK8 kinase function. Understanding the role and interaction network of the Mediator complex during HS-induced transcriptional memory will be an exciting aspect of future HS memory research. The second characterized mutant, rein2, was selected based on its strongly impaired pAPX2::LUC re-induction phenotype. In gene expression analysis, the mutant revealed additional defects in the initial induction of HS memory genes. Along with this observation, basal thermotolerance was impaired similarly as HS memory at the physiological level in rein2. Sequencing of backcrossed bulk segregants with subsequent fine mapping narrowed the location of REIN2 to a 1 Mb region on chromosome 1. This interval contains the At1g65440 gene, which encodes the histone chaperone SPT6L. SPT6L interacts with chromatin remodelers and bridges them to the transcription machinery to regulate nucleosome and Pol II occupancy around the transcriptional start site. The EMS-induced missense mutation in SPT6L may cause altered HS-induced gene expression in rein2, possibly triggered by changes in the chromatin environment resulting from altered histone chaperone function. Expanding research on screen-derived factors that modify type II transcriptional memory has the potential to enhance our understanding of HS memory in plants. Discovering connections between previously identified memory factors will help to elucidate the underlying network of HS memory. This knowledge can initiate new approaches to improve heat resilience in crops.}, language = {en} } @phdthesis{Vyse2022, author = {Vyse, Kora}, title = {Elucidating molecular determinants of the loss of freezing tolerance during deacclimation after cold priming and low temperature memory after triggering}, school = {Universit{\"a}t Potsdam}, pages = {vii, 147}, year = {2022}, abstract = {W{\"a}hrend ihrer Entwicklung m{\"u}ssen sich Pflanzen an Temperaturschwankungen anpassen. Niedrige Temperaturen {\"u}ber dem Gefrierpunkt induzieren in Pflanzen eine K{\"a}lteakklimatisierung und h{\"o}here Frosttoleranz, die sich bei w{\"a}rmeren Temperaturen durch Deakklimatisierung wieder zur{\"u}ckbildet. Der Wechsel zwischen diesen beiden Prozessen ist f{\"u}r Pflanzen unerl{\"a}sslich, um als Reaktion auf unterschiedliche Temperaturbedingungen eine optimale Fitness zu erreichen. Die K{\"a}lteakklimatisierung ist umfassend untersucht worden,{\"u}ber die Regulierung der Deakklimatisierung ist jedoch wenig bekannt. In dieser Arbeit wird der Prozess der Deakklimatisierung auf physiologischer und molekularer Ebene in Arabidopsis thaliana untersucht. Messungen des Elektrolytverlustes w{\"a}hrend der K{\"a}lteakklimatisierung und bis zu vier Tagen nach Deakklimatisierung erm{\"o}glichten die Identifizierung von vier Knockout-Mutanten (hra1, lbd41, mbf1c und jub1), die im Vergleich zum Wildtyp eine langsamere Deakklimatisierungsrate aufwiesen. Eine transkriptomische Studie mit Hilfe von RNA-Sequenzierung von A. thaliana Col-0, jub1 und mbf1c zeigte die Bedeutung der Hemmung von stressreaktiven und Jasmonat-ZIM-Dom{\"a}nen-Genen sowie die Regulierung von Zellwandmodifikationen w{\"a}hrend der Deakklimatisierung. Dar{\"u}ber hinaus zeigten Messungen der Alkoholdehydrogenase Aktivit{\"a}t und der Genexpressions{\"a}nderungen von Hypoxiemarkern w{\"a}hrend der ersten vier Tagen der Deakklimatisierung, dass eine Hypoxie-Reaktion w{\"a}hrend der Deakklimatisierung aktiviert wird. Es wurde gezeigt, dass die epigenetische Regulierung w{\"a}hrend der K{\"a}lteakklimatisierung und der 24-st{\"u}ndigen Deakklimatisierung in A. thaliana eine große Rolle spielt. Dar{\"u}ber hinaus zeigten beide Deakklimatisierungsstudien, dass die fr{\"u}here Hypothese, dass Hitzestress eine Rolle bei der fr{\"u}hen Deakklimatisierung spielen k{\"o}nnte, unwahrscheinlich ist. Eine Reihe von DNA- und Histondemethylasen sowie Histonvarianten wurden w{\"a}hrend der Deakklimatisierung hochreguliert, was auf eine Rolle im pflanzlichen Ged{\"a}chtnis schließen l{\"a}sst. In j{\"u}ngster Zeit haben mehrere Studien gezeigt, dass Pflanzen in der Lage sind, die Erinnerung an einen vorangegangenen K{\"a}ltestress auch nach einer Woche Deakklimatisierung zu bewahren. In dieser Arbeit ergaben Transkriptom- und Metabolomanalysen von Arabidopsis w{\"a}hrend 24 Stunden Priming (K{\"a}lteakklimatisierung) und Triggering (wiederkehrender K{\"a}ltestress nach Deakklimatisierung) eine unikale signifikante und vor{\"u}bergehende Induktion der Transkriptionsfaktoren DREB1D, DREB1E und DREB1F w{\"a}hrend des Triggerings, die zur Feinabstimmung der zweiten K{\"a}ltestressreaktion beitr{\"a}gt. Dar{\"u}ber hinaus wurden Gene, die f{\"u}r Late Embryogenesis Abundant (LEA) und Frostschutzproteine kodieren, sowie Proteine, die reaktive Sauerstoffspezies entgiften, w{\"a}hrend des sp{\"a}ten Triggerings (24 Stunden) st{\"a}rker induziert als nach dem ersten K{\"a}lteimpuls, w{\"a}hrend Xyloglucan- Endotransglucosylase/Hydrolase Gene, deren Produkte f{\"u}r eine Restrukturierung der Zellwand verantwortlich sind, fr{\"u}h auf das Triggering reagierten. Die starke Induktion dieser Gene, sowohl bei der Deakklimatisierung als auch beim Triggering, l{\"a}sst vermuten, dass sie eine wesentliche Rolle bei der Stabilisierung der Zellen w{\"a}hrend des Wachstums und bei der Reaktion auf wiederkehrende Stressbedingungen spielen. Zusammenfassend gibt diese Arbeit neue Einblicke in die Regulierung der Deakklimatisierung und des K{\"a}ltestress-Ged{\"a}chtnisses in A. thaliana und er{\"o}ffnet neue M{\"o}glichkeiten f{\"u}r k{\"u}nftige, gezielte Studien von essentiellen Genen in diesem Prozess.}, language = {en} } @phdthesis{Eckert2022, author = {Eckert, Silvia}, title = {Trait variation in changing environments: Assessing the role of DNA methylation in non-native plant species}, doi = {10.25932/publishup-56884}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-568844}, school = {Universit{\"a}t Potsdam}, pages = {VIII, 134, CXXX}, year = {2022}, abstract = {The increasing introduction of non-native plant species may pose a threat to local biodiversity. However, the basis of successful plant invasion is not conclusively understood, especially since these plant species can adapt to the new range within a short period of time despite impoverished genetic diversity of the starting populations. In this context, DNA methylation is considered promising to explain successful adaptation mechanisms in the new habitat. DNA methylation is a heritable variation in gene expression without changing the underlying genetic information. Thus, DNA methylation is considered a so-called epigenetic mechanism, but has been studied in mainly clonally reproducing plant species or genetic model plants. An understanding of this epigenetic mechanism in the context of non-native, predominantly sexually reproducing plant species might help to expand knowledge in biodiversity research on the interaction between plants and their habitats and, based on this, may enable more precise measures in conservation biology. For my studies, I combined chemical DNA demethylation of field-collected seed material from predominantly sexually reproducing species and rearing offsping under common climatic conditions to examine DNA methylation in an ecological-evolutionary context. The contrast of chemically treated (demethylated) plants, whose variation in DNA methylation was artificially reduced, and untreated control plants of the same species allowed me to study the impact of this mechanism on adaptive trait differentiation and local adaptation. With this experimental background, I conducted three studies examining the effect of DNA methylation in non-native species along a climatic gradient and also between climatically divergent regions. The first study focused on adaptive trait differentiation in two invasive perennial goldenrod species, Solidago canadensis sensu latu and S. gigantea AITON, along a climate gradient of more than 1000 km in length in Central Europe. I found population differences in flowering timing, plant height, and biomass in the temporally longer-established S. canadensis, but only in the number of regrowing shoots for S. gigantea. While S. canadensis did not show any population structure, I was able to identify three genetic groups along this climatic gradient in S. gigantea. Surprisingly, demethylated plants of both species showed no change in the majority of traits studied. In the subsequent second study, I focused on the longer-established goldenrod species S. canadensis and used molecular analyses to infer spatial epigenetic and genetic population differences in the same specimens from the previous study. I found weak genetic but no epigenetic spatial variation between populations. Additionally, I was able to identify one genetic marker and one epigenetic marker putatively susceptible to selection. However, the results of this study reconfirmed that the epigenetic mechanism of DNA methylation appears to be hardly involved in adaptive processes within the new range in S. canadensis. Finally, I conducted a third study in which I reciprocally transplanted short-lived plant species between two climatically divergent regions in Germany to investigate local adaptation at the plant family level. For this purpose, I used four plant families (Amaranthaceae, Asteraceae, Plantaginaceae, Solanaceae) and here I additionally compared between non-native and native plant species. Seeds were transplanted to regions with a distance of more than 600 kilometers and had either a temperate-oceanic or a temperate-continental climate. In this study, some species were found to be maladapted to their own local conditions, both in non-native and native plant species alike. In demethylated individuals of the plant species studied, DNA methylation had inconsistent but species-specific effects on survival and biomass production. The results of this study highlight that DNA methylation did not make a substantial contribution to local adaptation in the non-native as well as native species studied. In summary, my work showed that DNA methylation plays a negligible role in both adaptive trait variation along climatic gradients and local adaptation in non-native plant species that either exhibit a high degree of genetic variation or rely mainly on sexual reproduction with low clonal propagation. I was able to show that the adaptive success of these non-native plant species can hardly be explained by DNA methylation, but could be a possible consequence of multiple introductions, dispersal corridors and meta-population dynamics. Similarly, my results illustrate that the use of plant species that do not predominantly reproduce clonally and are not model plants is essential to characterize the effect size of epigenetic mechanisms in an ecological-evolutionary context.}, language = {en} } @article{PerrellaBaeurlevanZanten2022, author = {Perrella, Giorgio and B{\"a}urle, Isabel and van Zanten, Martijn}, title = {Epigenetic regulation of thermomorphogenesis and heat stress tolerance}, series = {New phytologist : international journal of plant science}, volume = {234}, journal = {New phytologist : international journal of plant science}, number = {4}, publisher = {Wiley}, address = {Hoboken}, issn = {0028-646X}, doi = {10.1111/nph.17970}, pages = {1144 -- 1160}, year = {2022}, abstract = {Many environmental conditions fluctuate and organisms need to respond effectively. This is especially true for temperature cues that can change in minutes to seasons and often follow a diurnal rhythm. Plants cannot migrate and most cannot regulate their temperature. Therefore, a broad array of responses have evolved to deal with temperature cues from freezing to heat stress. A particular response to mildly elevated temperatures is called thermomorphogenesis, a suite of morphological adaptations that includes thermonasty, formation of thin leaves and elongation growth of petioles and hypocotyl. Thermomorphogenesis allows for optimal performance in suboptimal temperature conditions by enhancing the cooling capacity. When temperatures rise further, heat stress tolerance mechanisms can be induced that enable the plant to survive the stressful temperature, which typically comprises cellular protection mechanisms and memory thereof. Induction of thermomorphogenesis, heat stress tolerance and stress memory depend on gene expression regulation, governed by diverse epigenetic processes. In this Tansley review we update on the current knowledge of epigenetic regulation of heat stress tolerance and elevated temperature signalling and response, with a focus on thermomorphogenesis regulation and heat stress memory. In particular we highlight the emerging role of H3K4 methylation marks in diverse temperature signalling pathways.}, language = {en} } @article{MorenoRomeroProbstTrindadeetal.2020, author = {Moreno-Romero, Jordi and Probst, Aline V. and Trindade, In{\^e}s and Kalyanikrishna, and Engelhorn, Julia and Farrona, Sara}, title = {Looking At the Past and Heading to the Future}, series = {Frontiers in Plant Science}, volume = {10}, journal = {Frontiers in Plant Science}, number = {1795}, publisher = {Frontiers Media}, address = {Lausanne}, issn = {1664-462X}, doi = {10.3389/fpls.2019.01795}, pages = {1 -- 12}, year = {2020}, abstract = {In June 2019, more than a hundred plant researchers met in Cologne, Germany, for the 6th European Workshop on Plant Chromatin (EWPC). This conference brought together a highly dynamic community of researchers with the common aim to understand how chromatin organization controls gene expression, development, and plant responses to the environment. New evidence showing how epigenetic states are set, perpetuated, and inherited were presented, and novel data related to the three-dimensional organization of chromatin within the nucleus were discussed. At the level of the nucleosome, its composition by different histone variants and their specialized histone deposition complexes were addressed as well as the mechanisms involved in histone post-translational modifications and their role in gene expression. The keynote lecture on plant DNA methylation by Julie Law (SALK Institute) and the tribute session to Lars Hennig, honoring the memory of one of the founders of the EWPC who contributed to promote the plant chromatin and epigenetic field in Europe, added a very special note to this gathering. In this perspective article we summarize some of the most outstanding data and advances on plant chromatin research presented at this workshop.}, language = {en} } @misc{MorenoRomeroProbstTrindadeetal.2020, author = {Moreno-Romero, Jordi and Probst, Aline V. and Trindade, In{\^e}s and Kalyanikrishna, and Engelhorn, Julia and Farrona, Sara}, title = {Looking At the Past and Heading to the Future}, series = {Zweitver{\"o}ffentlichungen der Universit{\"a}t Potsdam : Mathematisch-Naturwissenschaftliche Reihe}, journal = {Zweitver{\"o}ffentlichungen der Universit{\"a}t Potsdam : Mathematisch-Naturwissenschaftliche Reihe}, issn = {1866-8372}, doi = {10.25932/publishup-51194}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-511942}, pages = {14}, year = {2020}, abstract = {In June 2019, more than a hundred plant researchers met in Cologne, Germany, for the 6th European Workshop on Plant Chromatin (EWPC). This conference brought together a highly dynamic community of researchers with the common aim to understand how chromatin organization controls gene expression, development, and plant responses to the environment. New evidence showing how epigenetic states are set, perpetuated, and inherited were presented, and novel data related to the three-dimensional organization of chromatin within the nucleus were discussed. At the level of the nucleosome, its composition by different histone variants and their specialized histone deposition complexes were addressed as well as the mechanisms involved in histone post-translational modifications and their role in gene expression. The keynote lecture on plant DNA methylation by Julie Law (SALK Institute) and the tribute session to Lars Hennig, honoring the memory of one of the founders of the EWPC who contributed to promote the plant chromatin and epigenetic field in Europe, added a very special note to this gathering. In this perspective article we summarize some of the most outstanding data and advances on plant chromatin research presented at this workshop.}, language = {en} } @article{GuerreroFickelBenhaiemetal.2020, author = {Guerrero, Tania P. and Fickel, J{\"o}rns and Benhaiem, Sarah and Weyrich, Alexandra}, title = {Epigenomics and gene regulation in mammalian social systems}, series = {Current zoology}, volume = {66}, journal = {Current zoology}, number = {3}, publisher = {Oxford Univ. Press}, address = {Oxford}, issn = {1674-5507}, doi = {10.1093/cz/zoaa005}, pages = {307 -- 319}, year = {2020}, abstract = {Social epigenomics is a new field of research that studies how the social environment shapes the epigenome and how in turn the epigenome modulates behavior. We focus on describing known gene-environment interactions (GEIs) and epigenetic mechanisms in different mammalian social systems. To illustrate how epigenetic mechanisms integrate GEls, we highlight examples where epigenetic mechanisms are associated with social behaviors and with their maintenance through neuroendocrine, locomotor, and metabolic responses. We discuss future research trajectories and open questions for the emerging field of social epigenomics in nonmodel and naturally occurring social systems. Finally, we outline the technological advances that aid the study of epigenetic mechanisms in the establishment of GEIs and vice versa.}, language = {en} } @article{HerdenEckertStiftetal.2019, author = {Herden, Jasmin and Eckert, Silvia and Stift, Marc and Joshi, Jasmin Radha and van Kleunen, Mark}, title = {No evidence for local adaptation and an epigenetic underpinning in native and non-native ruderal plant species in Germany}, series = {Ecology and evolution}, volume = {9}, journal = {Ecology and evolution}, number = {17}, publisher = {Wiley}, address = {Hoboken}, issn = {2045-7758}, doi = {10.1002/ece3.5325}, pages = {9412 -- 9426}, year = {2019}, abstract = {Many invasive species have rapidly adapted to different environments in their new ranges. This is surprising, as colonization is usually associated with reduced genetic variation. Heritable phenotypic variation with an epigenetic basis may explain this paradox. Here, we assessed the contribution of DNA methylation to local adaptation in native and naturalized non-native ruderal plant species in Germany. We reciprocally transplanted offspring from natural populations of seven native and five non-native plant species between the Konstanz region in the south and the Potsdam region in the north of Germany. Before the transplant, half of the seeds were treated with the demethylation agent zebularine. We recorded survival, flowering probability, and biomass production as fitness estimates. Contrary to our expectations, we found little evidence for local adaptation, both among the native and among the non-native plant species. Zebularine treatment had mostly negative effects on overall plant performance, regardless of whether plants were local or not, and regardless of whether they were native or non-native. Synthesis. We conclude that local adaptation, at least at the scale of our study, plays no major role in the success of non-native and native ruderal plants. Consequently, we found no evidence yet for an epigenetic basis of local adaptation.}, language = {en} } @article{LiuLaemkeLinetal.2018, author = {Liu, Hsiang-chin and L{\"a}mke, J{\"o}rn and Lin, Siou-ying and Hung, Meng-Ju and Liu, Kuan-Ming and Charng, Yee-yung and B{\"a}urle, Isabel}, title = {Distinct heat shock factors and chromatin modifications mediate the organ-autonomous transcriptional memory of heat stress}, series = {The plant journal}, volume = {95}, journal = {The plant journal}, number = {3}, publisher = {Wiley}, address = {Hoboken}, issn = {0960-7412}, doi = {10.1111/tpj.13958}, pages = {401 -- 413}, year = {2018}, abstract = {Plants can be primed by a stress cue to mount a faster or stronger activation of defense mechanisms upon subsequent stress. A crucial component of such stress priming is the modified reactivation of genes upon recurring stress; however, the underlying mechanisms of this are poorly understood. Here, we report that dozens of Arabidopsis thaliana genes display transcriptional memory, i.e. stronger upregulation after a recurring heat stress, that lasts for at least 3 days. We define a set of transcription factors involved in this memory response and show that the transcriptional memory results in enhanced transcriptional activation within minutes of the onset of a heat stress cue. Further, we show that the transcriptional memory is active in all tissues. It may last for up to a week, and is associated during this time with histone H3 lysine 4 hypermethylation. This transcriptional memory is cis-encoded, as we identify a promoter fragment that confers memory onto a heterologous gene. In summary, heat-induced transcriptional memory is a widespread and sustained response, and our study provides a framework for future mechanistic studies of somatic stress memory in higher plants.}, language = {en} } @misc{FriedrichFaivreBaeurleetal.2018, author = {Friedrich, Thomas and Faivre, Lea and B{\"a}urle, Isabel and Schubert, Daniel}, title = {Chromatin-based mechanisms of temperature memory in plants}, series = {Plant, cell \& environment : cell physiology, whole-plant physiology, community physiology}, volume = {42}, journal = {Plant, cell \& environment : cell physiology, whole-plant physiology, community physiology}, number = {3}, publisher = {Wiley}, address = {Hoboken}, issn = {0140-7791}, doi = {10.1111/pce.13373}, pages = {762 -- 770}, year = {2018}, abstract = {For successful growth and development, plants constantly have to gauge their environment. Plants are capable to monitor their current environmental conditions, and they are also able to integrate environmental conditions over time and store the information induced by the cues. In a developmental context, such an environmental memory is used to align developmental transitions with favourable environmental conditions. One temperature-related example of this is the transition to flowering after experiencing winter conditions, that is, vernalization. In the context of adaptation to stress, such an environmental memory is used to improve stress adaptation even when the stress cues are intermittent. A somatic stress memory has now been described for various stresses, including extreme temperatures, drought, and pathogen infection. At the molecular level, such a memory of the environment is often mediated by epigenetic and chromatin modifications. Histone modifications in particular play an important role. In this review, we will discuss and compare different types of temperature memory and the histone modifications, as well as the reader, writer, and eraser proteins involved.}, language = {en} }