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Crawford T, Siebler L, Sulkowska A, Nowack B, Jiang L, Pan Y, Lämke J, Kappel C, Bäurle I. The Mediator kinase module enhances polymerase activity to regulate transcriptional memory after heat stress in Arabidopsis. EMBO J 2024; 43:437-461. [PMID: 38228917 PMCID: PMC10897291 DOI: 10.1038/s44318-023-00024-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2023] [Revised: 12/12/2023] [Accepted: 12/14/2023] [Indexed: 01/18/2024] Open
Abstract
Plants are often exposed to recurring adverse environmental conditions in the wild. Acclimation to high temperatures entails transcriptional responses, which prime plants to better withstand subsequent stress events. Heat stress (HS)-induced transcriptional memory results in more efficient re-induction of transcription upon recurrence of heat stress. Here, we identified CDK8 and MED12, two subunits of the kinase module of the transcription co-regulator complex, Mediator, as promoters of heat stress memory and associated histone modifications in Arabidopsis. CDK8 is recruited to heat-stress memory genes by HEAT SHOCK TRANSCRIPTION FACTOR A2 (HSFA2). Like HSFA2, CDK8 is largely dispensable for the initial gene induction upon HS, and its function in transcriptional memory is thus independent of primary gene activation. In addition to the promoter and transcriptional start region of target genes, CDK8 also binds their 3'-region, where it may promote elongation, termination, or rapid re-initiation of RNA polymerase II (Pol II) complexes during transcriptional memory bursts. Our work presents a complex role for the Mediator kinase module during transcriptional memory in multicellular eukaryotes, through interactions with transcription factors, chromatin modifications, and promotion of Pol II efficiency.
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Affiliation(s)
- Tim Crawford
- Institute for Biochemistry and Biology, University of Potsdam, Potsdam, Germany
| | - Lara Siebler
- Institute for Biochemistry and Biology, University of Potsdam, Potsdam, Germany
| | | | - Bryan Nowack
- Institute for Biochemistry and Biology, University of Potsdam, Potsdam, Germany
| | - Li Jiang
- Institute for Biochemistry and Biology, University of Potsdam, Potsdam, Germany
| | - Yufeng Pan
- Institute for Biochemistry and Biology, University of Potsdam, Potsdam, Germany
| | - Jörn Lämke
- Institute for Biochemistry and Biology, University of Potsdam, Potsdam, Germany
| | - Christian Kappel
- Institute for Biochemistry and Biology, University of Potsdam, Potsdam, Germany
| | - Isabel Bäurle
- Institute for Biochemistry and Biology, University of Potsdam, Potsdam, Germany.
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2
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Pallarz S, Fiedler S, Wahler D, Lämke J, Grohmann L. Reproducibility of next-generation-sequencing-based analysis of a CRISPR/Cas9 genome edited oil seed rape. Food Chem (Oxf) 2023; 7:100182. [PMID: 37822547 PMCID: PMC10562171 DOI: 10.1016/j.fochms.2023.100182] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/08/2023] [Revised: 09/08/2023] [Accepted: 09/10/2023] [Indexed: 10/13/2023]
Abstract
Next-generation-sequencing (NGS) becomes increasingly important for laboratories tasked with the detection of genetically modified organisms (GMOs) in food, feed and seeds. Its implementation into standardized workflows demands reliable intra- and inter-laboratory reproducibility. Here, we analyze the reproducibility of short- and long-read targeted NGS and long-read whole genome sequencing (WGS) data between three independent laboratories. Replicate samples were submitted for sequencing and comparatively analyzed. The targeted-NGS-samples consisted of oil seed rape (OSR) sampled from a commodity shipment spiked with a genome edited (GE) OSR and the WGS-samples consisted of leaf material from the GMOs' parental line. All laboratories delivered highly reproducible high-quality targeted NGS data with little variation. The detection of GMO-related sequences works well regardless of the facility, while the mapping to the complex genome is superior using long read data. Long read WGS is currently not suitable for routine use in enforcement laboratories, due to a large inter-laboratory variation.
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Affiliation(s)
- Steffen Pallarz
- Department Genetic Engineering and Other Biotechnological Processes, Federal Office of Consumer Protection and Food Safety (BVL), P.O. Box 110260, 10832 Berlin, Germany
| | - Stefan Fiedler
- Department Method Standardisation, Reference Laboratories, Resistance To Antibiotics, Federal Office of Consumer Protection and Food Safety (BVL), P.O. Box 110260, 10832 Berlin, Germany
| | - Daniela Wahler
- Department Genetic Engineering and Other Biotechnological Processes, Federal Office of Consumer Protection and Food Safety (BVL), P.O. Box 110260, 10832 Berlin, Germany
| | - Jörn Lämke
- Department Method Standardisation, Reference Laboratories, Resistance To Antibiotics, Federal Office of Consumer Protection and Food Safety (BVL), P.O. Box 110260, 10832 Berlin, Germany
| | - Lutz Grohmann
- Department Genetic Engineering and Other Biotechnological Processes, Federal Office of Consumer Protection and Food Safety (BVL), P.O. Box 110260, 10832 Berlin, Germany
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Friedrich T, Oberkofler V, Trindade I, Altmann S, Brzezinka K, Lämke J, Gorka M, Kappel C, Sokolowska E, Skirycz A, Graf A, Bäurle I. Heteromeric HSFA2/HSFA3 complexes drive transcriptional memory after heat stress in Arabidopsis. Nat Commun 2021; 12:3426. [PMID: 34103516 PMCID: PMC8187452 DOI: 10.1038/s41467-021-23786-6] [Citation(s) in RCA: 75] [Impact Index Per Article: 25.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2019] [Accepted: 05/13/2021] [Indexed: 02/05/2023] Open
Abstract
Adaptive plasticity in stress responses is a key element of plant survival strategies. For instance, moderate heat stress (HS) primes a plant to acquire thermotolerance, which allows subsequent survival of more severe HS conditions. Acquired thermotolerance is actively maintained over several days (HS memory) and involves the sustained induction of memory-related genes. Here we show that FORGETTER3/ HEAT SHOCK TRANSCRIPTION FACTOR A3 (FGT3/HSFA3) is specifically required for physiological HS memory and maintaining high memory-gene expression during the days following a HS exposure. HSFA3 mediates HS memory by direct transcriptional activation of memory-related genes after return to normal growth temperatures. HSFA3 binds HSFA2, and in vivo both proteins form heteromeric complexes with additional HSFs. Our results indicate that only complexes containing both HSFA2 and HSFA3 efficiently promote transcriptional memory by positively influencing histone H3 lysine 4 (H3K4) hyper-methylation. In summary, our work defines the major HSF complex controlling transcriptional memory and elucidates the in vivo dynamics of HSF complexes during somatic stress memory.
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Affiliation(s)
- Thomas Friedrich
- grid.11348.3f0000 0001 0942 1117Institute for Biochemistry and Biology, University of Potsdam, Potsdam, Germany
| | - Vicky Oberkofler
- grid.11348.3f0000 0001 0942 1117Institute for Biochemistry and Biology, University of Potsdam, Potsdam, Germany
| | - Inês Trindade
- grid.11348.3f0000 0001 0942 1117Institute for Biochemistry and Biology, University of Potsdam, Potsdam, Germany
| | - Simone Altmann
- grid.11348.3f0000 0001 0942 1117Institute for Biochemistry and Biology, University of Potsdam, Potsdam, Germany ,grid.8241.f0000 0004 0397 2876Present Address: School of Life Sciences, University of Dundee, Dundee, UK
| | - Krzysztof Brzezinka
- grid.11348.3f0000 0001 0942 1117Institute for Biochemistry and Biology, University of Potsdam, Potsdam, Germany
| | - Jörn Lämke
- grid.11348.3f0000 0001 0942 1117Institute for Biochemistry and Biology, University of Potsdam, Potsdam, Germany
| | - Michal Gorka
- grid.418390.70000 0004 0491 976XMax-Planck-Institute for Molecular Plant Physiology, Potsdam, Germany
| | - Christian Kappel
- grid.11348.3f0000 0001 0942 1117Institute for Biochemistry and Biology, University of Potsdam, Potsdam, Germany
| | - Ewelina Sokolowska
- grid.418390.70000 0004 0491 976XMax-Planck-Institute for Molecular Plant Physiology, Potsdam, Germany
| | - Aleksandra Skirycz
- grid.418390.70000 0004 0491 976XMax-Planck-Institute for Molecular Plant Physiology, Potsdam, Germany
| | - Alexander Graf
- grid.418390.70000 0004 0491 976XMax-Planck-Institute for Molecular Plant Physiology, Potsdam, Germany
| | - Isabel Bäurle
- grid.11348.3f0000 0001 0942 1117Institute for Biochemistry and Biology, University of Potsdam, Potsdam, Germany
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Liu HC, Lämke J, Lin SY, Hung MJ, Liu KM, Charng YY, Bäurle I. Distinct heat shock factors and chromatin modifications mediate the organ-autonomous transcriptional memory of heat stress. Plant J 2018; 95:401-413. [PMID: 29752744 DOI: 10.1111/tpj.13958] [Citation(s) in RCA: 59] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/13/2017] [Revised: 03/21/2018] [Accepted: 04/25/2018] [Indexed: 05/26/2023]
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.
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Affiliation(s)
- Hsiang-Chin Liu
- Agricultural Biotechnology Research Center, Academia Sinica, Taipei, 11529, Taiwan
| | - Jörn Lämke
- University of Potsdam, Institute of Biochemistry and Biology, Karl-Liebknecht-Str. 24-25, D-14476, Potsdam, Germany
| | - Siou-Ying Lin
- Agricultural Biotechnology Research Center, Academia Sinica, Taipei, 11529, Taiwan
- Department of Biochemical Sciences and Technology, National Taiwan University, Taipei, 10617, Taiwan
| | - Meng-Ju Hung
- Agricultural Biotechnology Research Center, Academia Sinica, Taipei, 11529, Taiwan
| | - Kuan-Ming Liu
- Agricultural Biotechnology Research Center, Academia Sinica, Taipei, 11529, Taiwan
| | - Yee-Yung Charng
- Agricultural Biotechnology Research Center, Academia Sinica, Taipei, 11529, Taiwan
- Department of Biochemical Sciences and Technology, National Taiwan University, Taipei, 10617, Taiwan
| | - Isabel Bäurle
- University of Potsdam, Institute of Biochemistry and Biology, Karl-Liebknecht-Str. 24-25, D-14476, Potsdam, Germany
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5
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Liu HC, Lämke J, Lin SY, Hung MJ, Liu KM, Charng YY, Bäurle I. Distinct heat shock factors and chromatin modifications mediate the organ-autonomous transcriptional memory of heat stress. Plant J 2018; 95:399-400. [PMID: 29752744 DOI: 10.1111/tpj.14001] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/13/2017] [Revised: 03/21/2018] [Accepted: 04/25/2018] [Indexed: 05/18/2023]
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.
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Affiliation(s)
- Hsiang-Chin Liu
- Agricultural Biotechnology Research Center, Academia Sinica, Taipei, 11529, Taiwan
| | - Jörn Lämke
- University of Potsdam, Institute of Biochemistry and Biology, Karl-Liebknecht-Str. 24-25, D-14476, Potsdam, Germany
| | - Siou-Ying Lin
- Agricultural Biotechnology Research Center, Academia Sinica, Taipei, 11529, Taiwan
- Department of Biochemical Sciences and Technology, National Taiwan University, Taipei, 10617, Taiwan
| | - Meng-Ju Hung
- Agricultural Biotechnology Research Center, Academia Sinica, Taipei, 11529, Taiwan
| | - Kuan-Ming Liu
- Agricultural Biotechnology Research Center, Academia Sinica, Taipei, 11529, Taiwan
| | - Yee-Yung Charng
- Agricultural Biotechnology Research Center, Academia Sinica, Taipei, 11529, Taiwan
- Department of Biochemical Sciences and Technology, National Taiwan University, Taipei, 10617, Taiwan
| | - Isabel Bäurle
- University of Potsdam, Institute of Biochemistry and Biology, Karl-Liebknecht-Str. 24-25, D-14476, Potsdam, Germany
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6
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Abstract
Plants frequently have to weather both biotic and abiotic stressors, and have evolved sophisticated adaptation and defense mechanisms. In recent years, chromatin modifications, nucleosome positioning, and DNA methylation have been recognized as important components in these adaptations. Given their potential epigenetic nature, such modifications may provide a mechanistic basis for a stress memory, enabling plants to respond more efficiently to recurring stress or even to prepare their offspring for potential future assaults. In this review, we discuss both the involvement of chromatin in stress responses and the current evidence on somatic, intergenerational, and transgenerational stress memory.
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Affiliation(s)
- Jörn Lämke
- University of Potsdam, Institute for Biochemistry and Biology, Karl-Liebknecht-Strasse 24-25, 14476, Potsdam, Germany
| | - Isabel Bäurle
- University of Potsdam, Institute for Biochemistry and Biology, Karl-Liebknecht-Strasse 24-25, 14476, Potsdam, Germany.
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7
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Abstract
In nature, stress is typically chronic or recurring and stress exposure can prime modified responses to recurring stress. Such stress priming may occur at the level of transcription. Here, we discuss the connection between plant stress memory, transcription, and chromatin modifications using the example of recurring heat stress.
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Affiliation(s)
- Jörn Lämke
- a Institute for Biochemistry and Biology, University of Potsdam , Potsdam , Germany
| | - Krzysztof Brzezinka
- a Institute for Biochemistry and Biology, University of Potsdam , Potsdam , Germany
| | - Isabel Bäurle
- a Institute for Biochemistry and Biology, University of Potsdam , Potsdam , Germany
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Lämke J, Brzezinka K, Altmann S, Bäurle I. A hit-and-run heat shock factor governs sustained histone methylation and transcriptional stress memory. EMBO J 2015; 35:162-75. [PMID: 26657708 DOI: 10.15252/embj.201592593] [Citation(s) in RCA: 207] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2015] [Accepted: 11/13/2015] [Indexed: 01/19/2023] Open
Abstract
In nature, plants often encounter chronic or recurring stressful conditions. Recent results indicate that plants can remember a past exposure to stress to be better prepared for a future stress incident. However, the molecular basis of this is poorly understood. Here, we report the involvement of chromatin modifications in the maintenance of acquired thermotolerance (heat stress [HS] memory). HS memory is associated with the accumulation of histone H3 lysine 4 di- and trimethylation at memory-related loci. This accumulation outlasts their transcriptional activity and marks them as recently transcriptionally active. High accumulation of H3K4 methylation is associated with hyper-induction of gene expression upon a recurring HS. This transcriptional memory and the sustained accumulation of H3K4 methylation depend on HSFA2, a transcription factor that is required for HS memory, but not initial heat responses. Interestingly, HSFA2 associates with memory-related loci transiently during the early stages following HS. In summary, we show that transcriptional memory after HS is associated with sustained H3K4 hyper-methylation and depends on a hit-and-run transcription factor, thus providing a molecular framework for HS memory.
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Affiliation(s)
- Jörn Lämke
- Institute for Biochemistry and Biology, University of Potsdam, Potsdam, Germany
| | - Krzysztof Brzezinka
- Institute for Biochemistry and Biology, University of Potsdam, Potsdam, Germany
| | - Simone Altmann
- Institute for Biochemistry and Biology, University of Potsdam, Potsdam, Germany
| | - Isabel Bäurle
- Institute for Biochemistry and Biology, University of Potsdam, Potsdam, Germany
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Stief A, Brzezinka K, Lämke J, Bäurle I. Epigenetic responses to heat stress at different time scales and the involvement of small RNAs. Plant Signal Behav 2014; 9:e970430. [PMID: 25482804 PMCID: PMC4622961 DOI: 10.4161/15592316.2014.970430] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/18/2014] [Revised: 07/04/2014] [Accepted: 07/07/2014] [Indexed: 05/21/2023]
Abstract
The hypothesis that plants can benefit from a memory of past stress exposure has recently attracted a lot of attention. Here, we discuss two different examples of heat stress memory to elucidate the potential benefits that epigenetic responses may provide at both the level of acclimation of the individual plant and adaptation at a species-wide level. Specifically, we discuss how microRNAs regulate the heat stress memory and thereby increase survival upon a recurring heat stress. Secondly, we review how a prolonged heat stress in a small interfering RNA-deficient background induces retrotransposition that is transmitted to the next generation, thus creating genetic variation for natural selection to act on. Collectively, these studies reveal a crucial role of short RNAs in heat stress memory across different time scales.
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Affiliation(s)
- Anna Stief
- Institute for Biochemistry and Biology; University of Potsdam; Potsdam, Germany
| | - Krzysztof Brzezinka
- Institute for Biochemistry and Biology; University of Potsdam; Potsdam, Germany
| | - Jörn Lämke
- Institute for Biochemistry and Biology; University of Potsdam; Potsdam, Germany
| | - Isabel Bäurle
- Institute for Biochemistry and Biology; University of Potsdam; Potsdam, Germany
- Correspondence to: Isabel Bäurle;
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Hagl C, Lämke J, Bogdahn U, Buerger E, Winner B, Winkler J. Regulation der adulten Neurogenese durch Pramipexol. Akt Neurol 2007. [DOI: 10.1055/s-2007-987563] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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