TY - JOUR A1 - Kappel, Christian A1 - Friedrich, Thomas A1 - Oberkofler, Vicky A1 - Jiang, Li A1 - Crawford, Tim A1 - Lenhard, Michael A1 - Bäurle, Isabel T1 - Genomic and epigenomic determinants of heat stress-induced transcriptional memory in Arabidopsis JF - Genome biology : biology for the post-genomic era N2 - Background Transcriptional regulation is a key aspect of environmental stress responses. Heat stress induces transcriptional memory, i.e., sustained induction or enhanced re-induction of transcription, that allows plants to respond more efficiently to a recurrent HS. In light of more frequent temperature extremes due to climate change, improving heat tolerance in crop plants is an important breeding goal. However, not all heat stress-inducible genes show transcriptional memory, and it is unclear what distinguishes memory from non-memory genes. To address this issue and understand the genome and epigenome architecture of transcriptional memory after heat stress, we identify the global target genes of two key memory heat shock transcription factors, HSFA2 and HSFA3, using time course ChIP-seq. Results HSFA2 and HSFA3 show near identical binding patterns. In vitro and in vivo binding strength is highly correlated, indicating the importance of DNA sequence elements. In particular, genes with transcriptional memory are strongly enriched for a tripartite heat shock element, and are hallmarked by several features: low expression levels in the absence of heat stress, accessible chromatin environment, and heat stress-induced enrichment of H3K4 trimethylation. These results are confirmed by an orthogonal transcriptomic data set using both de novo clustering and an established definition of memory genes. Conclusions Our findings provide an integrated view of HSF-dependent transcriptional memory and shed light on its sequence and chromatin determinants, enabling the prediction and engineering of genes with transcriptional memory behavior. KW - Transcriptional memory KW - Priming KW - Heat stress KW - HSFA2 KW - HSFA3 KW - Arabidopsis thaliana KW - Histone H3K4 trimethylation KW - ChIP-seq Y1 - 2023 U6 - https://doi.org/10.1186/s13059-023-02970-5 SN - 1474-760X SN - 1465-6906 VL - 24 IS - 1 PB - BioMed Central CY - London ER - TY - JOUR A1 - Thirumalaikumar, Venkatesh P. A1 - Gorka, Michal A1 - Schulz, Karina A1 - Masclaux-Daubresse, Celine A1 - Sampathkumar, Arun A1 - Skirycz, Aleksandra A1 - Vierstra, Richard D. A1 - Balazadeh, Salma T1 - Selective autophagy regulates heat stress memory in Arabidopsis by NBR1-mediated targeting of HSP90.1 and ROF1 JF - Autophagy N2 - In nature, plants are constantly exposed to many transient, but recurring, stresses. Thus, to complete their life cycles, plants require a dynamic balance between capacities to recover following cessation of stress and maintenance of stress memory. Recently, we uncovered a new functional role for macroautophagy/autophagy in regulating recovery from heat stress (HS) and resetting cellular memory of HS inArabidopsis thaliana. Here, we demonstrated that NBR1 (next to BRCA1 gene 1) plays a crucial role as a receptor for selective autophagy during recovery from HS. Immunoblot analysis and confocal microscopy revealed that levels of the NBR1 protein, NBR1-labeled puncta, and NBR1 activity are all higher during the HS recovery phase than before. Co-immunoprecipitation analysis of proteins interacting with NBR1 and comparative proteomic analysis of annbr1-null mutant and wild-type plants identified 58 proteins as potential novel targets of NBR1. Cellular, biochemical and functional genetic studies confirmed that NBR1 interacts with HSP90.1 (heat shock protein 90.1) and ROF1 (rotamase FKBP 1), a member of the FKBP family, and mediates their degradation by autophagy, which represses the response to HS by attenuating the expression ofHSPgenes regulated by the HSFA2 transcription factor. Accordingly, loss-of-function mutation ofNBR1resulted in a stronger HS memory phenotype. Together, our results provide new insights into the mechanistic principles by which autophagy regulates plant response to recurrent HS. KW - Arabidopsis thaliana KW - heat stress KW - HSFA2 KW - HSP90.1 KW - NBR1 KW - ROF1 KW - selective autophagy KW - stress memory KW - stress recovery Y1 - 2020 U6 - https://doi.org/10.1080/15548627.2020.1820778 SN - 1554-8635 VL - 17 IS - 9 SP - 2184 EP - 2199 PB - Taylor & Francis CY - Abingdon ER - TY - THES A1 - Pan, Yufeng T1 - Genetic and molecular analysis of heat stress induced transcriptional memory T1 - Genetische und molekulare Analyse des durch Hitzestress ausgelösten transkriptionellen Gedächtnisses N2 - Heat stress (HS) is one of the most common abiotic stresses, frequently affecting plant growth and crop production. With its fluctuating nature, HS episodes are frequently interspersed by stress-free intervals. Plants can be primed by HS, allowing them to survive better a recurrent stress episode. A memory of this priming can be maintained during stress-free intervals and this memory is closely correlated with transcriptional memory at several HS-inducible loci. This transcriptional memory is evident from hyper-induction of a locus upon a recurrent HS. ASCORBATE PEROXIDASE 2 (APX2) shows such hyper-induction upon recurring HS, however, the molecular basis of this transcriptional memory is not understood. Previous research showed that the HSinduced transcriptional memory at APX2 can last for up to seven days, and that it is controlled by cis-regulatory elements within the APX2 promoter. To identify regulators involved in HS transcriptional memory, an unbiased forward genetic screening using EMS mutated seeds of pAPX2::LUC was performed from this screen. Two EMS mutants with affected transcriptional memory of LUC were identified. I confirmed that both two EMS mutants resulted from the gene mutations of HISTONE ACETYLTRANSFERASE 1 (HAC1). Besides pAPX2::LUC, the HS-induced transcription of other HS memory genes were also affected in hac1 mutants. Moreover, HAC1 may promote HS transcriptional memory by acetylating promoters of HS memory genes. On the other hand, to identify cis-regulatory elements that are required for transcriptional memory of APX2, I performed promoter analysis of the four conserved HSEs identified within a functional APX2 promoter. I found out that one of the HSEs (HSE1) is necessary for both HS-induced APX2 transcription and transcriptional memory, while another one of HSEs (HSE2) is important for HS-induced APX2 transcriptional memory. I also found out that the HSE1 itself (with 10 bp of flanking sequence) is sufficient to confer HS-induced APX2 transcriptional memory, and HSE1 is also necessary for HSFA2 to bind on APX2 promoter and activate APX2 transcription. The findings will provide important clues for the molecular mechanism of transcriptional memory and will enable engineering of enhanced stress tolerance in crops. N2 - Hitzestress (HS) ist einer der häufigsten abiotischen Stressfaktoren, der das Pflanzenwachstum und die Pflanzenproduktion häufig beeinträchtigt. Aufgrund seiner fluktuierenden Natur werden HS-Episoden häufig von stressfreien Intervallen unterbrochen. Pflanzen können durch HS vorbereitet werden, so dass sie eine wiederkehrende Stresssituation besser überstehen. Die Erinnerung an dieses Priming kann während stressfreier Intervalle aufrechterhalten werden, und diese Erinnerung ist eng mit der transkriptionellen Erinnerung an mehreren HS-induzierbaren Loci verbunden. Dieses transkriptionelle Gedächtnis zeigt sich in der Hyperinduktion eines Locus nach einem wiederholten HS. ASCORBATE PEROXIDASE 2 (APX2) zeigt eine solche Hyperinduktion bei wiederkehrendem HS, die molekulare Grundlage dieses Transkriptionsgedächtnisses ist jedoch nicht bekannt. Frühere Forschungsarbeiten haben gezeigt, dass das HS-induzierte Transkriptionsgedächtnis bei APX2 bis zu sieben Tage andauern kann und dass es durch cis-regulatorische Elemente innerhalb des APX2-Promotors gesteuert wird. Zur Identifizierung von Regulatoren, die am HS-Transkriptionsgedächtnis beteiligt sind, wurde ein unvoreingenommenes genetisches Vorwärtsscreening unter Verwendung von EMS-mutiertem Saatgut von pAPX2::LUC aus diesem Screening durchgeführt. Es wurden zwei EMS-Mutanten mit beeinträchtigtem Transkriptionsgedächtnis von LUC identifiziert. Ich bestätigte, dass beide EMS-Mutanten aus Genmutationen der HISTONE ACETYLTRANSFERASE 1 (HAC1) resultierten. Neben pAPX2::LUC war in den HAC1-Mutanten auch die HS-induzierte Transkription anderer HS-Gedächtnisgene beeinträchtigt. Darüber hinaus könnte HAC1 das HS-Transkriptionsgedächtnis durch Acetylierung der Promotoren von HS-Gedächtnisgenen fördern. Um andererseits cis-regulatorische Elemente zu identifizieren, die für das transkriptionelle Gedächtnis von APX2 erforderlich sind, habe ich eine Promotoranalyse der vier konservierten HSEs durchgeführt, die innerhalb eines funktionellen APX2-Promotors identifiziert wurden. Ich fand heraus, dass eine der HSEs (HSE1) sowohl für die HS-induzierte APX2-Transkription als auch für das Transkriptionsgedächtnis erforderlich ist, während eine andere HSE (HSE2) für das HS-induzierte APX2-Transkriptionsgedächtnis wichtig ist. Ich habe auch herausgefunden, dass das HSE1 selbst (mit 10 bp flankierender Sequenz) ausreicht, um HS-induziertes APX2-Transkriptionsgedächtnis zu verleihen, und dass HSE1 auch notwendig ist, damit HSFA2 an den APX2-Promotor binden und die APX2-Transkription aktivieren kann. Die Ergebnisse werden wichtige Hinweise auf den molekularen Mechanismus des Transkriptionsgedächtnisses liefern und die Entwicklung einer verbesserten Stresstoleranz bei Nutzpflanzen ermöglichen. KW - HS transcriptional memory KW - APX2 KW - HSFA2 KW - HAC1 KW - H3K9ac KW - HSE KW - HS-Transkriptionsgedächtnis KW - APX2 KW - HSFA2 KW - HAC1 KW - H3K9ac KW - HSE Y1 - 2022 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus4-560119 ER -