Ontology highlight
ABSTRACT:
PROVIDER: PRJNA369777 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR5227660.fastq.gz | Fastqsanger.gz | |||
| SRR5227661.fastq.gz | Fastqsanger.gz | |||
| SRR5227652.fastq.gz | Fastqsanger.gz | |||
| SRR5227662.fastq.gz | Fastqsanger.gz | |||
| SRR5227653.fastq.gz | Fastqsanger.gz |
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Project description:New shoot growth from underground adventitious buds of leafy spurge is critical for survival of this invasive perennial weed after episodes of severe abiotic stress. Because global climate change is expected to increase abiotic stress, such as dehydration, objectives of this study include examining the impact that dehydration stress has on molecular mechanisms associated with vegetative reproduction. Greenhouse plants were exposed to mild- (3-day), intermediate- (7-day), severe- (14-day) and extended- (21-day) dehydration treatments, prior to decapitation of aerial tissue and rehydration of soil to induce new vegetative shoot growth. Compared to well-watered control plants, mild-dehydration accelerated new vegetative shoot growth but intermediate- and severe-dehydration treatments both delayed and reduced shoot growth, and 21-day dehydration treatment inhibited initiation of new vegetative shoots and was considered a lethal treatment. Overall, transcriptome profiles revealed that 2109 genes were differentially-expressed (P<0.05) in crown buds in response to the various dehydration treatments. Sub-network enrichment analyses identified central hubs of over-represented genes involved in processes such as hormone responses and signaling (e.g., ABA, auxin, ethylene, GA, and JA), response to abiotic stress (DREB1A/2A) and light (PIF3), phosphorylation (CLV1, MPK3/4/6, SOS2), gene silencing (miRNA156/172a), circadian regulation (CRY2, LHY, PHYA/B), and flowering (AGL8/20, AP2, FLC). Further, results from this and previous studies highlight HY5, MAF3, MYB-like/RVE1 and RD22 as molecular markers for endodormancy in crown buds of leafy spurge. Early response to dehydration also highlighted involvement of upstream ethylene and jasmonate signaling, whereas longer-term dehydration impacted ABA signaling. The identification of conserved ABRE- and MYC-consensus, cis-acting elements in the promoter of a leafy spurge gene similar to Arabidopsis MYB-like/RVE1 (AT5G17300) implicates a potential role for ABA signaling in its dehydration-induced expression. Response of these molecular mechanisms to dehydration-stress provides insights on the ability of invasive perennial weeds to adapt and survive under harsh environments, which provide new insights for addressing future management practices. Changes in transcript abundance for underground adventitious buds of leafy spurge which were exposed various levels of dehydration stress (Day-3, -7, -14, -16, -21) are analysed relative to controls (Day-0).
2014-05-31 | E-GEOD-55133 | biostudies-arrayexpress
Project description:The signaling pathway of the phytohormone abscisic acid (ABA) regulates responses towards abiotic stress such as drought and high osmotic conditions. The multitude of functionally redundant components involved in ABA signaling, poses a major challenge for elucidating the largely unresolved response selectivity. We decided rebuilding single linear ABA signaling pathways in yeast for combinatoric permutation of ABA receptors and coreceptors, as well as the response-mediating SnRK2 protein kinases and their targeted transcription factors to drive luciferase expression in a heterologous host. We show that SnRK2s differ in the regulation by ABA receptor complexes, affect ABA responsiveness of the pathway, and differ in their transactivation activity but have similar preferences for ABA-responsive transcription factors. SnRK2s thought to act ABA-independently and known to be activated under osmotic stress in plants were regulated by ABA receptor complexes in yeast and competed with ABA receptor components in an ABA-dependent manner in plant tissue. The study reveals the suitability of the yeast system for analysis of ABA signaling factors and allowing the future dissection of ligand-receptor specificities in a functional response pathway. The analysis provides new insights into SnRK2 regulation indicating that four SnRK2 members of the osmotic stress response are tightly embedded into the ABA signaling pathway.
2019-07-30 | PXD013669 | Pride
Project description:Resistance (R) genes are very effective for disease control in plants. Current research shows that R genes predominantly function by inducing a hypersensitive reaction (HR), which results in localized cell death thought to restrict pathogen spread. Some R genes elicit a more atypical response where resistance is not associated with HR or the associated gene expression changes, termed extreme resistance (ER). The molecular regulatory mechanism underlying ER is largely unexplored. One of the few known, naturally occurring, instances of ER is resistance derived from the soybean Rsv3 gene, which confers resistance against the most virulent strains of soybean mosaic virus (SMV). To discern the regulatory mechanism underlying the Rsv3-mediated ER reaction, we generated a gene regulatory network using transcriptomic data from a time course comparison of SMV-G7-infected resistant (L29, Rsv3-genotype) and susceptible (Williams82, rsv3-genotype) soybean cultivars. We identified putative interactions between transcription factors (TFs) regulating gene expression in hormone regulatory pathways, such as abscisic acid (ABA) and jasmonic acid (JA). This is consistent with the demonstrated involvement of these pathways in Rsv3-mediated resistance. We found significant enrichment for the G-box motif (“CACGTG”) among genes implicated in ABA- and JA-related activities. This motif is specifically recognized by MYC2, which is a master regulator of ABA and JA signaling. Our network identified a MYC2 TF encoded by Glyma.07G051500 as a putative transcriptional regulator whose expression was significantly down-regulated in L29. This correlated with the down-regulation of expression of genes involved in ABA and JA processes. Our results suggest an important function for Glyma.07G051500 in ABA and JA derived defense signaling. Additionally, our regulatory network found other putative TFs with differential expression, such as MYBs and ERFs, which may also be involved in regulating ABA and JA signaling for defense. The regulatory network presented here offers new insights into the regulation of the molecular defense mechanism underlying Rsv3-mediated ER against SMV.
2020-03-31 | GSE137263 | GEO
Project description:New shoot growth from underground adventitious buds of leafy spurge is critical for survival of this invasive perennial weed after episodes of severe abiotic stress. Because global climate change is expected to increase abiotic stress, such as dehydration, objectives of this study include examining the impact that dehydration stress has on molecular mechanisms associated with vegetative reproduction. Greenhouse plants were exposed to mild- (3-day), intermediate- (7-day), severe- (14-day) and extended- (21-day) dehydration treatments, prior to decapitation of aerial tissue and rehydration of soil to induce new vegetative shoot growth. Compared to well-watered control plants, mild-dehydration accelerated new vegetative shoot growth but intermediate- and severe-dehydration treatments both delayed and reduced shoot growth, and 21-day dehydration treatment inhibited initiation of new vegetative shoots and was considered a lethal treatment. Overall, transcriptome profiles revealed that 2109 genes were differentially-expressed (P<0.05) in crown buds in response to the various dehydration treatments. Sub-network enrichment analyses identified central hubs of over-represented genes involved in processes such as hormone responses and signaling (e.g., ABA, auxin, ethylene, GA, and JA), response to abiotic stress (DREB1A/2A) and light (PIF3), phosphorylation (CLV1, MPK3/4/6, SOS2), gene silencing (miRNA156/172a), circadian regulation (CRY2, LHY, PHYA/B), and flowering (AGL8/20, AP2, FLC). Further, results from this and previous studies highlight HY5, MAF3, MYB-like/RVE1 and RD22 as molecular markers for endodormancy in crown buds of leafy spurge. Early response to dehydration also highlighted involvement of upstream ethylene and jasmonate signaling, whereas longer-term dehydration impacted ABA signaling. The identification of conserved ABRE- and MYC-consensus, cis-acting elements in the promoter of a leafy spurge gene similar to Arabidopsis MYB-like/RVE1 (AT5G17300) implicates a potential role for ABA signaling in its dehydration-induced expression. Response of these molecular mechanisms to dehydration-stress provides insights on the ability of invasive perennial weeds to adapt and survive under harsh environments, which provide new insights for addressing future management practices.
2014-05-31 | GSE55133 | GEO
Project description:CDK8 is a key subunit of Mediator complex, a large multiprotein complex that is a fundamental part of the conserved eukaryotic transcriptional machinery. However, the biological functions of CDK8 in plant abiotic stress responses remain largely unexplored. Here, we demonstrated CDK8 as a critical regulator in the abscisic acid (ABA) signaling and drought response pathways in Arabidopsis. Compared to wild-type, cdk8 mutants showed reduced sensitivity to ABA, impaired stomatal apertures and hypersensitivity to drought stress. Transcriptomic and chromatin immunoprecipitation analysis revealed that CDK8 positively regulates the transcription of several ABA-responsive genes, probably through promoting the recruitment of RNA polymerase II to their promoters. We discovered that both CDK8 and SnRK2.6 interact physically with an ERF/AP2 transcription factor RAP2.6, which can directly bind to the promoters of RD29A and COLD-REGULATED 15A (COR15A) with GCC or DRE elements, thereby promoting their expression. Importantly, we also showed that CDK8 is essential for the ABA-induced expression of RAP2.6 and RAP2.6-mediated upregulation of ABA-responsive genes, indicating that CDK8 could link the SnRK2.6-mediated ABA signaling to RNA polymerase II to promote immediate transcriptional response to ABA and drought signals. Overall, our data provide new insights into the roles of CDK8 in modulating ABA signaling and drought responses.
2021-10-11 | GSE135607 | GEO
Project description:Abscisic acid (ABA) is a plant hormone that is important in responding to various environmental stresses. Using an ABA auxotroph in Arabidopsis (aba2-2) as the plant material, we would like to identify early downstream targets of transcription in response to a small dose of ABA, 1 uM. We also added cycloheximide to preferentially obtain immediate targets of ABA addition. We believe that using a sensitized background of an ABA auxotroph would yield a set of genes that are very closely regulated by ABA at the transcriptional level. This data set will be used for network analysis of ABA signaling.
2011-10-30 | E-MEXP-3404 | biostudies-arrayexpress
Project description:The signaling pathway of the phytohormone abscisic acid (ABA) regulates responses towards abiotic stress such as drought and high osmotic conditions. The multitude of functionally redundant components involved in ABA signaling, poses a major challenge for elucidating the largely unresolved response selectivity. We decided rebuilding single linear ABA signaling pathways in yeast for combinatoric permutation of ABA receptors and coreceptors, as well as the response-mediating SnRK2 protein kinases and their targeted transcription factors to drive luciferase expression in a heterologous host. We show that SnRK2s differ in the regulation by ABA receptor complexes, affect ABA responsiveness of the pathway, and differ in their transactivation activity but have similar preferences for ABA-responsive transcription factors. SnRK2s thought to act ABA-independently and known to be activated under osmotic stress in plants were regulated by ABA receptor complexes in yeast and competed with ABA receptor components in an ABA-dependent manner in plant tissue. The study reveals the suitability of the yeast system for analysis of ABA signaling factors and allowing the future dissection of ligand-receptor specificities in a functional response pathway. The analysis provides new insights into SnRK2 regulation indicating that four SnRK2 members of the osmotic stress response are tightly embedded into the ABA signaling pathway.
2019-08-13 | PXD013849 | panorama
Project description:Abscisic acid (ABA) is an essential hormone that allows plants to respond to environmental stresses such as high salinity, drought and cold. It also plays a pivotal role in seed maturation and germination. Because of its importance, transcriptome changes in response to ABA have been profiled extensively by the plant community. Very few ChIP-chip/seq of ABA-related TFs have been reported to date. To fill the knowledge gap about how ABA works at the transcriptional level, we carried out ChIP-seq on 21 TFs from 11 different families using both mock- and ABA-treated conditions. Analyses of the resulting 122 ChIP-seq datasets identified 326,698 TF binding events using a stringent statistical cutoff. Based on our data, a comprehensive regulatory network in Arabidopsis thaliana was constructed. We uncovered determinants of dynamic TF binding and defined a hierarchy among TFs to explain differential gene expression and pathway feedback regulation. By extrapolating regulatory characteristics observed for the canonical ABA pathway components, we identified a new family of transcriptional regulators modulating ABA and salt responsiveness, and demonstrate their utility to modulate plant resilience to osmotic stress.
2017-02-03 | GSE80566 | GEO
Project description:Abscisic acid (ABA) is an essential hormone that allows plants to respond to environmental stresses such as high salinity, drought and cold. It also plays a pivotal role in seed maturation and germination. Because of its importance, transcriptome changes in response to ABA have been profiled extensively by the plant community. Very few ChIP-chip/seq of ABA-related TFs have been reported to date. To fill the knowledge gap about how ABA works at the transcriptional level, we carried out ChIP-seq on 21 TFs from 11 different families using both mock- and ABA-treated conditions. Analyses of the resulting 122 ChIP-seq datasets identified 326,698 TF binding events using a stringent statistical cutoff. Based on our data, a comprehensive regulatory network in Arabidopsis thaliana was constructed. We uncovered determinants of dynamic TF binding and defined a hierarchy among TFs to explain differential gene expression and pathway feedback regulation. By extrapolating regulatory characteristics observed for the canonical ABA pathway components, we identified a new family of transcriptional regulators modulating ABA and salt responsiveness, and demonstrate their utility to modulate plant resilience to osmotic stress.
2017-02-03 | GSE80564 | GEO
Project description:Mapping ultra-high resolution of Sp1:DNA interaction would provide us with valuable new mechanistic insights into Sp1-mediated gene regulatory network in Huntington Disease cell culture model. STHdh Q7/Q7 cells were directly fixed and used for the ChIP-exo experiment.
2016-07-15 | E-GEOD-84056 | biostudies-arrayexpress