Arabidopsis thaliana
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA301696 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR2932370.fastq.gz | Fastqsanger.gz | |||
| SRR2932371.fastq.gz | Fastqsanger.gz | |||
| SRR2932372.fastq.gz | Fastqsanger.gz | |||
| SRR2932373.fastq.gz | Fastqsanger.gz | |||
| SRR2932374.fastq.gz | Fastqsanger.gz |
Items per page: 5 1 - 5 of 15 |
Similar Datasets
Project description:The 3' untranslated regions (3' UTRs) of mRNAs play important roles in the regulation of mRNA localization, translation, and stability. Alternative cleavage and polyadenylation (APA) generates mRNAs with different 3' UTRs, but the involvement of this process in stress response has not been clarified. Here, we report that a subset of stress-related genes exhibits 3' UTR extensions of their mRNAs during dehydration stress. These extended 3' UTRs have characteristics of long noncoding RNAs and likely do not interact with miRNAs. Functional studies using T-DNA insertion mutants reveal that they can function as antisense transcripts to repress expression levels of sense genes from the opposite strand, or can activate the transcription of downstream genes from the same strand. Poly(A) signal analysis reveal that mRNAs with 3' UTR extensions have weaker poly(A) signals than mRNAs without 3' UTR extensions. Finally, we show that their biogenesis is partially dependent on a trans-acting factor FPA. Taken together, we report that dehydration stress could induce mRNA 3' UTR extensions, and elucidate a novel function for these stress-induced 3' UTR extensions as long noncoding RNAs in the regulation of their neighboring genes.
2017-04-05 | GSE74864 | GEO
Project description:Arabidopsis thaliana plants that have experienced an initial exposure to dehydration stress (“trained plants”) have an increased ability to maintain leaf relative water content (RWC) during subsequent stresses than plants experiencing the stress for the first time and transcription of selected dehydration response genes is altered during successive exposures to dehydration stress. This physiological and transcriptional behavior of trained plants is consistent with a “memory “of an earlier stress. It is unknown whether such memory is present in other Angiosperm lineages and whether it is an evolutionarily conserved response to stress. Here, we analyzed the behavior and transcriptomes of maize (Zea mays) plants experiencing multiple dehydration stresses and compare them with responses of the evolutionarily distant A. thaliana. We found structurally related genes in maize that displayed the same memory-type responses as in A. thaliana, providing evidence of the conservation of function and transcriptional memory in the evolution of plants’ dehydration stress response systems. Similar to A. thaliana, trained Z. mays plants retained higher RWC during dehydration stress than untrained plants, due in part to maintaining reduced stomatal conductance, despite full recovery of RWC, after the first stress. Divergent transcriptional memory responses were also expressed, suggesting diversification of function among stress memory genes. Some dehydration stress memory genes were also shared with other stress and hormone responding pathways, indicating complex and dynamic interactions between different plant signaling networks. The results provide new insight into how plants respond to multiple dehydration stresses and provide a platform for studies of the functions of memory genes in adaptive responses to water deficit in monocot and eudicot plants .
2014-08-01 | GSE48507 | GEO
Project description:Arabidopsis thaliana plants that have experienced an initial exposure to dehydration stress (“trained plants”) have an increased ability to maintain leaf relative water content (RWC) during subsequent stresses than plants experiencing the stress for the first time and transcription of selected dehydration response genes is altered during successive exposures to dehydration stress. This physiological and transcriptional behavior of trained plants is consistent with a “memory “of an earlier stress. It is unknown whether such memory is present in other Angiosperm lineages and whether it is an evolutionarily conserved response to stress (see E-GEOD-48235). Here, we analyzed the behavior and transcriptomes of maize (Zea mays) plants experiencing multiple dehydration stresses and compare them with responses of the evolutionarily distant A. thaliana. We found structurally related genes in maize that displayed the same memory-type responses as in A. thaliana, providing evidence of the conservation of function and transcriptional memory in the evolution of plants’ dehydration stress response systems. Similar to A. thaliana, trained Z. mays plants retained higher RWC during dehydration stress than untrained plants, due in part to maintaining reduced stomatal conductance, despite full recovery of RWC, after the first stress. Divergent transcriptional memory responses were also expressed, suggesting diversification of function among stress memory genes. Some dehydration stress memory genes were also shared with other stress and hormone responding pathways, indicating complex and dynamic interactions between different plant signaling networks. The results provide new insight into how plants respond to multiple dehydration stresses and provide a platform for studies of the functions of memory genes in adaptive responses to water deficit in monocot and eudicot plants . For each condition (water, S1, and S3) the transcriptome was sequenced for two replicates. The watered condition is considered the control.
2014-08-01 | E-GEOD-48507 | biostudies-arrayexpress
Project description:Arabidopsis plants that have experienced stress from water withdrawal show an improved ability to tolerate subsequent exposures as a ‘memory’ from the previous stress. This physiological stress memory is associated with ‘transcriptional memory’ illustrated by a subset of dehydrations stress responding genes that produce significantly different transcript amounts during repeated dehydration stresses relative to their response in the first. Here we report the genome-wide representation of dehydration stress transcriptional memory genes in A. thaliana. We identify four novel transcription patterns in response to repeated dehydration stress treatments. The nature of the proteins encoded by genes from each type of memory-response pattern is analyzed and the consequences of the genes’ memory behavior are considered in the context of possible biological relevance. The memory behavior of genes co-regulated by the dehydration/ABA and other abiotic stress and hormone responding pathways suggested that the crosstalk at the transcriptional level between them was affected as well. The intensity and the nature of specific biochemical, membrane, chloroplast, and stress response-related interactions during multiple exposures to dehydration stress are different from the responses to a single dehydration stress. The results reveal additional, hitherto unknown, levels of complexity of the plants’ transcriptional behavior when adjusting and adapting to recurring water deficits.
2014-01-01 | GSE48235 | GEO
Project description:Arabidopsis plants that have experienced stress from water withdrawal show an improved ability to tolerate subsequent exposures as a ‘memory’ from the previous stress. This physiological stress memory is associated with ‘transcriptional memory’ illustrated by a subset of dehydrations stress responding genes that produce significantly different transcript amounts during repeated dehydration stresses relative to their response in the first. Here we report the genome-wide representation of dehydration stress transcriptional memory genes in A. thaliana. We identify four novel transcription patterns in response to repeated dehydration stress treatments. The nature of the proteins encoded by genes from each type of memory-response pattern is analyzed and the consequences of the genes’ memory behavior are considered in the context of possible biological relevance. The memory behavior of genes co-regulated by the dehydration/ABA and other abiotic stress and hormone responding pathways suggested that the crosstalk at the transcriptional level between them was affected as well. The intensity and the nature of specific biochemical, membrane, chloroplast, and stress response-related interactions during multiple exposures to dehydration stress are different from the responses to a single dehydration stress. The results reveal additional, hitherto unknown, levels of complexity of the plants’ transcriptional behavior when adjusting and adapting to recurring water deficits. For each condition (water, S1, and S3) the transcriptome was sequenced for two replicates. The watered condition is considered the control.
2014-01-01 | E-GEOD-48235 | biostudies-arrayexpress
Project description:Four distinct types of dehydration stress memory genes in Arabidopsis thaliana
| PRJNA209324 | ENA
Project description:Effect of single or double knock-out mutation of subclass III SnRK2 protein kinases in Arabidopsis after 6 h of treatment with dehydration stress.
2009-12-17 | E-MEXP-2355 | biostudies-arrayexpress
Project description:Studies have revealed dozens of functional peptides in putative ‘noncoding’ regions and raised the question of how many proteins are encoded by noncanonical open reading frames (ORFs). We comprehensively annotated genome-wide translated ORFs across five eukaryotic by analyzing ribosome profiling reads. We revealed pervasive translation in annotated untranslated regions of mRNAs or off-frame regions (i.e., uORFs, dORFs, and iORFs). We developed a logistic regression model based on ORF features to calculate the peptide functional probability in humans. Systematic ectopic expression experiments showed that peptides encoded by ncORFs follow the basic principles governing conventional protein subcellular localization and carry out diverse biological functions.
2024-05-23 | PXD037658 | Pride
Project description:Background The homeodomain leucine zipper (HD-Zip) transcription factor family is one of the largest plant specific superfamilies, and includes genes with roles in modulation of plant growth and response to environmental stresses. Many HD-Zip genes are characterized in Arabidopsis (Arabidopsis thaliana), and members of the family are being investigated for abiotic stress responses in rice (Oryza sativa), maize (Zea mays), poplar (Populus trichocarpa) and cucumber (Cucmis sativus). Findings in these species suggest HD-Zip genes as high priority candidates for crop improvement. Results In this study we have identified members of the HD-Zip gene family in soybean cv. 'Williams 82', and characterized their expression under dehydration and salt stress. Homology searches with BLASTP and Hidden Markov Model guided sequence alignments identified 101 HD-Zip genes in the soybean genome. Phylogeny reconstruction coupled with domain and gene structure analyses using soybean, Arabidopsis, rice, grape (Vitis vinifera), and Medicago truncatula homologues enabled placement of these sequences into four previously described subfamilies. Of the 101 HD-Zip genes identified in soybean, 88 exist as whole-genome duplication-derived gene pairs, indicating high retention of these genes following polyploidy in Glycine ~10 Mya. The HD-Zip genes exhibit ubiquitous expression patterns across 24 conditions that include 17 tissues of soybean. An RNA-Seq experiment performed to study differential gene expression at 0, 1, 6 and 12 hr soybean roots under dehydration and salt stress identified 20 differentially expressed (DE) genes. Several of these DE genes are orthologs of genes previously reported to play a role under abiotic stress, implying conservation of HD-Zip gene functions across species. Screening of HD-Zip promoters identified transcription factor binding sites that are overrepresented in the DE genes under both dehydration and salt stress, providing further support for the role of HD-Zip genes in abiotic stress responses. Conclusions We provide a thorough description of soybean HD-Zip genes, and identify potential candidates with probable roles in dehydration and salt stress. Expression profiles generated for all soybean genes, under dehydration and salt stress, at four time points, will serve as an important resource for the soybean research community, and will aid in understanding plant responses to abiotic stress. We sequenced mRNA from soybean cv. "Williams 82" root samples that includes three control samples (0 hr), and three biological replicates for each of the three time points 1, 6 and 12 hr under dehydration and salt stress
2014-11-01 | E-GEOD-57252 | biostudies-arrayexpress