Identification of abscisic acid-associated known and novel miRNAs and their target genes in Arabidopsis thaliana
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA723054 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR14276943_1.fastq.gz | Fastqsanger.gz | |||
| SRR14276943_2.fastq.gz | Fastqsanger.gz | |||
| SRR14276944_1.fastq.gz | Fastqsanger.gz | |||
| SRR14276944_2.fastq.gz | Fastqsanger.gz | |||
| SRR14276945_1.fastq.gz | Fastqsanger.gz |
Items per page: 5 1 - 5 of 48 |
Similar Datasets
Project description:Using RNA-Seq, we identified miRNAs in the WT Col-0 strain of Arabidopsis and its abi1td, mkkk17 and mkkk18 mutant lines that are differentially expressed in response to ABA treatment. Both known and novel miRNAs were characterized and the expression profiles of a subset were validated by qRT-PCR; we also verified the potential target genes of selected novel miRNAs by 5′ RLM-RACE. GO annotation revealed that the top-ranked miRNA target genes were involved in diverse biological processes, including regulation of transcription, response to stress, biosynthetic processes, and signaling pathways.
2021-07-15 | GSE172377 | GEO
Project description:Heterotrimeric G proteins mediate crucial and diverse signaling pathways in eukaryotes. To gain insights into the regulatory modes of the G protein and the co-regulatory modes of the G protein and the stress hormone abscisic acid (ABA), we generated and analyzed gene expression in G protein subunit single and double mutants of the model plant Arabidopsis thaliana. Through a Boolean modeling approach, our analysis reveals novel modes of heterotrimeric G protein action. Keywords: transcriptome analysis; G protein subunit mutants; abscisic acid (ABA)
2010-12-06 | GSE19520 | GEO
Project description:Seed germination is a critical developmental stage in the life cycle of plants, and its regulation is essential for ensuring crop productivity, particularly under adverse environmental conditions. Here, we find that the Arabidopsis thaliana PRE-MRNA-PROCESSING (PRP21) is crucial for the regulation of abscisic acid (ABA) response of seed germination. Our RNA deep sequencing and poly(A) tag sequencing analyses reveal that PRP21 is involved in pre-mRNA splicing, genome-wide gene transcription, and mRNA 3' end processing, highlighting its multifunctional role in gene regulation. Furthermore, we find that PRP21 interacts with various splicing factors and small nuclear ribonucleoproteins, suggesting its involvement in spliceosome assembly. Additionally, we demonstrate that PRP21 negatively regulates the expression of ABA-responsive genes, such as ABSCISIC ACID-INSENSITIVE 3 (ABI3), ABSCISIC ACID-INSENSITIVE 5 (ABI5), EARLY METHIONINE-LABELED 1 (EM1), and EARLY METHIONINE-LABELED 6 (EM6), thereby modulating ABA response and seed germination. Our findings underscore the importance of PRP21 in coordinating transcriptional and post-transcriptional processes, and provide insights into the molecular mechanisms underlying seed germination, potentially guiding crop improvement for stress tolerance.
2025-04-21 | GSE278189 | GEO
Project description:Seed germination is a critical developmental stage in the life cycle of plants, and its regulation is essential for ensuring crop productivity, particularly under adverse environmental conditions. Here, we find that the Arabidopsis thaliana PRE-MRNA-PROCESSING (PRP21) is crucial for the regulation of abscisic acid (ABA) response of seed germination. Our RNA deep sequencing and poly(A) tag sequencing analyses reveal that PRP21 is involved in pre-mRNA splicing, genome-wide gene transcription, and mRNA 3' end processing, highlighting its multifunctional role in gene regulation. Furthermore, we find that PRP21 interacts with various splicing factors and small nuclear ribonucleoproteins, suggesting its involvement in spliceosome assembly. Additionally, we demonstrate that PRP21 negatively regulates the expression of ABA-responsive genes, such as ABSCISIC ACID-INSENSITIVE 3 (ABI3), ABSCISIC ACID-INSENSITIVE 5 (ABI5), EARLY METHIONINE-LABELED 1 (EM1), and EARLY METHIONINE-LABELED 6 (EM6), thereby modulating ABA response and seed germination. Our findings underscore the importance of PRP21 in coordinating transcriptional and post-transcriptional processes, and provide insights into the molecular mechanisms underlying seed germination, potentially guiding crop improvement for stress tolerance.
2025-04-21 | GSE291571 | GEO
Project description:Seed germination is a critical developmental stage in the life cycle of plants, and its regulation is essential for ensuring crop productivity, particularly under adverse environmental conditions. Here, we find that the Arabidopsis thaliana PRE-MRNA-PROCESSING (PRP21) is crucial for the regulation of abscisic acid (ABA) response of seed germination. Our RNA deep sequencing and poly(A) tag sequencing analyses reveal that PRP21 is involved in pre-mRNA splicing, genome-wide gene transcription, and mRNA 3' end processing, highlighting its multifunctional role in gene regulation. Furthermore, we find that PRP21 interacts with various splicing factors and small nuclear ribonucleoproteins, suggesting its involvement in spliceosome assembly. Additionally, we demonstrate that PRP21 negatively regulates the expression of ABA-responsive genes, such as ABSCISIC ACID-INSENSITIVE 3 (ABI3), ABSCISIC ACID-INSENSITIVE 5 (ABI5), EARLY METHIONINE-LABELED 1 (EM1), and EARLY METHIONINE-LABELED 6 (EM6), thereby modulating ABA response and seed germination. Our findings underscore the importance of PRP21 in coordinating transcriptional and post-transcriptional processes, and provide insights into the molecular mechanisms underlying seed germination, potentially guiding crop improvement for stress tolerance.
2025-04-21 | GSE278188 | 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 | GSE80565 | 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:Arabidopsis thaliana Col-0 wildtype plants were grown on soil (Jiffy7 peat pellets 42 mm) to the respective developmental stage (1.04 or 1.08 Boyes scale). The plants were sprayed with 50 µM Abscisic acid and incubated for 15 min or 2 hours under normal growth conditions. Leaves 1 and 2 were harvested and immediately frozen in liquid nitrogen.
2006-10-31 | E-CAGE-48 | biostudies-arrayexpress
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 | GSE80567 | 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 | GSE80566 | GEO