|
| Status |
Public on Apr 01, 2021 |
| Title |
A dynamic network reveals the novel characteristics of miRNA regulation over time in response to the ABA hormone in Arabidopsis (mRNA) |
| Organism |
Arabidopsis thaliana |
| Experiment type |
Expression profiling by high throughput sequencing
|
| Summary |
MicroRNAs (miRNAs) participate in post-transcriptional regulation as short non-coding RNAs together with the transcription factors (TFs) and other regulatory factors such as alternative splicing (AS), which constitute complex gene regulatory networks. Following stimulation with ABA in Arabidopsis, we performed RNA-seq and small RNA-seq simultaneously at consecutive time points, and found that miRNAs respond rapidly under stress condition. Further functional analyses revealed that miRNAs classified according to different response time points play a role by binding different target genes. Systematic analysis including the static network of TF-target, TF-miRNA, miRNA-target and the time series DEGs and DE-miRNAs revealed a miRNA-mRNA dynamic regulatory network. We found that miRNAs in miRNA-containing feed-forward loops (M-FFLs) could enhance co-expression and crosstalks between different FFLs of network. Additionally, the differential transcript usage (DTU) and differential alternative splicing (DAS) analysis increased regulatory diversity between miRNA and its target genes. Collectively, our findings highlighted the systematical and precise post-transcriptional regulation of miRNAs in plant.
|
| |
|
| Overall design |
Totally fifty-six samples, two treatments with seven time points and two replicates, and each sample has two files of paired-end data.
|
| |
|
| Contributor(s) |
Gao Z, Yu R, Li L, Deng XW, He H |
| Citation missing |
Has this study been published? Please login to update or notify GEO. |
| |
| Submission date |
Feb 12, 2020 |
| Last update date |
Apr 01, 2021 |
| Contact name |
Xu Zhao Gao |
| E-mail(s) |
gaozx@pku.edu.cn
|
| Organization name |
Peking University
|
| Department |
College of Biological Sciences
|
| Lab |
Plant molecular genetics and agricultural biotechnology research laboratory
|
| Street address |
The Summer Palace Road No. 5
|
| City |
Beijing |
| State/province |
Beijing |
| ZIP/Postal code |
100871 |
| Country |
China |
| |
|
| Platforms (1) |
| GPL13222 |
Illumina HiSeq 2000 (Arabidopsis thaliana) |
|
| Samples (28)
|
|
| This SubSeries is part of SuperSeries: |
| GSE145209 |
A dynamic network reveals the novel characteristics of miRNA regulation over time in response to the ABA hormone in Arabidopsis |
|
| Relations |
| BioProject |
PRJNA606323 |
| SRA |
SRP248470 |
Less...
More...