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RNA-seq of abscisic acid-reponsive transcription factors

ABSTRACT: 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.

ORGANISM(S): Arabidopsis thaliana

PROVIDER: GSE80565 | GEO | 2017/02/03

SECONDARY ACCESSION(S): PRJNA319318

REPOSITORIES: GEO

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Project description:Background: Abscisic acid (ABA) regulates various developmental processes and stress responses over both short (i.e. hours or days) and longer (i.e. months or seasons) time frames. To elucidate the transcriptional regulation of early responses of grapevine (Vitis vinifera) responding to ABA, different organs of grape (berries, shoot tips, leaves, roots and cell cultures) were treated with 10 μM (S)-(+)-ABA for 2 h. NimbleGen whole genome microarrays of Vitis vinifera were used to determine the effects of ABA on organ-specific mRNA expression patterns. Results: Transcriptomic analysis revealed 839 genes whose transcript abundances varied significantly in a specific organ in response to ABA treatment. No single gene exhibited the same changes in transcript abundance across all organs in response to ABA. The biochemical pathways affected by ABA were identified using the Cytoscape program with the BiNGO plug-in software. The results indicated that these 839 genes were involved in several biological processes such as flavonoid metabolism, response to reactive oxygen species, response to light, and response to temperature stimulus. ABA affected ion and water transporters, particularly in the root. The protein amino acid phosphorylation process was significantly overrepresented in shoot tips and roots treated with ABA. ABA affected mRNA abundance of genes (CYP707As, UGTs, and PP2Cs) associated with ABA degradation, conjugation, and the ABA signaling pathway. ABA also significantly affected the expression of several transcription factors (e.g. AP2/ERF, MYC/MYB, and bZIP/AREB). The greatest number of significantly differentially expressed genes was observed in the roots followed by cell cultures, leaves, berries, and shoot tips, respectively. Each organ had a unique set of gene responses to ABA. Conclusions: This study examined the short-term effects of ABA on different organs of grapevine. The responses of each organ were unique indicating that ABA signaling varies with the organ. Understanding the ABA responses in an organ-specific manner is crucial to fully understand hormone action and plant responses to water deficit.

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RNA-seq of abscisic acid-reponsive transcription factors

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