Chromatin retained MUSHER lncRNA integrates ABA and DOG1 signalling pathways to enhance Arabidopsis seeds dormancy.
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PROVIDER: PRJNA1147759 | ENA |
REPOSITORIES: ENA
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Project description:Many plant lncRNAs regulate gene expression by binding to chromatin, but how they are retained at the target loci is unclear. We identify a new, chromatin-localized lncRNA - MUSHER, which activates two parallel regulatory pathways to increase Arabidopsis seed dormancy. MUSHER is upregulated in response to high temperatures, contributing to the induction of secondary dormancy. It promotes DOG1 expression by recruitment of the CPSF complex to enhance the proximal cleavage and polyadenylation at the DOG1 transcript. It also increases ABA sensitivity in seeds by activating PIR1 gene transcription. These genes, located on different chromosomes, are both bound by MUSHER, despite lacking sequence homology. The chromatin association of MUSHER enables the integration of the DOG1- and ABA pathways to adjust seed germination timing. Additionally, MUSHER and other lncRNAs interact with U1 snRNP, which is required for their chromatin localisation, revealing a novel function of U1 snRNP in plants.
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Project description:Abscisic acid (ABA) regulates abiotic stress and developmental responses including regulation of seed dormancy to prevent seeds from germinating under unfavorable environmental conditions. ABA HYPERSENSITIVE GERMINATION1 (AHG1) encoding a type 2C protein phosphatase (PP2C) is a central negative regulator of the ABA response in germination; however, the molecular function and regulation of AHG1 remain elusive. Here we report that AHG1 interacts with DELAY OF GERMINATION1 (DOG1), which is a pivotal positive regulator in seed dormancy. DOG1 acts upstream of AHG1 and impairs the PP2C activity of AHG1 in vitro. Furthermore, DOG1 has the ability to bind heme. Binding of DOG1 to AHG1 and heme are independent processes but both are essential for DOG1 function in vivo. Our study demonstrates that AHG1 and DOG1 constitute an important regulatory system for seed dormancy and germination by integrating multiple environmental signals, in parallel with the PYL/RCAR ABA receptor-mediated regulatory system.
2018-06-10 | PXD009392 | Pride
Project description:Production of morphologically and physiologically variable seeds is an important strategy that helps plants to survive in unpredictable natural conditions. However, the model plant Arabidopsis thaliana and most agronomically essential crops yield visually homogenous seeds. Using automated phenotype analysis, we observed that in Arabidopsis small seeds tend to have higher primary and secondary dormancy levels when compared to large ones. Transcriptomic analysis revealed distinct gene expression profiles between large and small seeds. Large seeds had higher expression of translation-related genes implicated in germination competence. In contrast, small seeds showed elevated expression of many positive regulators of dormancy, including a key regulator of this process – the DOG1 gene. Differences in DOG1 expression were associated with differential production of its alternative cleavage and polyadenylation isoforms where in small seeds proximal poly(A) site is selected resulting in a short mRNA isoform. Furthermore, single-seed RNA-seq analysis demonstrated that large seeds resemble DOG1 knockout mutant seeds. Finally, on the single seed level, the expression of genes affected by seed size was correlated with the expression of genes positioning seeds on the path towards germination. Our results demonstrate an unexpected link between seed size and dormancy phenotypes in a species producing highly homogenous seed pools, suggesting that the correlation between seed morphology and physiology is more widespread than initially assumed.
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Project description:Through a genetic screening in 3μM (+)-S-ABA, we have isolated the anac089-2 mutant, which was obtained from fast neutron-mutagenized Col-0 M2 seeds. This mutant showed ABA-insensitive phenotypes in the transition from dormancy to germination. anac089-2 mutant line was subjected to mapping based on Col/Ler polymorphisms. This mutation was independently mapped to the top arm of Chromosome 5. The anac089-2 mutation is located in a 25 kb region between CAPS markers MWD9/EcoRV and MWD9-25.3/AccI. This 25 kb region contains 8 genes, and sequencing of these genes revealed that anac089-2 mutant contained a mutation in the At5g22290. This gene encodes ANAC089, a nuclear localized NAC transcription factor, with the deduced protein of 340 amino acids. Southern blot analysis suggests that anac089-2 mutation is a ~700 bp deletion that includes the C-terminal region. ANAC089 is involved in an ABA signaling pathway during seed germination and stress responses (Osuna et al., 2011).
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