Spatio-Temporal Transcript Profiling of Rice Roots and Shoots in Response to Phosphate Starvation and Recovery
David Secco,Mehdi Jabnoune,Hayden Walker,Huixia Shou,Ping Wu,Yves Poirier,James Whelan,James Whelan,James Whelan +8 more
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TLDR
A comprehensive spatio-temporal transcriptome analysis of plant responses to Pi stress is presented, revealing a large number of potential key regulators of Pi homeostasis in plants.Abstract:
Using rice (Oryza sativa) as a model crop species, we performed an in-depth temporal transcriptome analysis, covering the early and late stages of Pi deprivation as well as Pi recovery in roots and shoots, using next-generation sequencing Analyses of 126 paired-end RNA sequencing libraries, spanning nine time points, provided a comprehensive overview of the dynamic responses of rice to Pi stress Differentially expressed genes were grouped into eight sets based on their responses to Pi starvation and recovery, enabling the complex signaling pathways involved in Pi homeostasis to be untangled A reference annotation-based transcript assembly was also generated, identifying 438 unannotated loci that were differentially expressed under Pi starvation Several genes also showed induction of unannotated splice isoforms under Pi starvation Among these, PHOSPHATE2 (PHO2), a key regulator of Pi homeostasis, displayed a Pi starvation–induced isoform, which was associated with increased translation activity In addition, microRNA (miRNA) expression profiles after long-term Pi starvation in roots and shoots were assessed, identifying 20 miRNA families that were not previously associated with Pi starvation, such as miR6250 In this article, we present a comprehensive spatio-temporal transcriptome analysis of plant responses to Pi stress, revealing a large number of potential key regulators of Pi homeostasis in plantsread more
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Widespread noncoding circular RNAs in plants
TL;DR: It is demonstrated that circRNAs are widespread in plants, revealed the common and distinct features ofcircRNAs between plants and animals, and suggested that circ RNAs could be a critical class of noncoding regulators in plants.
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Stress induced gene expression drives transient DNA methylation changes at adjacent repetitive elements
David Secco,Chuang Wang,Huixia Shou,Matthew D. Schultz,Serge Chiarenza,Laurent Nussaume,Joseph R. Ecker,James Whelan,Ryan Lister +8 more
TL;DR: In this paper, the authors used whole genome bisulfite sequencing to assess the spatio-temporal dynamics of mC in rice grown under phosphate starvation and recovery conditions, and identified widespread phosphate starvation-induced changes in mC, preferentially localized in transposable elements (TEs) close to highly induced genes.
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Complex Regulation of Plant Phosphate Transporters and the Gap between Molecular Mechanisms and Practical Application: What Is Missing?
TL;DR: Here, an increasing number of yeast PHO84 homologs as well as other genes encoding proteins with phosphate (Pi) transport activities have been identified and functionally characterized in diverse plant species and potential strategies for effective use of PTs are proposed in improving plant growth and development.
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Long non-coding RNAs and their biological roles in plants
TL;DR: In plants, although a large number of lncRNA transcripts have been predicted and identified in few species, current knowledge of their biological functions is still limited and here, recent studies on their identification, characteristics, classification, bioinformatics, resources, and current exploration of their Biological functions in plants are summarized.
Journal ArticleDOI
Identification of primary and secondary metabolites with phosphorus status‐dependent abundance in Arabidopsis, and of the transcription factor PHR1 as a major regulator of metabolic changes during phosphorus limitation
Bikram Datt Pant,Pooja Pant,Alexander Erban,David V. Huhman,Joachim Kopka,Wolf-Rüdiger Scheible +5 more
TL;DR: The phr1 mutation had a remarkably pronounced effect on the metabolic P-limitation response, providing evidence that PHR1 is a key factor for metabolic reprogramming during P limitation in Arabidopsis thaliana.
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PHYTOCHELATINS AND METALLOTHIONEINS: Roles in Heavy Metal Detoxification and Homeostasis
TL;DR: Recent advances in understanding the regulation of PC biosynthesis and MT gene expression and the possible roles of PCs and MTs in heavy metal detoxification and homeostasis are reviewed.