1
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Reynoso MA, Borowsky AT, Pauluzzi GC, Yeung E, Zhang J, Formentin E, Velasco J, Cabanlit S, Duvenjian C, Prior MJ, Akmakjian GZ, Deal RB, Sinha NR, Brady SM, Girke T, Bailey-Serres J. Gene regulatory networks shape developmental plasticity of root cell types under water extremes in rice. Dev Cell 2022; 57:1177-1192.e6. [PMID: 35504287 DOI: 10.1016/j.devcel.2022.04.013] [Citation(s) in RCA: 23] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2021] [Revised: 02/10/2022] [Accepted: 04/07/2022] [Indexed: 12/11/2022]
Abstract
Understanding how roots modulate development under varied irrigation or rainfall is crucial for development of climate-resilient crops. We established a toolbox of tagged rice lines to profile translating mRNAs and chromatin accessibility within specific cell populations. We used these to study roots in a range of environments: plates in the lab, controlled greenhouse stress and recovery conditions, and outdoors in a paddy. Integration of chromatin and mRNA data resolves regulatory networks of the following: cycle genes in proliferating cells that attenuate DNA synthesis under submergence; genes involved in auxin signaling, the circadian clock, and small RNA regulation in ground tissue; and suberin biosynthesis, iron transporters, and nitrogen assimilation in endodermal/exodermal cells modulated with water availability. By applying a systems approach, we identify known and candidate driver transcription factors of water-deficit responses and xylem development plasticity. Collectively, this resource will facilitate genetic improvements in root systems for optimal climate resilience.
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Affiliation(s)
- Mauricio A Reynoso
- Center for Plant Cell Biology, Department of Botany and Plant Sciences, University of California, Riverside, Riverside, CA 92521, USA; IBBM, FCE-UNLP CONICET, La Plata 1900, Argentina
| | - Alexander T Borowsky
- Center for Plant Cell Biology, Department of Botany and Plant Sciences, University of California, Riverside, Riverside, CA 92521, USA
| | - Germain C Pauluzzi
- Center for Plant Cell Biology, Department of Botany and Plant Sciences, University of California, Riverside, Riverside, CA 92521, USA
| | - Elaine Yeung
- Center for Plant Cell Biology, Department of Botany and Plant Sciences, University of California, Riverside, Riverside, CA 92521, USA
| | - Jianhai Zhang
- Center for Plant Cell Biology, Department of Botany and Plant Sciences, University of California, Riverside, Riverside, CA 92521, USA
| | - Elide Formentin
- Center for Plant Cell Biology, Department of Botany and Plant Sciences, University of California, Riverside, Riverside, CA 92521, USA; Department of Biology, University of Padova, Padova, Italy
| | - Joel Velasco
- Center for Plant Cell Biology, Department of Botany and Plant Sciences, University of California, Riverside, Riverside, CA 92521, USA
| | - Sean Cabanlit
- Center for Plant Cell Biology, Department of Botany and Plant Sciences, University of California, Riverside, Riverside, CA 92521, USA
| | - Christine Duvenjian
- Center for Plant Cell Biology, Department of Botany and Plant Sciences, University of California, Riverside, Riverside, CA 92521, USA
| | - Matthew J Prior
- Center for Plant Cell Biology, Department of Botany and Plant Sciences, University of California, Riverside, Riverside, CA 92521, USA
| | - Garo Z Akmakjian
- Center for Plant Cell Biology, Department of Botany and Plant Sciences, University of California, Riverside, Riverside, CA 92521, USA
| | - Roger B Deal
- Department of Biology, Emory University, Atlanta, GA 30322, USA
| | - Neelima R Sinha
- Department of Plant Biology, University of California, Davis, Davis, CA 95616, USA
| | - Siobhan M Brady
- Department of Plant Biology and Genome Center, University of California, Davis, Davis, CA 95616, USA
| | - Thomas Girke
- Center for Plant Cell Biology, Department of Botany and Plant Sciences, University of California, Riverside, Riverside, CA 92521, USA
| | - Julia Bailey-Serres
- Center for Plant Cell Biology, Department of Botany and Plant Sciences, University of California, Riverside, Riverside, CA 92521, USA; Plant Ecophysiology, Institute of Environmental Biology, Utrecht University, 3584 Utrecht, the Netherlands.
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2
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Gray SB, Rodriguez‐Medina J, Rusoff S, Toal TW, Kajala K, Runcie DE, Brady SM. Translational regulation contributes to the elevated CO 2 response in two Solanum species. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2020; 102:383-397. [PMID: 31797460 PMCID: PMC7216843 DOI: 10.1111/tpj.14632] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/30/2019] [Revised: 11/17/2019] [Accepted: 11/20/2019] [Indexed: 05/12/2023]
Abstract
Understanding the impact of elevated CO2 (eCO2 ) in global agriculture is important given climate change projections. Breeding climate-resilient crops depends on genetic variation within naturally varying populations. The effect of genetic variation in response to eCO2 is poorly understood, especially in crop species. We describe the different ways in which Solanum lycopersicum and its wild relative S. pennellii respond to eCO2 , from cell anatomy, to the transcriptome, and metabolome. We further validate the importance of translational regulation as a potential mechanism for plants to adaptively respond to rising levels of atmospheric CO2 .
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Affiliation(s)
- Sharon B. Gray
- Department of Plant Biology and Genome CenterUniversity of California, Davis451 Health Sciences DriveDavisCA95616USA
| | - Joel Rodriguez‐Medina
- Department of Plant Biology and Genome CenterUniversity of California, Davis451 Health Sciences DriveDavisCA95616USA
| | - Samuel Rusoff
- Department of Plant Biology and Genome CenterUniversity of California, Davis451 Health Sciences DriveDavisCA95616USA
| | - Ted W. Toal
- Department of Plant Biology and Genome CenterUniversity of California, Davis451 Health Sciences DriveDavisCA95616USA
| | - Kaisa Kajala
- Department of Plant Biology and Genome CenterUniversity of California, Davis451 Health Sciences DriveDavisCA95616USA
- Present address:
Plant EcophysiologyUtrecht UniversityPadualaan 83584 CHUtrechtthe Netherlands
| | - Daniel E. Runcie
- Department of Plant SciencesUniversity of California, DavisOne Shields AvenueDavisCA95616USA
| | - Siobhan M. Brady
- Department of Plant Biology and Genome CenterUniversity of California, Davis451 Health Sciences DriveDavisCA95616USA
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3
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Buijs G, Vogelzang A, Nijveen H, Bentsink L. Dormancy cycling: translation-related transcripts are the main difference between dormant and non-dormant seeds in the field. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2020; 102:327-339. [PMID: 31785171 PMCID: PMC7217185 DOI: 10.1111/tpj.14626] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/16/2019] [Revised: 11/08/2019] [Accepted: 11/13/2019] [Indexed: 05/20/2023]
Abstract
Primary seed dormancy is a mechanism that orchestrates the timing of seed germination in order to prevent out-of-season germination. Secondary dormancy can be induced in imbibed seeds when they encounter prolonged unfavourable conditions. Secondary dormancy is not induced during dry storage, and therefore the mechanisms underlying this process have remained largely unexplored. Here, a 2-year seed burial experiment in which dormancy cycling was studied at the physiological and transcriptional level is presented. For these analyses six different Arabidopsis thaliana genotypes were used: Landsberg erecta (Ler) and the dormancy associated DELAY OF GERMINATION (DOG) near-isogenic lines 1, 2, 3, 6 and 22 (NILDOG1, 2, 3, 6 and 22). The germination potential of seeds exhumed from the field showed that these seeds go through dormancy cycling and that the dynamics of this cycling is genotype dependent. RNA-seq analysis revealed large transcriptional changes during dormancy cycling, especially at the time points preceding shifts in dormancy status. Dormancy cycling is driven by soil temperature and the endosperm is important in the perception of the environment. Genes that are upregulated in the low- to non-dormant stages are enriched for genes involved in translation, indicating that the non-dormant seeds are prepared for rapid seed germination.
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Affiliation(s)
- Gonda Buijs
- Wageningen Seed LaboratoryLaboratory of Plant PhysiologyWageningen UniversityWageningenthe Netherlands
| | - Afke Vogelzang
- Wageningen Seed LaboratoryLaboratory of Plant PhysiologyWageningen UniversityWageningenthe Netherlands
| | - Harm Nijveen
- Bioinformatics GroupWageningen UniversityWageningenthe Netherlands
| | - Leónie Bentsink
- Wageningen Seed LaboratoryLaboratory of Plant PhysiologyWageningen UniversityWageningenthe Netherlands
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4
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Ruocco N, Bertocci I, Munari M, Musco L, Caramiello D, Danovaro R, Zupo V, Costantini M. Morphological and molecular responses of the sea urchin Paracentrotus lividus to highly contaminated marine sediments: The case study of Bagnoli-Coroglio brownfield (Mediterranean Sea). MARINE ENVIRONMENTAL RESEARCH 2020; 154:104865. [PMID: 32056706 DOI: 10.1016/j.marenvres.2019.104865] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/10/2019] [Revised: 12/12/2019] [Accepted: 12/14/2019] [Indexed: 06/10/2023]
Abstract
Marine sediments store complex mixtures of compounds, including heavy metals, organotins and a large array of other contaminants. Sediment quality monitoring, characterization and management are priorities, due to potential impacts of the above compounds on coastal waters and their biota, especially in cases of pollutants released during dredging activities. Harbours and marinas, as well as estuaries and bays, where limited exchanges of water occurr, the accumulation of toxic compounds poses major concerns for human and environmental health. Here we report the effects of highly contaminated sediments from the site of national interest Bagnoli-Coroglio (Tyrrhenian Sea, Western Mediterranean) on the sea urchin Paracentrotus lividus, considered a good model for ecotoxicological studies. Adult sea urchins were reared one month in aquaria in the presence of contaminated sediment that was experimentally subject to different patterns of re-suspension events (mimicking the effect of natural storms occurring in the field), crossed with O2 enrichment versus natural gas exchanges in the water. The development of embryos deriving from adult urchins exposed to such experimental conditions was followed until the pluteus stage, checking the power of contaminated sediment to induce morphological malformations and its eventual buffering by high oxygenation. Real-Time qPCR analysis revealed that the expression of several genes (among the fifty analyzed, involved in different functional processes) was targeted by contaminated sediments more than those exposed in oxygen-enriched condition. Our findings have biological and ecological relevance in terms of assessing the actual impact on local organisms of chronic environmental contamination by heavy metals and polycyclic aromatic hydrocarbons affecting the Bagnoli-Coroglio area, and of exploring enhanced sediment and water oxygenation as a promising tool to mitigate the effects of contamination in future environmental restoration actions.
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Affiliation(s)
- Nadia Ruocco
- Department of Marine Biotechnology, Stazione Zoologica Anton Dohrn, Villa Comunale, 80121, Naples, Italy
| | - Iacopo Bertocci
- Department of Biology, University of Pisa, CoNISMa, Via Derna 1, 56126, Pisa, Italy; Department of Integrative Marine Ecology, Stazione Zoologica Anton Dohrn,Villa Comunale, 80121, Naples, Italy
| | - Marco Munari
- Department of Integrative Marine Ecology, Stazione Zoologica Anton Dohrn,Villa Comunale, 80121, Naples, Italy
| | - Luigi Musco
- Department of Integrative Marine Ecology, Stazione Zoologica Anton Dohrn,Villa Comunale, 80121, Naples, Italy
| | - Davide Caramiello
- Unit Marine Resources for Research, Stazione Zoologica Anton Dohrn, 80121, Naples, Italy
| | - Roberto Danovaro
- Stazione Zoologica Anton Dohrn, Villa Comunale, 80121, Naples, Italy; Department of Life and Environmental Sciences, Polytechnic University of Marche, Ancona, 60131, Italy
| | - Valerio Zupo
- Department of Marine Biotechnology, Stazione Zoologica Anton Dohrn, Villa Comunale, 80121, Naples, Italy.
| | - Maria Costantini
- Department of Marine Biotechnology, Stazione Zoologica Anton Dohrn, Villa Comunale, 80121, Naples, Italy.
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5
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ANAC032 regulates root growth through the MYB30 gene regulatory network. Sci Rep 2019; 9:11358. [PMID: 31388054 PMCID: PMC6684591 DOI: 10.1038/s41598-019-47822-0] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2019] [Accepted: 07/24/2019] [Indexed: 01/03/2023] Open
Abstract
Reactive oxygen species (ROS) play important roles as root growth regulators. We previously reported a comprehensive transcriptomic atlas, which we named ROS-map, that revealed ROS-responsible genes in Arabidopsis root tips. By using ROS-map, we have characterised an early ROS response key transcription factor, MYB30, as a regulator of root cell elongation under ROS signals. However, there are other ROS-responsible transcription factors which have the potential to regulate root growth. In the present study, we characterised the function of another early ROS-responsible transcription factor, ANAC032, that was selected from ROS-map. Overexpression of ANAC032 fused with the transcriptional activation domain, VP16, inhibited root growth, especially decreasing cell elongation. By transcriptome analysis, we revealed that ANAC032 regulated many stress-responsible genes in the roots. Intriguingly, ANAC032 upregulated MYB30 and its target genes. The upregulation of MYB30 target genes was completely abolished in the ANAC032-VP16x2 OX and ANAC032 estradiol-inducible line in myb30-2 mutants. Moreover, root growth inhibition was alleviated in ANAC032-OX in myb30-2 mutants. Overall, we characterised an upstream transcription factor, ANAC032, of the MYB30 transcriptional cascade which is a key regulator for root cell elongation under ROS signalling.
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6
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Youssef MS, Mira MM, Millar JL, Becker MG, Belmonte MF, Hill RD, Stasolla C. Spatial identification of transcripts and biological processes in laser micro-dissected sub-regions of waterlogged corn roots with altered expression of phytoglobin. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2019; 139:350-365. [PMID: 30952087 DOI: 10.1016/j.plaphy.2019.03.036] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/08/2019] [Revised: 03/25/2019] [Accepted: 03/25/2019] [Indexed: 05/27/2023]
Abstract
Over-expression of the corn phytoglobin ZmPgb1.2 increases tolerance to waterlogging, while suppression of ZmPgb1.2 compromises plant growth. To unravel compartment-specific transcriptional changes evoked by ZmPgb1.2 during hypoxia, laser micro-dissected sub-regions from waterlogged roots of WT and ZmPgb1.2 overexpressing [ZmPgb1.2(S)] plants were probed for global transcriptional analysis using next generation RNA sequencing. These sub-regions included compartments within the meristematic, elongation, and maturation zone. Of the 149 genes differentially expressed by the up-regulation of ZmPgb1.2, 78 occurred within the meristematic region and included genes involved in jasmonic acid synthesis and response, ascorbic acid metabolism, and ethylene signalling. The ZmPgb1.2 regulation of these genes, discussed in the context of known functions of Pgbs, was further validated by monitoring their expression in meristematic cells of waterlogged roots suppressing ZmPgb1.2. Of the 27 genes differentially expressed by the over-expression of ZmPgb1.2 in the elongation zone, pyruvate kinase and alcohol dehydrogenase showed an expression pattern correlated to the level of ZmPgb1.2 in the tissue. The transcriptional induction of these two enzymes in hypoxic domains of the elongation zone over-expressing ZmPgb1.2 suggests the activation of the fermentation pathway which might be required to sustain metabolic flux and production of ATP in support of cell elongation.
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Affiliation(s)
- Mohamed S Youssef
- Botany Department, Faculty of Science, Kafrelsheikh University, 33516, Kafr El-Sheikh, Egypt
| | - Mohamed M Mira
- Department of Botany, Faculty of Science, Tanta University, Tanta, 31527, Gharbia, Egypt
| | - Jenna L Millar
- Department of Biological Sciences, University of Manitoba, Winnipeg, Manitoba, R3T 2N2, Canada
| | - Michael G Becker
- Department of Biological Sciences, University of Manitoba, Winnipeg, Manitoba, R3T 2N2, Canada
| | - Mark F Belmonte
- Department of Biological Sciences, University of Manitoba, Winnipeg, Manitoba, R3T 2N2, Canada
| | - Robert D Hill
- Department of Plant Science, University of Manitoba, Winnipeg, Manitoba, R3T 2N2, Canada
| | - Claudio Stasolla
- Department of Plant Science, University of Manitoba, Winnipeg, Manitoba, R3T 2N2, Canada.
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7
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Di Mambro R, Svolacchia N, Dello Ioio R, Pierdonati E, Salvi E, Pedrazzini E, Vitale A, Perilli S, Sozzani R, Benfey PN, Busch W, Costantino P, Sabatini S. The Lateral Root Cap Acts as an Auxin Sink that Controls Meristem Size. Curr Biol 2019; 29:1199-1205.e4. [PMID: 30880016 DOI: 10.1016/j.cub.2019.02.022] [Citation(s) in RCA: 44] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2018] [Revised: 12/27/2018] [Accepted: 02/06/2019] [Indexed: 12/28/2022]
Abstract
Plant developmental plasticity relies on the activities of meristems, regions where stem cells continuously produce new cells [1]. The lateral root cap (LRC) is the outermost tissue of the root meristem [1], and it is known to play an important role during root development [2-6]. In particular, it has been shown that mechanical or genetic ablation of LRC cells affect meristem size [7, 8]; however, the molecular mechanisms involved are unknown. Root meristem size and, consequently, root growth depend on the position of the transition zone (TZ), a boundary that separates dividing from differentiating cells [9, 10]. The interaction of two phytohormones, cytokinin and auxin, is fundamental in controlling the position of the TZ [9, 10]. Cytokinin via the ARABIDOPSIS RESPONSE REGULATOR 1 (ARR1) control auxin distribution within the meristem, generating an instructive auxin minimum that positions the TZ [10]. We identify a cytokinin-dependent molecular mechanism that acts in the LRC to control the position of the TZ and meristem size. We show that auxin levels within the LRC cells depends on PIN-FORMED 5 (PIN5), a cytokinin-activated intracellular transporter that pumps auxin from the cytoplasm into the endoplasmic reticulum, and on irreversible auxin conjugation mediated by the IAA-amino synthase GRETCHEN HAGEN 3.17 (GH3.17). By titrating auxin in the LRC, the PIN5 and the GH3.17 genes control auxin levels in the entire root meristem. Overall, our results indicate that the LRC serves as an auxin sink that, under the control of cytokinin, regulates meristem size and root growth.
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Affiliation(s)
- Riccardo Di Mambro
- Department of Biology, University of Pisa - via L. Ghini, 13 - 56126 Pisa, Italy.
| | - Noemi Svolacchia
- Dipartimento di Biologia e Biotecnologie, Laboratory of Functional Genomics and Proteomics of Model Systems, Università di Roma, Sapienza - via dei Sardi, 70 - 00185 Rome, Italy
| | - Raffaele Dello Ioio
- Dipartimento di Biologia e Biotecnologie, Laboratory of Functional Genomics and Proteomics of Model Systems, Università di Roma, Sapienza - via dei Sardi, 70 - 00185 Rome, Italy
| | - Emanuela Pierdonati
- Dipartimento di Biologia e Biotecnologie, Laboratory of Functional Genomics and Proteomics of Model Systems, Università di Roma, Sapienza - via dei Sardi, 70 - 00185 Rome, Italy
| | - Elena Salvi
- Dipartimento di Biologia e Biotecnologie, Laboratory of Functional Genomics and Proteomics of Model Systems, Università di Roma, Sapienza - via dei Sardi, 70 - 00185 Rome, Italy
| | - Emanuela Pedrazzini
- Istituto di Biologia e Biotecnologia Agraria, Consiglio Nazionale delle Ricerche - Via Alfonso Corti, 12 - 20133 Milano, Italy
| | - Alessandro Vitale
- Istituto di Biologia e Biotecnologia Agraria, Consiglio Nazionale delle Ricerche - Via Alfonso Corti, 12 - 20133 Milano, Italy
| | - Serena Perilli
- Dipartimento di Biologia e Biotecnologie, Laboratory of Functional Genomics and Proteomics of Model Systems, Università di Roma, Sapienza - via dei Sardi, 70 - 00185 Rome, Italy
| | - Rosangela Sozzani
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh, NC, United States
| | - Philip N Benfey
- Department of Biology and Howard Hughes Medical Institute, Duke University, Durham, NC 27708, USA
| | - Wolfgang Busch
- Plant Molecular and Cellular Biology Laboratory, Salk Institute for Biological Studies, La Jolla, CA 92037, USA
| | - Paolo Costantino
- Dipartimento di Biologia e Biotecnologie, Laboratory of Functional Genomics and Proteomics of Model Systems, Università di Roma, Sapienza - via dei Sardi, 70 - 00185 Rome, Italy
| | - Sabrina Sabatini
- Dipartimento di Biologia e Biotecnologie, Laboratory of Functional Genomics and Proteomics of Model Systems, Università di Roma, Sapienza - via dei Sardi, 70 - 00185 Rome, Italy.
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8
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Palovaara J, Weijers D. Adapting INTACT to analyse cell-type-specific transcriptomes and nucleocytoplasmic mRNA dynamics in the Arabidopsis embryo. PLANT REPRODUCTION 2019; 32:113-121. [PMID: 30430248 DOI: 10.1007/s00497-018-0347-0] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/05/2018] [Accepted: 10/31/2018] [Indexed: 05/06/2023]
Abstract
In the early embryo of vascular plants, the different cell types and stem cells of the seedling are specified as the embryo develops from a zygote towards maturity. How the key steps in cell and tissue specification are instructed by genome-wide transcriptional activity is poorly understood. Progress in defining transcriptional regulation at the genome-wide level in plant embryos has been hampered by difficulties associated with capturing cell-type-specific transcriptomes in this small and inaccessible structure. We recently adapted a two-component genetic nucleus labelling system called INTACT to isolate nuclei from distinct cell types at different stages of Arabidopsis thaliana embryogenesis. We have used these to generate a transcriptomic atlas of embryo development following microarray-based expression profiling. Here, we present a general description of the adapted INTACT procedure, including the two-component labelling system, seed isolation, nuclei preparation and purification, as well as transcriptomic profiling. We also compare nuclear and cellular transcriptomes from the early Arabidopsis embryo to assess nucleocytoplasmic differences and discuss how these differences can be used to infer regulation of gene activity.
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Affiliation(s)
- Joakim Palovaara
- Laboratory of Biochemistry, Wageningen University, 6708 WE, Wageningen, The Netherlands
- Molecular Genetics, University of Bremen, 28359, Bremen, Germany
| | - Dolf Weijers
- Laboratory of Biochemistry, Wageningen University, 6708 WE, Wageningen, The Netherlands.
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9
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Gaudinier A, Rodriguez-Medina J, Zhang L, Olson A, Liseron-Monfils C, Bågman AM, Foret J, Abbitt S, Tang M, Li B, Runcie DE, Kliebenstein DJ, Shen B, Frank MJ, Ware D, Brady SM. Transcriptional regulation of nitrogen-associated metabolism and growth. Nature 2018; 563:259-264. [PMID: 30356219 DOI: 10.1038/s41586-018-0656-3] [Citation(s) in RCA: 158] [Impact Index Per Article: 26.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2017] [Accepted: 08/22/2018] [Indexed: 11/09/2022]
Abstract
Nitrogen is an essential macronutrient for plant growth and basic metabolic processes. The application of nitrogen-containing fertilizer increases yield, which has been a substantial factor in the green revolution1. Ecologically, however, excessive application of fertilizer has disastrous effects such as eutrophication2. A better understanding of how plants regulate nitrogen metabolism is critical to increase plant yield and reduce fertilizer overuse. Here we present a transcriptional regulatory network and twenty-one transcription factors that regulate the architecture of root and shoot systems in response to changes in nitrogen availability. Genetic perturbation of a subset of these transcription factors revealed coordinate transcriptional regulation of enzymes involved in nitrogen metabolism. Transcriptional regulators in the network are transcriptionally modified by feedback via genetic perturbation of nitrogen metabolism. The network, genes and gene-regulatory modules identified here will prove critical to increasing agricultural productivity.
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Affiliation(s)
- Allison Gaudinier
- Department of Plant Biology and Genome Center, University of California, Davis, Davis, CA, USA
| | - Joel Rodriguez-Medina
- Department of Plant Biology and Genome Center, University of California, Davis, Davis, CA, USA
| | - Lifang Zhang
- Cold Spring Harbor Laboratory, Cold Spring Harbor, Cold Spring Harbor, NY, USA
| | - Andrew Olson
- Cold Spring Harbor Laboratory, Cold Spring Harbor, Cold Spring Harbor, NY, USA
| | | | - Anne-Maarit Bågman
- Department of Plant Biology and Genome Center, University of California, Davis, Davis, CA, USA
| | - Jessica Foret
- Department of Plant Biology and Genome Center, University of California, Davis, Davis, CA, USA
| | | | - Michelle Tang
- Department of Plant Biology and Genome Center, University of California, Davis, Davis, CA, USA.,Department of Plant Sciences, University of California, Davis, Davis, CA, USA
| | - Baohua Li
- Department of Plant Sciences, University of California, Davis, Davis, CA, USA
| | - Daniel E Runcie
- Department of Plant Sciences, University of California, Davis, Davis, CA, USA
| | - Daniel J Kliebenstein
- Department of Plant Sciences, University of California, Davis, Davis, CA, USA.,DynaMo Center of Excellence, University of Copenhagen, Frederiksberg C, Denmark
| | - Bo Shen
- DuPont Pioneer, Johnston, IA, USA
| | | | - Doreen Ware
- Cold Spring Harbor Laboratory, Cold Spring Harbor, Cold Spring Harbor, NY, USA.,US Department of Agriculture, Agricultural Research Service, Ithaca, NY, USA
| | - Siobhan M Brady
- Department of Plant Biology and Genome Center, University of California, Davis, Davis, CA, USA.
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10
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MYB30 links ROS signaling, root cell elongation, and plant immune responses. Proc Natl Acad Sci U S A 2018; 115:E4710-E4719. [PMID: 29712840 DOI: 10.1073/pnas.1804233115] [Citation(s) in RCA: 69] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Reactive oxygen species (ROS) are known to be important signal molecules that are involved in biotic and abiotic stress responses as well as in growth regulation. However, the molecular mechanisms by which ROS act as a growth regulator, as well as how ROS-dependent growth regulation relates to its roles in stress responses, are not well understood. We performed a time-course microarray analysis of Arabidopsis root tips upon treatment with hydrogen peroxide, which we named "ROS-map." Using the ROS-map, we identified an MYB transcription factor, MYB30, which showed a strong response to ROS treatment and is the key regulator of a gene network that leads to the hydrogen peroxide-dependent inhibition of root cell elongation. Intriguingly, this network contained multiple genes involved in very-long-chain fatty acid (VLCFA) transport. Finally, we showed that MYB30 is necessary for root growth regulation during defense responses, thus providing a molecular link between these two ROS-associated processes.
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11
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Palovaara J, Saiga S, Wendrich JR, van 't Wout Hofland N, van Schayck JP, Hater F, Mutte S, Sjollema J, Boekschoten M, Hooiveld GJ, Weijers D. Transcriptome dynamics revealed by a gene expression atlas of the early Arabidopsis embryo. NATURE PLANTS 2017; 3:894-904. [PMID: 29116234 PMCID: PMC5687563 DOI: 10.1038/s41477-017-0035-3] [Citation(s) in RCA: 55] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/15/2017] [Accepted: 09/19/2017] [Indexed: 05/02/2023]
Abstract
During early plant embryogenesis, precursors for all major tissues and stem cells are formed. While several components of the regulatory framework are known, how cell fates are instructed by genome-wide transcriptional activity remains unanswered-in part because of difficulties in capturing transcriptome changes at cellular resolution. Here, we have adapted a two-component transgenic labelling system to purify cell-type-specific nuclear RNA and generate a transcriptome atlas of early Arabidopsis embryo development, with a focus on root stem cell niche formation. We validated the dataset through gene expression analysis, and show that gene activity shifts in a spatio-temporal manner, probably signifying transcriptional reprogramming, to induce developmental processes reflecting cell states and state transitions. This atlas provides the most comprehensive tissue- and cell-specific description of genome-wide gene activity in the early plant embryo, and serves as a valuable resource for understanding the genetic control of early plant development.
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Affiliation(s)
- Joakim Palovaara
- Laboratory of Biochemistry, Wageningen University, 6708 WE, Wageningen, The Netherlands
| | - Shunsuke Saiga
- Laboratory of Biochemistry, Wageningen University, 6708 WE, Wageningen, The Netherlands
| | - Jos R Wendrich
- Laboratory of Biochemistry, Wageningen University, 6708 WE, Wageningen, The Netherlands
- Department of Plant Biotechnology and Bioinformatics and VIB Center for Plant Systems Biology, Ghent University, Technologiepark 927, 9052, Ghent, Belgium
| | | | - J Paul van Schayck
- Laboratory of Biochemistry, Wageningen University, 6708 WE, Wageningen, The Netherlands
| | - Friederike Hater
- Laboratory of Biochemistry, Wageningen University, 6708 WE, Wageningen, The Netherlands
| | - Sumanth Mutte
- Laboratory of Biochemistry, Wageningen University, 6708 WE, Wageningen, The Netherlands
| | - Jouke Sjollema
- Laboratory of Biochemistry, Wageningen University, 6708 WE, Wageningen, The Netherlands
| | - Mark Boekschoten
- Nutrition, Metabolism and Genomics Group, Division of Human Nutrition, Wageningen University, 6708 WE, Wageningen, The Netherlands
| | - Guido J Hooiveld
- Nutrition, Metabolism and Genomics Group, Division of Human Nutrition, Wageningen University, 6708 WE, Wageningen, The Netherlands
| | - Dolf Weijers
- Laboratory of Biochemistry, Wageningen University, 6708 WE, Wageningen, The Netherlands.
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12
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Silva AT, Ligterink W, Hilhorst HWM. Metabolite profiling and associated gene expression reveal two metabolic shifts during the seed-to-seedling transition in Arabidopsis thaliana. PLANT MOLECULAR BIOLOGY 2017; 95:481-496. [PMID: 29046998 PMCID: PMC5688192 DOI: 10.1007/s11103-017-0665-x] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/18/2017] [Accepted: 10/04/2017] [Indexed: 05/02/2023]
Abstract
Metabolic and transcriptomic correlation analysis identified two distinctive profiles involved in the metabolic preparation for seed germination and seedling establishment, respectively. Transcripts were identified that may control metabolic fluxes. The transition from a quiescent metabolic state (dry seed) to the active state of a vigorous seedling is crucial in the plant's life cycle. We analysed this complex physiological trait by measuring the changes in primary metabolism that occur during the transition in order to determine which metabolic networks are operational. The transition involves several developmental stages from seed germination to seedling establishment, i.e. between imbibition of the mature dry seed and opening of the cotyledons, the final stage of seedling establishment. We hypothesized that the advancement of growth is associated with certain signature metabolite profiles. Metabolite-metabolite correlation analysis underlined two specific profiles which appear to be involved in the metabolic preparation for seed germination and efficient seedling establishment, respectively. Metabolite profiles were also compared to transcript profiles and although transcriptional changes did not always equate to a proportional metabolic response, in depth correlation analysis identified several transcripts that may directly influence the flux through metabolic pathways during the seed-to-seedling transition. This correlation analysis also pinpointed metabolic pathways which are significant for the seed-to-seedling transition, and metabolite contents that appeared to be controlled directly by transcript abundance. This global view of the transcriptional and metabolic changes during the seed-to-seedling transition in Arabidopsis opens up new perspectives for understanding the complex regulatory mechanism underlying this transition.
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Affiliation(s)
- Anderson Tadeu Silva
- Laboratory of Plant Physiology, Wageningen University, Droevendaalsesteeg 1, 6708 PB, Wageningen, The Netherlands.
- Interdisciplinary Plant Group, University of Missouri, Columbia, MO, USA.
| | - Wilco Ligterink
- Laboratory of Plant Physiology, Wageningen University, Droevendaalsesteeg 1, 6708 PB, Wageningen, The Netherlands
| | - Henk W M Hilhorst
- Laboratory of Plant Physiology, Wageningen University, Droevendaalsesteeg 1, 6708 PB, Wageningen, The Netherlands.
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13
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Garg R, Singh VK, Rajkumar MS, Kumar V, Jain M. Global transcriptome and coexpression network analyses reveal cultivar-specific molecular signatures associated with seed development and seed size/weight determination in chickpea. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2017; 91:1088-1107. [PMID: 28640939 DOI: 10.1111/tpj.13621] [Citation(s) in RCA: 88] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/15/2017] [Revised: 06/02/2017] [Accepted: 06/09/2017] [Indexed: 05/22/2023]
Abstract
Seed development is an intricate process regulated via a complex transcriptional regulatory network. To understand the molecular mechanisms governing seed development and seed size/weight in chickpea, we performed a comprehensive analysis of transcriptome dynamics during seed development in two cultivars with contrasting seed size/weight (small-seeded, Himchana 1 and large-seeded, JGK 3). Our analysis identified stage-specific expression for a significant proportion (>13%) of the genes in each cultivar. About one half of the total genes exhibited significant differential expression in JGK 3 as compared with Himchana 1. We found that different seed development stages can be delineated by modules of coexpressed genes. A comparative analysis revealed differential developmental stage specificity of some modules between the two cultivars. Furthermore, we constructed transcriptional regulatory networks and identified key components determining seed size/weight. The results suggested that extended period of cell division during embryogenesis and higher level of endoreduplication along with more accumulation of storage compounds during maturation determine large seed size/weight. Further, we identified quantitative trait loci-associated candidate genes harboring single nucleotide polymorphisms in the promoter sequences that differentiate small- and large-seeded chickpea cultivars. The results provide a valuable resource to dissect the role of candidate genes governing seed development and seed size/weight in chickpea.
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Affiliation(s)
- Rohini Garg
- National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi, 110067, India
- Department of Life Sciences, School of Natural Sciences, Shiv Nadar University, Gautam Buddha Nagar, Uttar Pradesh, 201314, India
| | - Vikash K Singh
- National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi, 110067, India
| | - Mohan Singh Rajkumar
- National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi, 110067, India
| | - Vinay Kumar
- National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi, 110067, India
| | - Mukesh Jain
- National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi, 110067, India
- School of Computational & Integrative Sciences, Jawaharlal Nehru University, New Delhi, 110067, India
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14
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Ruocco N, Maria Fedele A, Costantini S, Romano G, Ianora A, Costantini M. New inter-correlated genes targeted by diatom-derived polyunsaturated aldehydes in the sea urchin Paracentrotus lividus. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2017; 142:355-362. [PMID: 28437727 DOI: 10.1016/j.ecoenv.2017.04.022] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/23/2017] [Revised: 04/10/2017] [Accepted: 04/11/2017] [Indexed: 06/07/2023]
Abstract
The marine environment is continually subjected to the action of stressors (including natural toxins), which represent a constant danger for benthic communities. In the present work using network analysis we identified ten genes on the basis of associated functions (FOXA, FoxG, GFI-1, nodal, JNK, OneCut/Hnf6, TAK1, tcf4, TCF7, VEGF) in the sea urchin Paracentrotus lividus, having key roles in different processes, such as embryonic development and asymmetry, cell fate specification, cell differentiation and morphogenesis, and skeletogenesis. These genes are correlated with three HUB genes, Foxo, Jun and HIF1A. Real Time qPCR revealed that during sea urchin embryonic development the expression levels of these genes were modulated by three diatom-derived polyunsaturated aldehydes (PUAs), decadienal, heptadienal and octadienal. Our findings show how changes in gene expression levels may be used as an early indicator of stressful conditions in the marine environment. The identification of key genes and the molecular pathways in which they are involved represents a fundamental tool in understanding how marine organisms try to afford protection against toxicants, to avoid deleterious consequences and irreversible damages. The genes identified in this work as targets for PUAs can be considered as possible biomarkers to detect exposure to different environmental pollutants.
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Affiliation(s)
- Nadia Ruocco
- Department of Biology and Evolution of Marine Organisms, Stazione Zoologica Anton Dohrn, Villa Comunale, 80121 Napoli, Italy; Department of Biology, University of Naples Federico II, Complesso Universitario di Monte Sant'Angelo, Via Cinthia, 80126 Napoli, Italy; Bio-Organic Chemistry Unit, Institute of Biomolecular Chemistry-CNR, Via Campi Flegrei 34, Pozzuoli, Naples 80078, Italy
| | - Anna Maria Fedele
- Department of Biology and Evolution of Marine Organisms, Stazione Zoologica Anton Dohrn, Villa Comunale, 80121 Napoli, Italy
| | - Susan Costantini
- Unità di Farmacologia Sperimentale, Istituto Nazionale Tumori "Fondazione G. Pascale", IRCCS, 80131 Napoli, Italy
| | - Giovanna Romano
- Department of Integrative Marine Ecology, Stazione Zoologica Anton Dohrn, Villa Comunale, 80121 Napoli, Italy
| | - Adrianna Ianora
- Department of Integrative Marine Ecology, Stazione Zoologica Anton Dohrn, Villa Comunale, 80121 Napoli, Italy
| | - Maria Costantini
- Department of Biology and Evolution of Marine Organisms, Stazione Zoologica Anton Dohrn, Villa Comunale, 80121 Napoli, Italy.
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15
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Becker MG, Walker PL, Pulgar-Vidal NC, Belmonte MF. SeqEnrich: A tool to predict transcription factor networks from co-expressed Arabidopsis and Brassica napus gene sets. PLoS One 2017; 12:e0178256. [PMID: 28575075 PMCID: PMC5456048 DOI: 10.1371/journal.pone.0178256] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2017] [Accepted: 05/10/2017] [Indexed: 01/08/2023] Open
Abstract
Transcription factors and their associated DNA binding sites are key regulatory elements of cellular differentiation, development, and environmental response. New tools that predict transcriptional regulation of biological processes are valuable to researchers studying both model and emerging-model plant systems. SeqEnrich predicts transcription factor networks from co-expressed Arabidopsis or Brassica napus gene sets. The networks produced by SeqEnrich are supported by existing literature and predicted transcription factor–DNA interactions that can be functionally validated at the laboratory bench. The program functions with gene sets of varying sizes and derived from diverse tissues and environmental treatments. SeqEnrich presents as a powerful predictive framework for the analysis of Arabidopsis and Brassica napus co-expression data, and is designed so that researchers at all levels can easily access and interpret predicted transcriptional circuits. The program outperformed its ancestral program ChipEnrich, and produced detailed transcription factor networks from Arabidopsis and Brassica napus gene expression data. The SeqEnrich program is ideal for generating new hypotheses and distilling biological information from large-scale expression data.
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Affiliation(s)
- Michael G. Becker
- Department of Biological Sciences, University of Manitoba, Winnipeg, Manitoba, Canada
| | - Philip L. Walker
- Department of Biological Sciences, University of Manitoba, Winnipeg, Manitoba, Canada
| | | | - Mark F. Belmonte
- Department of Biological Sciences, University of Manitoba, Winnipeg, Manitoba, Canada
- * E-mail:
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16
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Becker MG, Zhang X, Walker PL, Wan JC, Millar JL, Khan D, Granger MJ, Cavers JD, Chan AC, Fernando DWG, Belmonte MF. Transcriptome analysis of the Brassica napus-Leptosphaeria maculans pathosystem identifies receptor, signaling and structural genes underlying plant resistance. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2017; 90:573-586. [PMID: 28222234 DOI: 10.1111/tpj.13514] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/16/2016] [Revised: 02/05/2017] [Accepted: 02/10/2017] [Indexed: 05/18/2023]
Abstract
The hemibiotrophic fungal pathogen Leptosphaeria maculans is the causal agent of blackleg disease in Brassica napus (canola, oilseed rape) and causes significant loss of yield worldwide. While genetic resistance has been used to mitigate the disease by means of traditional breeding strategies, there is little knowledge about the genes that contribute to blackleg resistance. RNA sequencing and a streamlined bioinformatics pipeline identified unique genes and plant defense pathways specific to plant resistance in the B. napus-L. maculans LepR1-AvrLepR1 interaction over time. We complemented our temporal analyses by monitoring gene activity directly at the infection site using laser microdissection coupled to quantitative PCR. Finally, we characterized genes involved in plant resistance to blackleg in the Arabidopsis-L. maculans model pathosystem. Data reveal an accelerated activation of the plant transcriptome in resistant host cotyledons associated with transcripts coding for extracellular receptors and phytohormone signaling molecules. Functional characterization provides direct support for transcriptome data and positively identifies resistance regulators in the Brassicaceae. Spatial gradients of gene activity were identified in response to L. maculans proximal to the site of infection. This dataset provides unprecedented spatial and temporal resolution of the genes required for blackleg resistance and serves as a valuable resource for those interested in host-pathogen interactions.
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Affiliation(s)
- Michael G Becker
- Department of Biological Sciences, University of Manitoba, Winnipeg, MB, R3T2N2, Canada
| | - Xuehua Zhang
- Department of Plant Science, University of Manitoba, Winnipeg, MB, R3T2N2, Canada
| | - Philip L Walker
- Department of Biological Sciences, University of Manitoba, Winnipeg, MB, R3T2N2, Canada
| | - Joey C Wan
- Department of Biological Sciences, University of Manitoba, Winnipeg, MB, R3T2N2, Canada
| | - Jenna L Millar
- Department of Biological Sciences, University of Manitoba, Winnipeg, MB, R3T2N2, Canada
| | - Deirdre Khan
- Department of Biological Sciences, University of Manitoba, Winnipeg, MB, R3T2N2, Canada
| | - Matthew J Granger
- Department of Biological Sciences, University of Manitoba, Winnipeg, MB, R3T2N2, Canada
| | - Jacob D Cavers
- Department of Biological Sciences, University of Manitoba, Winnipeg, MB, R3T2N2, Canada
| | - Ainsley C Chan
- Department of Biological Sciences, University of Manitoba, Winnipeg, MB, R3T2N2, Canada
| | | | - Mark F Belmonte
- Department of Biological Sciences, University of Manitoba, Winnipeg, MB, R3T2N2, Canada
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17
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Schaefer RJ, Michno JM, Myers CL. Unraveling gene function in agricultural species using gene co-expression networks. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2017; 1860:53-63. [DOI: 10.1016/j.bbagrm.2016.07.016] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/04/2016] [Revised: 07/23/2016] [Accepted: 07/25/2016] [Indexed: 10/21/2022]
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18
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Chan AC, Khan D, Girard IJ, Becker MG, Millar JL, Sytnik D, Belmonte MF. Tissue-specific laser microdissection of the Brassica napus funiculus improves gene discovery and spatial identification of biological processes. JOURNAL OF EXPERIMENTAL BOTANY 2016; 67:3561-71. [PMID: 27194740 PMCID: PMC4892738 DOI: 10.1093/jxb/erw179] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
The three primary tissue systems of the funiculus each undergo unique developmental programs to support the growth and development of the filial seed. To understand the underlying transcriptional mechanisms that orchestrate development of the funiculus at the globular embryonic stage of seed development, we used laser microdissection coupled with RNA-sequencing to produce a high-resolution dataset of the mRNAs present in the epidermis, cortex, and vasculature of the Brassica napus (canola) funiculus. We identified 7761 additional genes in these tissues compared with the whole funiculus organ alone using this technology. Differential expression and enrichment analyses were used to identify several biological processes associated with each tissue system. Our data show that cell wall modification and lipid metabolism are prominent in the epidermis, cell growth and modification occur in the cortex, and vascular tissue proliferation and differentiation occur in the central vascular strand. We provide further evidence that each of the three tissue systems of the globular stage funiculus are involved in specific biological processes that all co-ordinate to support seed development. The identification of genes and gene regulators responsible for tissue-specific developmental processes of the canola funiculus now serves as a valuable resource for seed improvement research.
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Affiliation(s)
- Ainsley C Chan
- University of Manitoba, Department of Biological Sciences, 50 Sifton Road, Winnipeg, MB R3T 2N2, Canada
| | - Deirdre Khan
- University of Manitoba, Department of Biological Sciences, 50 Sifton Road, Winnipeg, MB R3T 2N2, Canada
| | - Ian J Girard
- University of Manitoba, Department of Biological Sciences, 50 Sifton Road, Winnipeg, MB R3T 2N2, Canada
| | - Michael G Becker
- University of Manitoba, Department of Biological Sciences, 50 Sifton Road, Winnipeg, MB R3T 2N2, Canada
| | - Jenna L Millar
- University of Manitoba, Department of Biological Sciences, 50 Sifton Road, Winnipeg, MB R3T 2N2, Canada
| | - David Sytnik
- University of Manitoba, Department of Biological Sciences, 50 Sifton Road, Winnipeg, MB R3T 2N2, Canada
| | - Mark F Belmonte
- University of Manitoba, Department of Biological Sciences, 50 Sifton Road, Winnipeg, MB R3T 2N2, Canada
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19
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Silva AT, Ribone PA, Chan RL, Ligterink W, Hilhorst HWM. A Predictive Coexpression Network Identifies Novel Genes Controlling the Seed-to-Seedling Phase Transition in Arabidopsis thaliana. PLANT PHYSIOLOGY 2016; 170:2218-31. [PMID: 26888061 PMCID: PMC4825141 DOI: 10.1104/pp.15.01704] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/05/2015] [Accepted: 02/15/2016] [Indexed: 05/18/2023]
Abstract
The transition from a quiescent dry seed to an actively growing photoautotrophic seedling is a complex and crucial trait for plant propagation. This study provides a detailed description of global gene expression in seven successive developmental stages of seedling establishment in Arabidopsis (Arabidopsis thaliana). Using the transcriptome signature from these developmental stages, we obtained a coexpression gene network that highlights interactions between known regulators of the seed-to-seedling transition and predicts the functions of uncharacterized genes in seedling establishment. The coexpressed gene data sets together with the transcriptional module indicate biological functions related to seedling establishment. Characterization of the homeodomain leucine zipper I transcription factor AtHB13, which is expressed during the seed-to-seedling transition, demonstrated that this gene regulates some of the network nodes and affects late seedling establishment. Knockout mutants for athb13 showed increased primary root length as compared with wild-type (Columbia-0) seedlings, suggesting that this transcription factor is a negative regulator of early root growth, possibly repressing cell division and/or cell elongation or the length of time that cells elongate. The signal transduction pathways present during the early phases of the seed-to-seedling transition anticipate the control of important events for a vigorous seedling, such as root growth. This study demonstrates that a gene coexpression network together with transcriptional modules can provide insights that are not derived from comparative transcript profiling alone.
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Affiliation(s)
- Anderson Tadeu Silva
- Wageningen Seed Laboratory, Laboratory of Plant Physiology, Wageningen University, 6708 PB Wageningen, The Netherlands (A.T.S., W.L., H.W.M.H.); andInstituto de Agrobiotecnología del Litoral, Universidad Nacional del Litoral, Consejo Nacional de Investigaciones Científicas y Técnicas, 3000 Santa Fe, Argentina (P.A.R., R.L.C.)
| | - Pamela A Ribone
- Wageningen Seed Laboratory, Laboratory of Plant Physiology, Wageningen University, 6708 PB Wageningen, The Netherlands (A.T.S., W.L., H.W.M.H.); andInstituto de Agrobiotecnología del Litoral, Universidad Nacional del Litoral, Consejo Nacional de Investigaciones Científicas y Técnicas, 3000 Santa Fe, Argentina (P.A.R., R.L.C.)
| | - Raquel L Chan
- Wageningen Seed Laboratory, Laboratory of Plant Physiology, Wageningen University, 6708 PB Wageningen, The Netherlands (A.T.S., W.L., H.W.M.H.); andInstituto de Agrobiotecnología del Litoral, Universidad Nacional del Litoral, Consejo Nacional de Investigaciones Científicas y Técnicas, 3000 Santa Fe, Argentina (P.A.R., R.L.C.)
| | - Wilco Ligterink
- Wageningen Seed Laboratory, Laboratory of Plant Physiology, Wageningen University, 6708 PB Wageningen, The Netherlands (A.T.S., W.L., H.W.M.H.); andInstituto de Agrobiotecnología del Litoral, Universidad Nacional del Litoral, Consejo Nacional de Investigaciones Científicas y Técnicas, 3000 Santa Fe, Argentina (P.A.R., R.L.C.)
| | - Henk W M Hilhorst
- Wageningen Seed Laboratory, Laboratory of Plant Physiology, Wageningen University, 6708 PB Wageningen, The Netherlands (A.T.S., W.L., H.W.M.H.); andInstituto de Agrobiotecnología del Litoral, Universidad Nacional del Litoral, Consejo Nacional de Investigaciones Científicas y Técnicas, 3000 Santa Fe, Argentina (P.A.R., R.L.C.)
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20
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Winter CM, Yamaguchi N, Wu MF, Wagner D. Transcriptional programs regulated by both LEAFY and APETALA1 at the time of flower formation. PHYSIOLOGIA PLANTARUM 2015; 155:55-73. [PMID: 26096587 PMCID: PMC5757833 DOI: 10.1111/ppl.12357] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/26/2014] [Accepted: 06/09/2015] [Indexed: 05/24/2023]
Abstract
Two key regulators of the switch to flower formation and of flower patterning in Arabidopsis are the plant-specific helix-turn-helix transcription factor LEAFY (LFY) and the MADS box transcription factor APETALA1 (AP1). The interactions between these two transcriptional regulators are complex. AP1 is both a direct target of LFY and can act in parallel with LFY. Available genetic and molecular evidence suggests that LFY and AP1 together orchestrate the switch to flower formation and early events during flower morphogenesis by altering transcriptional programs. However, very little is known about target genes regulated by both transcription factors. Here, we performed a meta-analysis of public datasets to identify genes that are likely to be regulated by both LFY and AP1. Our analyses uncovered known and novel direct LFY and AP1 targets with a role in the control of onset of flower formation. It also identified additional families of proteins and regulatory pathways that may be under transcriptional control by both transcription factors. In particular, several of these genes are linked to response to hormones, to transport and to development. Finally, we show that the gibberellin catabolism enzyme ELA1, which was recently shown to be important for the timing of the switch to flower formation, is positively feedback-regulated by AP1. Our study contributes to the elucidation of the regulatory network that leads to formation of a vital plant organ system, the flower.
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Affiliation(s)
- Cara M. Winter
- Department of Biology, Duke University, Durham, NC, 27708, USA
| | - Nobutoshi Yamaguchi
- Department of Biology, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Miin-Feng Wu
- Department of Biology, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Doris Wagner
- Department of Biology, University of Pennsylvania, Philadelphia, PA, 19104, USA
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21
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Tsukagoshi H, Suzuki T, Nishikawa K, Agarie S, Ishiguro S, Higashiyama T. RNA-seq analysis of the response of the halophyte, Mesembryanthemum crystallinum (ice plant) to high salinity. PLoS One 2015; 10:e0118339. [PMID: 25706745 PMCID: PMC4338230 DOI: 10.1371/journal.pone.0118339] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2014] [Accepted: 01/14/2015] [Indexed: 01/08/2023] Open
Abstract
Understanding the molecular mechanisms that convey salt tolerance in plants is a crucial issue for increasing crop yield. The ice plant (Mesembryanthemum crystallinum) is a halophyte that is capable of growing under high salt conditions. For example, the roots of ice plant seedlings continue to grow in 140 mM NaCl, a salt concentration that completely inhibits Arabidopsis thaliana root growth. Identifying the molecular mechanisms responsible for this high level of salt tolerance in a halophyte has the potential of revealing tolerance mechanisms that have been evolutionarily successful. In the present study, deep sequencing (RNAseq) was used to examine gene expression in ice plant roots treated with various concentrations of NaCl. Sequencing resulted in the identification of 53,516 contigs, 10,818 of which were orthologs of Arabidopsis genes. In addition to the expression analysis, a web-based ice plant database was constructed that allows broad public access to the data. The results obtained from an analysis of the RNAseq data were confirmed by RT-qPCR. Novel patterns of gene expression in response to high salinity within 24 hours were identified in the ice plant when the RNAseq data from the ice plant was compared to gene expression data obtained from Arabidopsis plants exposed to high salt. Although ABA responsive genes and a sodium transporter protein (HKT1), are up-regulated and down-regulated respectively in both Arabidopsis and the ice plant; peroxidase genes exhibit opposite responses. The results of this study provide an important first step towards analyzing environmental tolerance mechanisms in a non-model organism and provide a useful dataset for predicting novel gene functions.
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Affiliation(s)
- Hironaka Tsukagoshi
- The Center for Gene Research, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Aichi, Japan
- Program for leading graduate schools, PhD Professional: Gateway to Success in Frontier Asia, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Aichi, Japan
- PRESTO, JST, Honcho, Kawaguchi, Saitama, Japan
| | - Takamasa Suzuki
- Division of Biological Science, Graduate School of Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Aichi, Japan
- JST, ERATO, Higashiyama Live-Holonics Project, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Aichi, Japan
| | - Kouki Nishikawa
- Graduate School of Bioagricultural Sciences, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Aichi, Japan
| | - Sakae Agarie
- Faculty of Agriculture, Kagawa university, Saiwaicho 1-1, Takamatsu, Kagawa, Japan
| | - Sumie Ishiguro
- Graduate School of Bioagricultural Sciences, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Aichi, Japan
| | - Tetsuya Higashiyama
- Division of Biological Science, Graduate School of Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Aichi, Japan
- JST, ERATO, Higashiyama Live-Holonics Project, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Aichi, Japan
- WPI-ITbM, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Aichi, Japan
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22
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Lo HY, Li CC, Huang HC, Lin LJ, Hsiang CY, Ho TY. Application of transcriptomics in Chinese herbal medicine studies. J Tradit Complement Med 2014; 2:105-14. [PMID: 24716122 PMCID: PMC3942912 DOI: 10.1016/s2225-4110(16)30083-9] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Transcriptomics using DNA microarray has become a practical and popular tool for herbal medicine study because of high throughput, sensitivity, accuracy, specificity, and reproducibility. Therefore, this article focuses on the overview of DNA microarray technology and the application of DNA microarray in Chinese herbal medicine study. To understand the number and the objectives of articles utilizing DNA microarray for herbal medicine study, we surveyed 297 frequently used Chinese medicinal herbs listed in Pharmacopoeia Commission of People's Republic of China. We classified these medicinal herbs into 109 families and then applied PudMed search using “microarray” and individual herbal family as keywords. Although thousands of papers applying DNA microarray in Chinese herbal studies have been published since 1998, most of the articles focus on the elucidation of mechanisms of certain biological effects of herbs. Construction of the bioactivity database containing large-scaled gene expression profiles of quality control herbs can be applied in the future to analyze the biological events induced by herbs, predict the therapeutic potential of herbs, evaluate the safety of herbs, and identify the drug candidate of herbs. Moreover, the linkage of systems biology tools, such as functional genomics, transcriptomics, proteomics, metabolomics, pharmacogenomics and toxicogenomics, will become a new translational platform between Western medicine and Chinese herbal medicine.
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Affiliation(s)
- Hsin-Yi Lo
- Graduate Institute of Chinese Medicine, China Medical University, Taichung 40402, Taiwan
| | - Chia-Cheng Li
- Graduate Institute of Chinese Medicine, China Medical University, Taichung 40402, Taiwan
| | - Hui-Chi Huang
- School of Pharmaceutical Sciences and Chinese Medicine Resources, China Medical University, Taichung 40402, Taiwan
| | - Li-Jen Lin
- School of Chinese Medicine, China Medical University, Taichung 40402, Taiwan
| | - Chien-Yun Hsiang
- Department of Microbiology, China Medical University, Taichung 40402, Taiwan
| | - Tin-Yun Ho
- Department of Microbiology, China Medical University, Taichung 40402, Taiwan
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Discovering functional modules across diverse maize transcriptomes using COB, the Co-expression Browser. PLoS One 2014; 9:e99193. [PMID: 24922320 PMCID: PMC4055606 DOI: 10.1371/journal.pone.0099193] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2014] [Accepted: 05/12/2014] [Indexed: 01/13/2023] Open
Abstract
Tools that provide improved ability to relate genotype to phenotype have the potential to accelerate breeding for desired traits and to improve our understanding of the molecular variants that underlie phenotypes. The availability of large-scale gene expression profiles in maize provides an opportunity to advance our understanding of complex traits in this agronomically important species. We built co-expression networks based on genome-wide expression data from a variety of maize accessions as well as an atlas of different tissues and developmental stages. We demonstrate that these networks reveal clusters of genes that are enriched for known biological function and contain extensive structure which has yet to be characterized. Furthermore, we found that co-expression networks derived from developmental or tissue atlases as compared to expression variation across diverse accessions capture unique functions. To provide convenient access to these networks, we developed a public, web-based Co-expression Browser (COB), which enables interactive queries of the genome-wide networks. We illustrate the utility of this system through two specific use cases: one in which gene-centric queries are used to provide functional context for previously characterized metabolic pathways, and a second where lists of genes produced by mapping studies are further resolved and validated using co-expression networks.
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Khan D, Chan A, Millar JL, Girard IJ, Belmonte MF. Predicting transcriptional circuitry underlying seed coat development. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2014; 223:146-52. [PMID: 24767124 DOI: 10.1016/j.plantsci.2014.03.016] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/09/2013] [Revised: 03/16/2014] [Accepted: 03/17/2014] [Indexed: 05/27/2023]
Abstract
Filling, protection, and dispersal of angiosperm seeds are largely dependent on the development of the maternally derived seed coat. The development of the seed coat in plants such as Arabidopsis thaliana and Glycine max (soybean) is regulated by a complex network of genes and gene products responsible for the establishment and identity of this multicellular structure. Recent studies support the hypothesis that the structure, development, and function of the seed coat are under the control of transcriptional regulators that are specified in space and time. Furthermore, these transcriptional regulators can act in combination to orchestrate the expression of large gene sets. We discuss the underlying transcriptional circuits of the seed coat sub-regions through the interrogation of large-scale datasets, and also provide some ideas on how the identification and analysis of these datasets can be further improved in these two model oilseed systems.
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Affiliation(s)
- Deirdre Khan
- Department of Biological Sciences, University of Manitoba, Winnipeg R3T 2N2, Canada
| | - Ainsley Chan
- Department of Biological Sciences, University of Manitoba, Winnipeg R3T 2N2, Canada
| | - Jenna L Millar
- Department of Biological Sciences, University of Manitoba, Winnipeg R3T 2N2, Canada
| | - Ian J Girard
- Department of Biological Sciences, University of Manitoba, Winnipeg R3T 2N2, Canada
| | - Mark F Belmonte
- Department of Biological Sciences, University of Manitoba, Winnipeg R3T 2N2, Canada.
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25
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Yamaguchi N, Winter CM, Wu MF, Kanno Y, Yamaguchi A, Seo M, Wagner D. Gibberellin acts positively then negatively to control onset of flower formation in Arabidopsis. Science 2014; 344:638-41. [PMID: 24812402 DOI: 10.1126/science.1250498] [Citation(s) in RCA: 157] [Impact Index Per Article: 15.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
The switch to reproductive development is biphasic in many plants, a feature important for optimal pollination and yield. We show that dual opposite roles of the phytohormone gibberellin underpin this phenomenon in Arabidopsis. Although gibberellin promotes termination of vegetative development, it inhibits flower formation. To overcome this effect, the transcription factor LEAFY induces expression of a gibberellin catabolism gene; consequently, increased LEAFY activity causes reduced gibberellin levels. This allows accumulation of gibberellin-sensitive DELLA proteins. The DELLA proteins are recruited by SQUAMOSA PROMOTER BINDING PROTEIN-LIKE transcription factors to regulatory regions of the floral commitment gene APETALA1 and promote APETALA1 up-regulation and floral fate synergistically with LEAFY. The two opposing functions of gibberellin may facilitate evolutionary and environmental modulation of plant inflorescence architecture.
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Affiliation(s)
- Nobutoshi Yamaguchi
- Department of Biology, University of Pennsylvania, 415 South University Avenue, Philadelphia, PA 19104-6018, USA
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26
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Comprehensive developmental profiles of gene activity in regions and subregions of the Arabidopsis seed. Proc Natl Acad Sci U S A 2013; 110:E435-44. [PMID: 23319655 DOI: 10.1073/pnas.1222061110] [Citation(s) in RCA: 292] [Impact Index Per Article: 26.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023] Open
Abstract
Seeds are complex structures that consist of the embryo, endosperm, and seed-coat regions that are of different ontogenetic origins, and each region can be further divided into morphologically distinct subregions. Despite the importance of seeds for food, fiber, and fuel globally, little is known of the cellular processes that characterize each subregion or how these processes are integrated to permit the coordinated development of the seed. We profiled gene activity genome-wide in every organ, tissue, and cell type of Arabidopsis seeds from fertilization through maturity. The resulting mRNA datasets offer the most comprehensive description of gene activity in seeds with high spatial and temporal resolution,providing unique insights into the function of understudied seed regions. Global comparisons of mRNA populations reveal unexpected overlaps in the functional identities of seed subregions. Analyses of coexpressed gene sets suggest that processes that regulate seed size and filling are coordinated across several subregions. Predictions of gene regulatory networks based on the association of transcription factors with enriched DNA sequence motifs upstream of coexpressed genes identify regulators of seed development. These studies emphasize the utility of these data sets as an essential resource for the study of seed biology.
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Bailey-Serres J. Microgenomics: genome-scale, cell-specific monitoring of multiple gene regulation tiers. ANNUAL REVIEW OF PLANT BIOLOGY 2013; 64:293-325. [PMID: 23451787 DOI: 10.1146/annurev-arplant-050312-120035] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
The expression of nuclear protein-coding genes is controlled by dynamic mechanisms ranging from DNA methylation, chromatin modification, and gene transcription to mRNA maturation, turnover, and translation and the posttranslational control of protein function. A genome-scale assessment of the spatiotemporal regulation of gene expression is essential for a comprehensive understanding of gene regulatory networks. However, there are major obstacles to the precise evaluation of gene regulation in multicellular plant organs; these include the monitoring of regulatory processes at levels other than steady-state transcript abundance, resolution of gene regulation in individual cells or cell types, and effective assessment of transient gene activity manifested during development or in response to external cues. This review surveys the advantages and applications of microgenomics technologies that enable panoramic quantitation of cell-type-specific expression in plants, focusing on the importance of querying gene activity at multiple steps in the continuum, from histone modification to selective translation.
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Affiliation(s)
- J Bailey-Serres
- Center for Plant Cell Biology and Department of Botany and Plant Sciences, University of California, Riverside, CA 92521, USA.
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28
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Bargmann BOR, Vanneste S, Krouk G, Nawy T, Efroni I, Shani E, Choe G, Friml J, Bergmann DC, Estelle M, Birnbaum KD. A map of cell type-specific auxin responses. Mol Syst Biol 2013; 9:688. [PMID: 24022006 PMCID: PMC3792342 DOI: 10.1038/msb.2013.40] [Citation(s) in RCA: 115] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2013] [Accepted: 07/23/2013] [Indexed: 12/31/2022] Open
Abstract
In plants, changes in local auxin concentrations can trigger a range of developmental processes as distinct tissues respond differently to the same auxin stimulus. However, little is known about how auxin is interpreted by individual cell types. We performed a transcriptomic analysis of responses to auxin within four distinct tissues of the Arabidopsis thaliana root and demonstrate that different cell types show competence for discrete responses. The majority of auxin-responsive genes displayed a spatial bias in their induction or repression. The novel data set was used to examine how auxin influences tissue-specific transcriptional regulation of cell-identity markers. Additionally, the data were used in combination with spatial expression maps of the root to plot a transcriptomic auxin-response gradient across the apical and basal meristem. The readout revealed a strong correlation for thousands of genes between the relative response to auxin and expression along the longitudinal axis of the root. This data set and comparative analysis provide a transcriptome-level spatial breakdown of the response to auxin within an organ where this hormone mediates many aspects of development.
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Affiliation(s)
- Bastiaan O R Bargmann
- Biology Department, Center for Genomics and Systems Biology, New York University, New York, NY, USA
- Department of Cell and Developmental Biology, UCSD, La Jolla, CA, USA
| | - Steffen Vanneste
- Department of Plant Systems Biology, VIB, Ghent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
| | - Gabriel Krouk
- Laboratoire de Biochimie et Physiologie Moléculaire des Plantes, Institut de Biologie Intégrative des Plantes—Claude Grignon, Montpellier, France
| | - Tal Nawy
- Biology Department, Center for Genomics and Systems Biology, New York University, New York, NY, USA
| | - Idan Efroni
- Biology Department, Center for Genomics and Systems Biology, New York University, New York, NY, USA
| | - Eilon Shani
- Department of Cell and Developmental Biology, UCSD, La Jolla, CA, USA
| | - Goh Choe
- Department of Cell and Developmental Biology, UCSD, La Jolla, CA, USA
| | - Jiří Friml
- Department of Plant Systems Biology, VIB, Ghent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- Institute of Science and Technology Austria (IST Austria), Klosterneuburg, Austria
| | | | - Mark Estelle
- Department of Cell and Developmental Biology, UCSD, La Jolla, CA, USA
| | - Kenneth D Birnbaum
- Biology Department, Center for Genomics and Systems Biology, New York University, New York, NY, USA
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Mustroph A, Zanetti ME, Girke T, Bailey-Serres J. Isolation and analysis of mRNAs from specific cell types of plants by ribosome immunopurification. Methods Mol Biol 2013; 959:277-302. [PMID: 23299683 DOI: 10.1007/978-1-62703-221-6_19] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
Multiple ribosomes assemble onto an individual mRNA to form a polyribosome (polysome) complex. The epitope tagging of specific ribosomal proteins can enable the immunopurification of polysomes from crude cell extracts derived from cryopreserved tissue samples. Through expression of the epitope-tagged ribosomal protein in cell-type and regional specific domains of Arabidopsis thaliana and other organisms it is feasible to quantitatively assess the mRNAs that are associated with ribosomes with cell-specific resolution. Here we present detailed methods for development of transgenics that express a FLAG-tagged version of ribosomal protein L18 (RPL18) under the direction of individual promoters with specific domains of expression, the immunopurification of ribosomes, and bioinformatic analyses of the resultant datasets obtained by microarray profiling. This methodology provides researchers with the opportunity to assess rapid changes at the organ, tissue, regional or cell-type specific level of mRNAs that are associated with ribosomes and therefore engaged in translation.
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Affiliation(s)
- Angelika Mustroph
- Department of Plant Physiology, University of Bayreuth, Bayreuth, Germany.
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30
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Avin-Wittenberg T, Tzin V, Angelovici R, Less H, Galili G. Deciphering energy-associated gene networks operating in the response of Arabidopsis plants to stress and nutritional cues. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2012; 70:954-66. [PMID: 22288575 DOI: 10.1111/j.1365-313x.2012.04926.x] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
Plants need to continuously adjust their transcriptome in response to various stresses that lead to inhibition of photosynthesis and the deprivation of cellular energy. This adjustment is triggered in part by a coordinated re-programming of the energy-associated transcriptome to slow down photosynthesis and activate other energy-promoting gene networks. Therefore, understanding the stress-related transcriptional networks of genes belonging to energy-associated pathways is of major importance for engineering stress tolerance. In a bioinformatics approach developed by our group, termed 'gene coordination', we previously divided genes encoding for enzymes and transcription factors in Arabidopsis thaliana into three clusters, displaying altered coordinated transcriptional behaviors in response to multiple biotic and abiotic stresses (Plant Cell, 23, 2011, 1264). Enrichment analysis indicated further that genes controlling energy-associated metabolism operate as a compound network in response to stress. In the present paper, we describe in detail the network association of genes belonging to six central energy-associated pathways in each of these three clusters described in our previous paper. Our results expose extensive stress-associated intra- and inter-pathway interactions between genes from these pathways, indicating that genes encoding proteins involved in energy-associated metabolism are expressed in a highly coordinated manner. We also provide examples showing that this approach can be further utilized to elucidate candidate genes for stress tolerance and functions of isozymes.
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Affiliation(s)
- Tamar Avin-Wittenberg
- Department of Plant Sciences, The Weizmann Institute of Science, Rehovot 76100, Israel
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31
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Petricka JJ, Schauer MA, Megraw M, Breakfield NW, Thompson JW, Georgiev S, Soderblom EJ, Ohler U, Moseley MA, Grossniklaus U, Benfey PN. The protein expression landscape of the Arabidopsis root. Proc Natl Acad Sci U S A 2012. [PMID: 22447775 DOI: 10.1073/pnas,0.1202546109] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/26/2023] Open
Abstract
Because proteins are the major functional components of cells, knowledge of their cellular localization is crucial to gaining an understanding of the biology of multicellular organisms. We have generated a protein expression map of the Arabidopsis root providing the identity and cell type-specific localization of nearly 2,000 proteins. Grouping proteins into functional categories revealed unique cellular functions and identified cell type-specific biomarkers. Cellular colocalization provided support for numerous protein-protein interactions. With a binary comparison, we found that RNA and protein expression profiles are weakly correlated. We then performed peak integration at cell type-specific resolution and found an improved correlation with transcriptome data using continuous values. We performed GeLC-MS/MS (in-gel tryptic digestion followed by liquid chromatography-tandem mass spectrometry) proteomic experiments on mutants with ectopic and no root hairs, providing complementary proteomic data. Finally, among our root hair-specific proteins we identified two unique regulators of root hair development.
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Affiliation(s)
- Jalean J Petricka
- Department of Biology, Duke Center for Systems Biology, and Institute for Genome Sciences and Policy, Duke University, Durham, NC 27708, USA
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32
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Abstract
Because proteins are the major functional components of cells, knowledge of their cellular localization is crucial to gaining an understanding of the biology of multicellular organisms. We have generated a protein expression map of the Arabidopsis root providing the identity and cell type-specific localization of nearly 2,000 proteins. Grouping proteins into functional categories revealed unique cellular functions and identified cell type-specific biomarkers. Cellular colocalization provided support for numerous protein-protein interactions. With a binary comparison, we found that RNA and protein expression profiles are weakly correlated. We then performed peak integration at cell type-specific resolution and found an improved correlation with transcriptome data using continuous values. We performed GeLC-MS/MS (in-gel tryptic digestion followed by liquid chromatography-tandem mass spectrometry) proteomic experiments on mutants with ectopic and no root hairs, providing complementary proteomic data. Finally, among our root hair-specific proteins we identified two unique regulators of root hair development.
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33
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Iyer-Pascuzzi AS, Jackson T, Cui H, Petricka JJ, Busch W, Tsukagoshi H, Benfey PN. Cell identity regulators link development and stress responses in the Arabidopsis root. Dev Cell 2011; 21:770-82. [PMID: 22014526 DOI: 10.1016/j.devcel.2011.09.009] [Citation(s) in RCA: 136] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2011] [Revised: 06/27/2011] [Accepted: 09/19/2011] [Indexed: 12/20/2022]
Abstract
Stress responses in plants are tightly coordinated with developmental processes, but interaction of these pathways is poorly understood. We used genome-wide assays at high spatiotemporal resolution to understand the processes that link development and stress in the Arabidopsis root. Our meta-analysis finds little evidence for a universal stress response. However, common stress responses appear to exist with many showing cell type specificity. Common stress responses may be mediated by cell identity regulators because mutations in these genes resulted in altered responses to stress. Evidence for a direct role for cell identity regulators came from genome-wide binding profiling of the key regulator SCARECROW, which showed binding to regulatory regions of stress-responsive genes. Coexpression in response to stress was used to identify genes involved in specific developmental processes. These results reveal surprising linkages between stress and development at cellular resolution, and show the power of multiple genome-wide data sets to elucidate biological processes.
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Affiliation(s)
- Anjali S Iyer-Pascuzzi
- Department of Biology and Institute for Genome Science and Policy Center for Systems Biology, Duke University, Durham, NC 27708, USA
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34
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Transcriptomic characterization of a synergistic genetic interaction during carpel margin meristem development in Arabidopsis thaliana. PLoS One 2011; 6:e26231. [PMID: 22031826 PMCID: PMC3198736 DOI: 10.1371/journal.pone.0026231] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2011] [Accepted: 09/22/2011] [Indexed: 11/19/2022] Open
Abstract
In flowering plants the gynoecium is the female reproductive structure. In Arabidopsis thaliana ovules initiate within the developing gynoecium from meristematic tissue located along the margins of the floral carpels. When fertilized the ovules will develop into seeds. SEUSS (SEU) and AINTEGUMENTA (ANT) encode transcriptional regulators that are critical for the proper formation of ovules from the carpel margin meristem (CMM). The synergistic loss of ovule initiation observed in the seu ant double mutant suggests that SEU and ANT share overlapping functions during CMM development. However the molecular mechanism underlying this synergistic interaction is unknown. Using the ATH1 transcriptomics platform we identified transcripts that were differentially expressed in seu ant double mutant relative to wild type and single mutant gynoecia. In particular we sought to identify transcripts whose expression was dependent on the coordinated activities of the SEU and ANT gene products. Our analysis identifies a diverse set of transcripts that display altered expression in the seu ant double mutant tissues. The analysis of overrepresented Gene Ontology classifications suggests a preponderance of transcriptional regulators including multiple members of the REPRODUCTIVE MERISTEMS (REM) and GROWTH-REGULATING FACTOR (GRF) families are mis-regulated in the seu ant gynoecia. Our in situ hybridization analyses indicate that many of these genes are preferentially expressed within the developing CMM. This study is the first step toward a detailed description of the transcriptional regulatory hierarchies that control the development of the CMM and ovule initiation. Understanding the regulatory hierarchy controlled by SEU and ANT will clarify the molecular mechanism of the functional redundancy of these two genes and illuminate the developmental and molecular events required for CMM development and ovule initiation.
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35
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Less H, Angelovici R, Tzin V, Galili G. Coordinated gene networks regulating Arabidopsis plant metabolism in response to various stresses and nutritional cues. THE PLANT CELL 2011; 23:1264-71. [PMID: 21487096 PMCID: PMC3101534 DOI: 10.1105/tpc.110.082867] [Citation(s) in RCA: 75] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/04/2011] [Revised: 03/03/2011] [Accepted: 03/12/2011] [Indexed: 05/18/2023]
Abstract
The expression pattern of any pair of genes may be negatively correlated, positively correlated, or not correlated at all in response to different stresses and even different progression stages of the stress. This makes it difficult to identify such relationships by classical statistical tools such as the Pearson correlation coefficient. Hence, dedicated bioinformatics approaches that are able to identify groups of cues in which there is a positive or negative expression correlation between pairs or groups of genes are called for. We herein introduce and discuss a bioinformatics approach, termed Gene Coordination, that is devoted to the identification of specific or multiple cues in which there is a positive or negative coordination between pairs of genes and can further incorporate additional coordinated genes to form large coordinated gene networks. We demonstrate the utility of this approach by providing a case study in which we were able to discover distinct expression behavior of the energy-associated gene network in response to distinct biotic and abiotic stresses. This bioinformatics approach is suitable to a broad range of studies that compare treatments versus controls, such as effects of various cues, or expression changes between a mutant and the control wild-type genotype.
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Affiliation(s)
| | | | | | - Gad Galili
- Department of Plant Sciences, Weizmann Institute of Science, Rehovot 76100, Israel
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36
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Hachez C, Ohashi-Ito K, Dong J, Bergmann DC. Differentiation of Arabidopsis guard cells: analysis of the networks incorporating the basic helix-loop-helix transcription factor, FAMA. PLANT PHYSIOLOGY 2011; 155:1458-72. [PMID: 21245191 PMCID: PMC3046599 DOI: 10.1104/pp.110.167718] [Citation(s) in RCA: 63] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/02/2023]
Abstract
Nearly all extant land plants possess stomata, the epidermal structures that mediate gas exchange between the plant and the environment. The developmental pathways, cell division patterns, and molecules employed in the generation of these structures are simple examples of processes used in many developmental contexts. One specific module is a set of "master regulator" basic helix-loop-helix transcription factors that regulate individual consecutive steps in stomatal development. Here, we profile transcriptional changes in response to inducible expression of Arabidopsis (Arabidopsis thaliana) FAMA, a basic helix-loop-helix protein whose actions during the final stage in stomatal development regulate both cell division and cell fate. Genes identified by microarray and candidate approaches were then further analyzed to test specific hypothesis about the activity of FAMA, the shape of its regulatory network, and to create a new set of stomata-specific or stomata-enriched reporters.
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Tsukagoshi H, Busch W, Benfey PN. Transcriptional Regulation of ROS Controls Transition from Proliferation to Differentiation in the Root. Cell 2010; 143:606-16. [DOI: 10.1016/j.cell.2010.10.020] [Citation(s) in RCA: 722] [Impact Index Per Article: 51.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2010] [Revised: 07/28/2010] [Accepted: 10/13/2010] [Indexed: 01/17/2023]
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38
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Sozzani R, Cui H, Moreno-Risueno MA, Busch W, Van Norman JM, Vernoux T, Brady SM, Dewitte W, Murray JAH, Benfey PN. Spatiotemporal regulation of cell-cycle genes by SHORTROOT links patterning and growth. Nature 2010; 466:128-32. [PMID: 20596025 DOI: 10.1038/nature09143] [Citation(s) in RCA: 296] [Impact Index Per Article: 21.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2010] [Accepted: 04/28/2010] [Indexed: 12/18/2022]
Abstract
The development of multicellular organisms relies on the coordinated control of cell divisions leading to proper patterning and growth. The molecular mechanisms underlying pattern formation, particularly the regulation of formative cell divisions, remain poorly understood. In Arabidopsis, formative divisions generating the root ground tissue are controlled by SHORTROOT (SHR) and SCARECROW (SCR). Here we show, using cell-type-specific transcriptional effects of SHR and SCR combined with data from chromatin immunoprecipitation-based microarray experiments, that SHR regulates the spatiotemporal activation of specific genes involved in cell division. Coincident with the onset of a specific formative division, SHR and SCR directly activate a D-type cyclin; furthermore, altering the expression of this cyclin resulted in formative division defects. Our results indicate that proper pattern formation is achieved through transcriptional regulation of specific cell-cycle genes in a cell-type- and developmental-stage-specific context. Taken together, we provide evidence for a direct link between developmental regulators, specific components of the cell-cycle machinery and organ patterning.
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Affiliation(s)
- R Sozzani
- Department of Biology and IGSP Center for Systems Biology, Duke University, Durham, North Carolina 27708, USA
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39
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Orlando DA, Brady SM, Fink TMA, Benfey PN, Ahnert SE. Detecting separate time scales in genetic expression data. BMC Genomics 2010; 11:381. [PMID: 20565716 PMCID: PMC3017766 DOI: 10.1186/1471-2164-11-381] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2009] [Accepted: 06/16/2010] [Indexed: 01/11/2023] Open
Abstract
Background Biological processes occur on a vast range of time scales, and many of them occur concurrently. As a result, system-wide measurements of gene expression have the potential to capture many of these processes simultaneously. The challenge however, is to separate these processes and time scales in the data. In many cases the number of processes and their time scales is unknown. This issue is particularly relevant to developmental biologists, who are interested in processes such as growth, segmentation and differentiation, which can all take place simultaneously, but on different time scales. Results We introduce a flexible and statistically rigorous method for detecting different time scales in time-series gene expression data, by identifying expression patterns that are temporally shifted between replicate datasets. We apply our approach to a Saccharomyces cerevisiae cell-cycle dataset and an Arabidopsis thaliana root developmental dataset. In both datasets our method successfully detects processes operating on several different time scales. Furthermore we show that many of these time scales can be associated with particular biological functions. Conclusions The spatiotemporal modules identified by our method suggest the presence of multiple biological processes, acting at distinct time scales in both the Arabidopsis root and yeast. Using similar large-scale expression datasets, the identification of biological processes acting at multiple time scales in many organisms is now possible.
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Affiliation(s)
- David A Orlando
- Department of Biology and IGSP Center for Systems Biology, Duke University, Durham, NC, USA
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40
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Moreno-Risueno MA, Busch W, Benfey PN. Omics meet networks - using systems approaches to infer regulatory networks in plants. CURRENT OPINION IN PLANT BIOLOGY 2010; 13:126-31. [PMID: 20036612 PMCID: PMC2862083 DOI: 10.1016/j.pbi.2009.11.005] [Citation(s) in RCA: 57] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/12/2009] [Revised: 11/18/2009] [Accepted: 11/25/2009] [Indexed: 05/19/2023]
Abstract
Many genomic-scale datasets in plants have been generated over the last few years. This substantial achievement has led to impressive progress, including some of the most detailed molecular maps in any multicellular organism. Networks and pathways have been reconstructed using transcriptome, genome-wide transcription factor binding, proteome and metabolome data, and subsequently used to infer functional interactions among genes, proteins, and metabolites. However, more sophisticated systems biology approaches are needed to integrate different omics datasets. Ultimately, the integration of diverse and massive datasets into coherent models will improve our understanding of the molecular networks that underlie biological processes.
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