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Mestinšek Mubi Š, Kunej U, Vogrinčič V, Jakše J, Murovec J. The effect of phytosulfokine alpha on haploid embryogenesis and gene expression of Brassica napus microspore cultures. FRONTIERS IN PLANT SCIENCE 2024; 15:1336519. [PMID: 38425801 PMCID: PMC10902448 DOI: 10.3389/fpls.2024.1336519] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/10/2023] [Accepted: 01/30/2024] [Indexed: 03/02/2024]
Abstract
Microspore embryogenesis (ME) is the most powerful tool for creating homozygous lines in plant breeding and molecular biology research. It is still based mainly on the reprogramming of microspores by temperature, osmotic and/or nutrient stress. New compounds are being sought that could increase the efficiency of microspore embryogenesis or even induce the formation of haploid embryos from recalcitrant genotypes. Among these, the mitogenic factor phytosulfokine alpha (PSK-α) is promising due to its broad spectrum of activity in vivo and in vitro. The aim of our study was to investigate the effect of PSK-α on haploid embryogenesis from microspores of oilseed rape (Brassica napus L., DH4079), one of the most important oil crops and a model plant for studying the molecular mechanisms controlling embryo formation. We tested different concentrations (0, 0.01, 0.1 and 1 µM) of the peptide and evaluated its effect on microspore viability and embryo regeneration after four weeks of culture. Our results showed a positive correlation between addition of PSK-α and cultured microspore viability and a positive effect also on the number of developed embryos. The analysis of transcriptomes across three time points (day 0, 2 and 4) with or without PSK-α supplementation (15 RNA libraries in total) unveiled differentially expressed genes pivotal in cell division, microspore embryogenesis, and subsequent regeneration. PCA grouped transcriptomes by RNA sampling time, with the first two principal components explaining 56.8% variability. On day 2 with PSK, 45 genes (15 up- and 30 down-regulated) were differentially expressed when PSK-α was added and their number increased to 304 by day 4 (30 up- and 274 down-regulated). PSK, PSKR, and PSI gene expression analysis revealed dynamic patterns, with PSK2 displaying the highest increase and overall expression during microspore culture at days 2 and 4. Despite some variations, only PSK1 showed significant differential expression upon PSK-α addition. Of 16 ME-related molecular markers, 3 and 15 exhibited significant differential expression in PSK-supplemented cultures at days 2 and 4, respectively. Embryo-specific markers predominantly expressed after 4 days of culture, with higher expression in medium without PSK, while on day 0, numerous sporophyte-specific markers were highly expressed.
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Li X, Liu Q, Liu J. Long Non-Coding RNAs: Discoveries, Mechanisms, and Research Strategies in Seeds. Genes (Basel) 2023; 14:2214. [PMID: 38137035 PMCID: PMC10742540 DOI: 10.3390/genes14122214] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2023] [Revised: 12/11/2023] [Accepted: 12/11/2023] [Indexed: 12/24/2023] Open
Abstract
Seeds provide nutrients for the embryo and allow for dormancy in stressed environments to better adapt the plant to its environment. In addition, seeds are an essential source of food for human survival and are the basis for the formation of food production and quality. Therefore, the research on the genetic mechanism of seed development and germination will provide a theoretical basis and technical support for the improvement of crop yield and quality. Recent studies have shown that long non-coding RNAs (lncRNAs) occupy a pivotal position in seed development and germination. In this review, we describe the key processes in seed biology and examine discoveries and insights made in seed lncRNA, with emphasis on lncRNAs that regulate seed biology through multiple mechanisms. Given that thousands of lncRNAs are present in the seed transcriptome, characterization has lagged far behind identification. We provide an overview of research strategies and approaches including some exciting new techniques that may uncover the function of lncRNAs in seed. Finally, we discuss the challenges facing the field and the opening questions. All in all, we hope to provide a clear perspective on discoveries of seed lncRNA by linking discoveries, mechanisms, and technologies.
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Affiliation(s)
| | | | - Jun Liu
- Guangdong Provincial Key Laboratory for Crop Germplasm Resources Preservation and Utilization, Agro-Biological Gene Research Center, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, China; (X.L.); (Q.L.)
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3
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Zhang Y, Xu T, Dong J. Asymmetric cell division in plant development. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2023; 65:343-370. [PMID: 36610013 PMCID: PMC9975081 DOI: 10.1111/jipb.13446] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/09/2022] [Accepted: 01/05/2023] [Indexed: 05/03/2023]
Abstract
Asymmetric cell division (ACD) is a fundamental process that generates new cell types during development in eukaryotic species. In plant development, post-embryonic organogenesis driven by ACD is universal and more important than in animals, in which organ pattern is preset during embryogenesis. Thus, plant development provides a powerful system to study molecular mechanisms underlying ACD. During the past decade, tremendous progress has been made in our understanding of the key components and mechanisms involved in this important process in plants. Here, we present an overview of how ACD is determined and regulated in multiple biological processes in plant development and compare their conservation and specificity among different model cell systems. We also summarize the molecular roles and mechanisms of the phytohormones in the regulation of plant ACD. Finally, we conclude with the overarching paradigms and principles that govern plant ACD and consider how new technologies can be exploited to fill the knowledge gaps and make new advances in the field.
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Affiliation(s)
- Yi Zhang
- Plant Synthetic Biology Center, Haixia Institute of Science and Technology, and College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China
- The Waksman Institute of Microbiology, Rutgers, the State University of New Jersey, Piscataway, NJ 08854, USA
- Correspondences: Yi Zhang (); Juan Dong (). Yi Zhang and Juan Dong are fully responsible for the distribution of all materials associated with this article
| | - Tongda Xu
- Plant Synthetic Biology Center, Haixia Institute of Science and Technology, and College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Juan Dong
- The Waksman Institute of Microbiology, Rutgers, the State University of New Jersey, Piscataway, NJ 08854, USA
- Department of Plant Biology, Rutgers, the State University of New Jersey, New Brunswick, NJ 08891, USA
- Correspondences: Yi Zhang (); Juan Dong (). Yi Zhang and Juan Dong are fully responsible for the distribution of all materials associated with this article
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Berendzen KW, Grefen C, Sakamoto T, Slane D. Analysis of Chromatin Accessibility, Histone Modifications, and Transcriptional States in Specific Cell Types Using Flow Cytometry. Methods Mol Biol 2023; 2698:57-73. [PMID: 37682469 DOI: 10.1007/978-1-0716-3354-0_5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/09/2023]
Abstract
The past two decades in biomedical research have experienced an explosion of cell type-specific and single-cell studies, especially concerning the concomitant dissection of regulatory and transcriptional landscapes of those under investigation. Additionally, leveraging next-generation sequencing (NGS) platforms efforts have been undertaken to evaluate the effects of chromatin accessibility, histone modifications, or even transcription factor binding sites. We have shown that Fluorescence-Activated Nuclear Sorting (FANS) is an effective means to characterize the transcriptomes of nuclei from different tissues. In light of our own technical and experimental developments, we extend this effort to combine FACS/FANS with Assay for Transposase-Accessible Chromatin using sequencing (ATAC-seq), Chromatin Immunoprecipitation sequencing (ChIP-seq), and RNA sequencing (RNA-seq) for profiling individual cell types according to their chromatin and transcriptional states.
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Affiliation(s)
- Kenneth W Berendzen
- Center for Plant Molecular Biology, University of Tübingen, Tübingen, Germany
| | - Christopher Grefen
- Faculty of Biology and Biotechnology, Molecular and Cellular Botany, University of Bochum, Bochum, Germany
| | - Takuya Sakamoto
- Department of Applied Biological Science, Faculty of Science and Technology, Tokyo University of Science, Chiba, Japan
| | - Daniel Slane
- Department of Applied Biological Science, Faculty of Science and Technology, Tokyo University of Science, Chiba, Japan.
- The University of Tokyo, Graduate School of Frontier Sciences, Department of Integrated Biosciences, Laboratory of Integrated Biology, Chiba, Japan.
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5
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Independent parental contributions initiate zygote polarization in Arabidopsis thaliana. Curr Biol 2021; 31:4810-4816.e5. [PMID: 34496220 DOI: 10.1016/j.cub.2021.08.033] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2021] [Revised: 07/09/2021] [Accepted: 08/11/2021] [Indexed: 12/24/2022]
Abstract
Embryogenesis of flowering plants is initiated by polarization of the zygote, a prerequisite for correct axis formation in the embryo. The daughter cells of the asymmetric zygote division form the pro-embryo and the mostly extra-embryonic suspensor.1 The suspensor plays a pivotal role in nutrient and hormone transport and rapid growth of the embryo.2,3 Zygote polarization is controlled by a MITOGEN-ACTIVATING PROTEIN (MAP) kinase signaling pathway including the MAPKK kinase (MAP3K) YODA (YDA)4 and the upstream membrane-associated proteins BRASINOSTEROID SIGNALING KINASE 1 (BSK1) and BSK2.5,6 Furthermore, suspensor development is controlled by cysteine-rich peptides of the EMBRYO SURROUNDING FACTOR 1 (ESF1) family.7 While they act genetically upstream of YDA, the corresponding receptor to perceive these potential ligands is unknown. In other developmental processes, such as stomata development, YDA activity is controlled by receptor kinases of the ERECTA family (ERf).8-12 While the receptor kinases upstream of BSK1/2 in the embryo have so far not been identified,1 YDA is in part activated by the sperm cell-derived BSK family member SHORT SUSPENSOR (SSP) that represents a naturally occurring, constitutively active variant of BSK1.5,13 It has been speculated that SSP might be a paternal component of a parental tug-of-war controlling resource allocation toward the embryo.2,13 Here, we show that in addition to SSP, the receptor kinase ERECTA plays a crucial role in zygote polarization as a maternally contributed part of the embryonic YDA pathway. We conclude that two independent parental contributions initiate zygote polarization and control embryo development.
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Kao P, Schon MA, Mosiolek M, Enugutti B, Nodine MD. Gene expression variation in Arabidopsis embryos at single-nucleus resolution. Development 2021; 148:dev199589. [PMID: 34142712 PMCID: PMC8276985 DOI: 10.1242/dev.199589] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2021] [Accepted: 05/24/2021] [Indexed: 12/17/2022]
Abstract
Soon after fertilization of egg and sperm, plant genomes become transcriptionally activated and drive a series of coordinated cell divisions to form the basic body plan during embryogenesis. Early embryonic cells rapidly diversify from each other, and investigation of the corresponding gene expression dynamics can help elucidate underlying cellular differentiation programs. However, current plant embryonic transcriptome datasets either lack cell-specific information or have RNA contamination from surrounding non-embryonic tissues. We have coupled fluorescence-activated nuclei sorting together with single-nucleus mRNA-sequencing to construct a gene expression atlas of Arabidopsis thaliana early embryos at single-cell resolution. In addition to characterizing cell-specific transcriptomes, we found evidence that distinct epigenetic and transcriptional regulatory mechanisms operate across emerging embryonic cell types. These datasets and analyses, as well as the approach we devised, are expected to facilitate the discovery of molecular mechanisms underlying pattern formation in plant embryos. This article has an associated 'The people behind the papers' interview.
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Affiliation(s)
- Ping Kao
- Gregor Mendel Institute (GMI), Austrian Academy of Sciences, Vienna Bio Center (VBC), Dr Bohr-Gasse 3, 1030 Vienna, Austria
| | - Michael A. Schon
- Gregor Mendel Institute (GMI), Austrian Academy of Sciences, Vienna Bio Center (VBC), Dr Bohr-Gasse 3, 1030 Vienna, Austria
| | - Magdalena Mosiolek
- Gregor Mendel Institute (GMI), Austrian Academy of Sciences, Vienna Bio Center (VBC), Dr Bohr-Gasse 3, 1030 Vienna, Austria
| | - Balaji Enugutti
- Gregor Mendel Institute (GMI), Austrian Academy of Sciences, Vienna Bio Center (VBC), Dr Bohr-Gasse 3, 1030 Vienna, Austria
| | - Michael D. Nodine
- Gregor Mendel Institute (GMI), Austrian Academy of Sciences, Vienna Bio Center (VBC), Dr Bohr-Gasse 3, 1030 Vienna, Austria
- Laboratory of Molecular Biology, Wageningen University, Wageningen 6708 PB, The Netherlands
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Seyfferth C, Renema J, Wendrich JR, Eekhout T, Seurinck R, Vandamme N, Blob B, Saeys Y, Helariutta Y, Birnbaum KD, De Rybel B. Advances and Opportunities in Single-Cell Transcriptomics for Plant Research. ANNUAL REVIEW OF PLANT BIOLOGY 2021; 72:847-866. [PMID: 33730513 PMCID: PMC7611048 DOI: 10.1146/annurev-arplant-081720-010120] [Citation(s) in RCA: 74] [Impact Index Per Article: 24.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
Single-cell approaches are quickly changing our view on biological systems by increasing the spatiotemporal resolution of our analyses to the level of the individual cell. The field of plant biology has fully embraced single-cell transcriptomics and is rapidly expanding the portfolio of available technologies and applications. In this review, we give an overview of the main advances in plant single-cell transcriptomics over the past few years and provide the reader with an accessible guideline covering all steps, from sample preparation to data analysis. We end by offering a glimpse of how these technologies will shape and accelerate plant-specific research in the near future.
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Affiliation(s)
- Carolin Seyfferth
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium;
- VIB Center for Plant Systems Biology, 9052 Ghent, Belgium
| | - Jim Renema
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium;
- VIB Center for Plant Systems Biology, 9052 Ghent, Belgium
| | - Jos R Wendrich
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium;
- VIB Center for Plant Systems Biology, 9052 Ghent, Belgium
| | - Thomas Eekhout
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium;
- VIB Center for Plant Systems Biology, 9052 Ghent, Belgium
| | - Ruth Seurinck
- Data Mining and Modeling for Biomedicine, VIB Center for Inflammation Research, 9052 Ghent, Belgium
- Department of Applied Mathematics, Computer Science and Statistics, Ghent University, 9000 Ghent, Belgium
| | - Niels Vandamme
- Data Mining and Modeling for Biomedicine, VIB Center for Inflammation Research, 9052 Ghent, Belgium
- Department of Applied Mathematics, Computer Science and Statistics, Ghent University, 9000 Ghent, Belgium
| | - Bernhard Blob
- The Sainsbury Laboratory, University of Cambridge, Cambridge CB2 1LR, United Kingdom
- Viikki Plant Science Centre, HiLIFE/Organismal and Evolutionary Biology Research Program, Institute of Biotechnology, Faculty of Biological and Environmental Sciences, University of Helsinki, 00014 Helsinki, Finland
| | - Yvan Saeys
- Data Mining and Modeling for Biomedicine, VIB Center for Inflammation Research, 9052 Ghent, Belgium
- Department of Applied Mathematics, Computer Science and Statistics, Ghent University, 9000 Ghent, Belgium
| | - Yrjo Helariutta
- The Sainsbury Laboratory, University of Cambridge, Cambridge CB2 1LR, United Kingdom
- Viikki Plant Science Centre, HiLIFE/Organismal and Evolutionary Biology Research Program, Institute of Biotechnology, Faculty of Biological and Environmental Sciences, University of Helsinki, 00014 Helsinki, Finland
| | - Kenneth D Birnbaum
- Center for Genomics and Systems Biology, Department of Biology, New York University, New York, NY 10003, USA;
| | - Bert De Rybel
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium;
- VIB Center for Plant Systems Biology, 9052 Ghent, Belgium
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8
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Hata T, Takada N, Hayakawa C, Kazama M, Uchikoba T, Tachikawa M, Matsuo M, Satoh S, Obokata J. De novo activated transcription of inserted foreign coding sequences is inheritable in the plant genome. PLoS One 2021; 16:e0252674. [PMID: 34111139 PMCID: PMC8191969 DOI: 10.1371/journal.pone.0252674] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2020] [Accepted: 05/19/2021] [Indexed: 01/16/2023] Open
Abstract
The manner in which inserted foreign coding sequences become transcriptionally activated and fixed in the plant genome is poorly understood. To examine such processes of gene evolution, we performed an artificial evolutionary experiment in Arabidopsis thaliana. As a model of gene-birth events, we introduced a promoterless coding sequence of the firefly luciferase (LUC) gene and established 386 T2-generation transgenic lines. Among them, we determined the individual LUC insertion loci in 76 lines and found that one-third of them were transcribed de novo even in the intergenic or inherently unexpressed regions. In the transcribed lines, transcription-related chromatin marks were detected across the newly activated transcribed regions. These results agreed with our previous findings in A. thaliana cultured cells under a similar experimental scheme. A comparison of the results of the T2-plant and cultured cell experiments revealed that the de novo-activated transcription concomitant with local chromatin remodelling was inheritable. During one-generation inheritance, it seems likely that the transcription activities of the LUC inserts trapped by the endogenous genes/transcripts became stronger, while those of de novo transcription in the intergenic/untranscribed regions became weaker. These findings may offer a clue for the elucidation of the mechanism by which inserted foreign coding sequences become transcriptionally activated and fixed in the plant genome.
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Affiliation(s)
- Takayuki Hata
- Graduate School of Life and Environfmental Sciences, Kyoto Prefectural University, Kyoto-shi, Kyoto, Japan
- Faculty of Agriculture, Setsunan University, Hirakata-shi, Osaka, Japan
| | - Naoto Takada
- Graduate School of Life and Environfmental Sciences, Kyoto Prefectural University, Kyoto-shi, Kyoto, Japan
| | - Chihiro Hayakawa
- Graduate School of Life and Environfmental Sciences, Kyoto Prefectural University, Kyoto-shi, Kyoto, Japan
| | - Mei Kazama
- Graduate School of Life and Environfmental Sciences, Kyoto Prefectural University, Kyoto-shi, Kyoto, Japan
| | - Tomohiro Uchikoba
- Faculty of Life and Environmental Sciences, Kyoto Prefectural University, Kyoto-shi, Kyoto, Japan
| | - Makoto Tachikawa
- Graduate School of Life and Environfmental Sciences, Kyoto Prefectural University, Kyoto-shi, Kyoto, Japan
| | - Mitsuhiro Matsuo
- Faculty of Agriculture, Setsunan University, Hirakata-shi, Osaka, Japan
| | - Soichirou Satoh
- Graduate School of Life and Environfmental Sciences, Kyoto Prefectural University, Kyoto-shi, Kyoto, Japan
- Faculty of Life and Environmental Sciences, Kyoto Prefectural University, Kyoto-shi, Kyoto, Japan
| | - Junichi Obokata
- Faculty of Agriculture, Setsunan University, Hirakata-shi, Osaka, Japan
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Antoniadi I, Skalický V, Sun G, Ma W, Galbraith DW, Novák O, Ljung K. Fluorescence activated cell sorting-A selective tool for plant cell isolation and analysis. Cytometry A 2021; 101:725-736. [PMID: 34028996 DOI: 10.1002/cyto.a.24461] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2021] [Revised: 04/27/2021] [Accepted: 05/03/2021] [Indexed: 12/13/2022]
Abstract
Instrumentation for flow cytometry and sorting is designed around the assumption that samples are single-cell suspensions. However, with few exceptions, higher plants comprise complex multicellular tissues and organs, in which the individual cells are held together by shared cell walls. Single-cell suspensions can be obtained through digestion of the cells walls and release of the so-called protoplasts (plants without their cell wall). Here we describe best practices for protoplast preparation, and for analysis through flow cytometry and cell sorting. Finally, the numerous downstream applications involving sorted protoplasts are discussed.
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Affiliation(s)
- Ioanna Antoniadi
- Umeå Plant Science Center, Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences, Umeå, Sweden
| | - Vladimír Skalický
- Laboratory of Growth Regulators, Institute of Experimental Botany, The Czech Academy of Sciences and Faculty of Science, Palacký University, Olomouc, Czech Republic
| | - Guiling Sun
- School of Life Sciences, Henan University, Institute of Plant Stress Biology, Kaifeng, China
| | - Wen Ma
- School of Life Sciences, Henan University, Institute of Plant Stress Biology, Kaifeng, China
| | - David W Galbraith
- Department of Biomedical Engineering, University of Arizona, School of Plant Sciences, BIO5 Institute, Arizona Cancer Center, Tucson, Arizona, USA.,School of Life Sciences, Henan University, Institute of Plant Stress Biology, Kaifeng, China
| | - Ondřej Novák
- Umeå Plant Science Center, Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences, Umeå, Sweden.,Laboratory of Growth Regulators, Institute of Experimental Botany, The Czech Academy of Sciences and Faculty of Science, Palacký University, Olomouc, Czech Republic
| | - Karin Ljung
- Umeå Plant Science Center, Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences, Umeå, Sweden
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Shi D, Jouannet V, Agustí J, Kaul V, Levitsky V, Sanchez P, Mironova VV, Greb T. Tissue-specific transcriptome profiling of the Arabidopsis inflorescence stem reveals local cellular signatures. THE PLANT CELL 2021; 33:200-223. [PMID: 33582756 PMCID: PMC8136906 DOI: 10.1093/plcell/koaa019] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/05/2020] [Accepted: 11/02/2020] [Indexed: 05/06/2023]
Abstract
Genome-wide gene expression maps with a high spatial resolution have substantially accelerated plant molecular science. However, the number of characterized tissues and growth stages is still small due to the limited accessibility of most tissues for protoplast isolation. Here, we provide gene expression profiles of the mature inflorescence stem of Arabidopsis thaliana covering a comprehensive set of distinct tissues. By combining fluorescence-activated nucleus sorting and laser-capture microdissection with next-generation RNA sequencing, we characterized the transcriptomes of xylem vessels, fibers, the proximal and distal cambium, phloem, phloem cap, pith, starch sheath, and epidermis cells. Our analyses classified more than 15,000 genes as being differentially expressed among different stem tissues and revealed known and novel tissue-specific cellular signatures. By determining overrepresented transcription factor binding regions in the promoters of differentially expressed genes, we identified candidate tissue-specific transcriptional regulators. Our datasets predict the expression profiles of an exceptional number of genes and allow hypotheses to be generated about the spatial organization of physiological processes. Moreover, we demonstrate that information about gene expression in a broad range of mature plant tissues can be established at high spatial resolution by nuclear mRNA profiling. Tissue-specific gene expression values can be accessed online at https://arabidopsis-stem.cos.uni-heidelberg.de/.
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Affiliation(s)
- Dongbo Shi
- Department of Developmental Physiology, Centre for Organismal Studies (COS), Heidelberg University, Im Neuenheimer Feld 230, 69120 Heidelberg, Germany
- Japan Science and Technology Agency (JST), Saitama, Kawaguchi, Japan
| | - Virginie Jouannet
- Department of Developmental Physiology, Centre for Organismal Studies (COS), Heidelberg University, Im Neuenheimer Feld 230, 69120 Heidelberg, Germany
| | - Javier Agustí
- Gregor Mendel Institute (GMI), Austrian Academy of Sciences, Vienna Biocenter (VBC), Dr. Bohr-Gasse 3, 1030 Vienna, Austria
- Instituto de Biología Molecular y Celular de Plantas (IBMCP), Universitat Politècnica de València (UPV)-Consejo Superior de Investigaciones Científicas (CSIC), C/Enginyer Fausto Elio S/N. 46011 Valencia, Spain
| | - Verena Kaul
- Department of Developmental Physiology, Centre for Organismal Studies (COS), Heidelberg University, Im Neuenheimer Feld 230, 69120 Heidelberg, Germany
| | - Victor Levitsky
- Faculty of Natural Sciences, Novosibirsk State University, Novosibirsk, 630090, Russia
- Department of Systems Biology, Institute of Cytology and Genetics, Siberian Branch, Russian Academy of Sciences, Novosibirsk, 630090, Russia
| | - Pablo Sanchez
- Gregor Mendel Institute (GMI), Austrian Academy of Sciences, Vienna Biocenter (VBC), Dr. Bohr-Gasse 3, 1030 Vienna, Austria
| | - Victoria V Mironova
- Faculty of Natural Sciences, Novosibirsk State University, Novosibirsk, 630090, Russia
- Department of Systems Biology, Institute of Cytology and Genetics, Siberian Branch, Russian Academy of Sciences, Novosibirsk, 630090, Russia
- Department of Plant Systems Physiology, Institute for Water and Wetland Research, Radboud University, Heyendaalseweg 135, 6525 AJ Nijmegen, The Netherlands
| | - Thomas Greb
- Department of Developmental Physiology, Centre for Organismal Studies (COS), Heidelberg University, Im Neuenheimer Feld 230, 69120 Heidelberg, Germany
- Author for correspondence:
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Zhang M, Xu X, Zheng Y, Zhang Y, Deng X, Luo S, Wu Q, Xu J, Zhang S. Expression of a plastid-localized sugar transporter in the suspensor is critical to embryogenesis. PLANT PHYSIOLOGY 2021; 185:1021-1038. [PMID: 33793862 PMCID: PMC8133565 DOI: 10.1093/plphys/kiaa084] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/14/2020] [Accepted: 11/29/2020] [Indexed: 05/05/2023]
Abstract
Plant growth and development rely on sugar transport between source and sink cells and between different organelles. The plastid-localized sugar transporter GLUCOSE-6-PHOSPHATE TRANSLOCATER1 (GPT1) is an essential gene in Arabidopsis (Arabidopsis thaliana). Using a partially rescued gpt1 mutant and cell-specific RNAi suppression of GPT1, we demonstrated that GPT1 is essential to the function of the embryo suspensor and the development of the embryo. GPT1 showed a dynamic expression/accumulation pattern during embryogenesis. Inhibition of GPT1 accumulation via RNAi using a suspensor-specific promoter resulted in embryos and seedlings with defects similar to auxin mutants. Loss of function of GPT1 in the suspensor also led to abnormal/ectopic cell division in the lower part of the suspensor, which gave rise to an ectopic embryo, resulting in twin embryos in some seeds. Furthermore, loss of function of GPT1 resulted in vacuolar localization of PIN-FORMED1 (PIN1) and altered DR5 auxin activity. Proper localization of PIN1 on the plasma membrane is essential to polar auxin transport and distribution, a key determinant of pattern formation during embryogenesis. Our findings suggest that the function of GPT1 in the embryo suspensor is linked to sugar and/or hormone distribution between the embryo proper and the maternal tissues, and is important for maintenance of suspensor identity and function during embryogenesis.
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Affiliation(s)
- Mengmeng Zhang
- College of Plant Protection, The Key Laboratory of Plant Immunity, Nanjing Agriculture University, Nanjing 210095, China
- State Key Laboratory of Plant Physiology and Biochemistry, College of Life Sciences, Zhejiang University, Hangzhou 310058, China
| | - Xuwen Xu
- State Key Laboratory of Plant Physiology and Biochemistry, College of Life Sciences, Zhejiang University, Hangzhou 310058, China
| | - Yueping Zheng
- State Key Laboratory of Plant Physiology and Biochemistry, College of Life Sciences, Zhejiang University, Hangzhou 310058, China
| | - Yan Zhang
- State Key Laboratory of Plant Physiology and Biochemistry, College of Life Sciences, Zhejiang University, Hangzhou 310058, China
| | - Xiangxiong Deng
- State Key Laboratory of Plant Physiology and Biochemistry, College of Life Sciences, Zhejiang University, Hangzhou 310058, China
| | - Suan Luo
- College of Plant Protection, The Key Laboratory of Plant Immunity, Nanjing Agriculture University, Nanjing 210095, China
| | - Qiuping Wu
- College of Plant Protection, The Key Laboratory of Plant Immunity, Nanjing Agriculture University, Nanjing 210095, China
| | - Juan Xu
- State Key Laboratory of Plant Physiology and Biochemistry, College of Life Sciences, Zhejiang University, Hangzhou 310058, China
| | - Shuqun Zhang
- Division of Biochemistry, University of Missouri, Columbia, MO 65211, USA
- Author for communication:
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12
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Do Plasmodesmata Play a Prominent Role in Regulation of Auxin-Dependent Genes at Early Stages of Embryogenesis? Cells 2021; 10:cells10040733. [PMID: 33810252 PMCID: PMC8066550 DOI: 10.3390/cells10040733] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2021] [Revised: 03/21/2021] [Accepted: 03/24/2021] [Indexed: 01/24/2023] Open
Abstract
Plasmodesmata form intercellular channels which ensure the transport of various molecules during embryogenesis and postembryonic growth. However, high permeability of plasmodesmata may interfere with the establishment of auxin maxima, which are required for cellular patterning and the development of distinct tissues. Therefore, diffusion through plasmodesmata is not always desirable and the symplastic continuum must be broken up to induce or accomplish some developmental processes. Many data show the role of auxin maxima in the regulation of auxin-responsive genes and the establishment of various cellular patterns. However, still little is known whether and how these maxima are formed in the embryo proper before 16-cell stage, that is, when there is still a nonpolar distribution of auxin efflux carriers. In this work, we focused on auxin-dependent regulation of plasmodesmata function, which may provide rapid and transient changes of their permeability, and thus take part in the regulation of gene expression.
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13
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Miya M, Yoshikawa T, Sato Y, Itoh JI. Genome-wide analysis of spatiotemporal expression patterns during rice leaf development. BMC Genomics 2021; 22:169. [PMID: 33750294 PMCID: PMC7941727 DOI: 10.1186/s12864-021-07494-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2020] [Accepted: 02/28/2021] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Rice leaves consist of three distinct regions along a proximal-distal axis, namely the leaf blade, sheath, and blade-sheath boundary region. Each region has a unique morphology and function, but the genetic programs underlying the development of each region are poorly understood. To fully elucidate rice leaf development and discover genes with unique functions in rice and grasses, it is crucial to explore genome-wide transcriptional profiles during the development of the three regions. RESULTS In this study, we performed microarray analysis to profile the spatial and temporal patterns of gene expression in the rice leaf using dissected parts of leaves sampled in broad developmental stages. The dynamics in each region revealed that the transcriptomes changed dramatically throughout the progress of tissue differentiation, and those of the leaf blade and sheath differed greatly at the mature stage. Cluster analysis of expression patterns among leaf parts revealed groups of genes that may be involved in specific biological processes related to rice leaf development. Moreover, we found novel genes potentially involved in rice leaf development using a combination of transcriptome data and in situ hybridization, and analyzed their spatial expression patterns at high resolution. We successfully identified multiple genes that exhibit localized expression in tissues characteristic of rice or grass leaves. CONCLUSIONS Although the genetic mechanisms of leaf development have been elucidated in several eudicots, direct application of that information to rice and grasses is not appropriate due to the morphological and developmental differences between them. Our analysis provides not only insights into the development of rice leaves but also expression profiles that serve as a valuable resource for gene discovery. The genes and gene clusters identified in this study may facilitate future research on the unique developmental mechanisms of rice leaves.
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Affiliation(s)
- Masayuki Miya
- Graduate School of Agricultural and Life Sciences, University of Tokyo, Tokyo, 113-8657, Japan
| | - Takanori Yoshikawa
- Graduate School of Agriculture, Kyoto University, Kyoto, 606-8502, Japan
| | - Yutaka Sato
- Institute of Crop Science, National Agriculture and Food Research Organization (NARO), Tsukuba, 305-8518, Japan
| | - Jun-Ichi Itoh
- Graduate School of Agricultural and Life Sciences, University of Tokyo, Tokyo, 113-8657, Japan.
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14
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Slane D, Berendzen KW, Witthöft J, Jürgens G. Transcriptomic Profiling of the Arabidopsis Embryonic Epidermis Using FANS in Combination with RNAseq. Methods Mol Biol 2021; 2122:151-164. [PMID: 31975302 DOI: 10.1007/978-1-0716-0342-0_12] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/01/2023]
Abstract
The fundamental mechanisms of cell identity and tissue establishment are important already from the very beginning of a plant's life and reiterate later during development. In order to unravel and understand the underlying mechanisms to generate differences that in turn lead to cell or tissue types, plant cells have to be separated and their transcriptional setup analyzed. We have previously demonstrated that fluorescence-activated nuclear sorting (FANS) is a powerful tool to generate nuclear transcriptomic profiles of the most inaccessible embryonic tissues. In this protocol, we extend this effort to combine FANS with next generation RNA sequencing (RNA-seq) to achieve early embryonic transcriptomes of Arabidopsis epidermis precursor tissue (protoderm) and the inner tissue counterpart.
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Affiliation(s)
- Daniel Slane
- Department of Cell Biology, Max Planck Institute for Developmental Biology, Tübingen, Germany
| | - Kenneth W Berendzen
- Center for Plant Molecular Biology, University of Tübingen, Tübingen, Germany
| | - Janika Witthöft
- Department of Cell Biology, Max Planck Institute for Developmental Biology, Tübingen, Germany
| | - Gerd Jürgens
- Department of Cell Biology, Max Planck Institute for Developmental Biology, Tübingen, Germany.
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15
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Armenta-Medina A, Gillmor CS, Gao P, Mora-Macias J, Kochian LV, Xiang D, Datla R. Developmental and genomic architecture of plant embryogenesis: from model plant to crops. PLANT COMMUNICATIONS 2021; 2:100136. [PMID: 33511346 PMCID: PMC7816075 DOI: 10.1016/j.xplc.2020.100136] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/12/2020] [Revised: 12/05/2020] [Accepted: 12/11/2020] [Indexed: 05/08/2023]
Abstract
Embryonic development represents an important reproductive phase of sexually reproducing plant species. The fusion of egg and sperm produces the plant zygote, a totipotent cell that, through cell division and cell identity specification in early embryogenesis, establishes the major cell lineages and tissues of the adult plant. The subsequent morphogenesis phase produces the full-sized embryo, while the late embryogenesis maturation process prepares the seed for dormancy and subsequent germination, ensuring continuation of the plant life cycle. In this review on embryogenesis, we compare the model eudicot Arabidopsis thaliana with monocot crops, focusing on genome activation, paternal and maternal regulation of early zygote development, and key organizers of patterning, such as auxin and WOX transcription factors. While the early stages of embryo development are apparently conserved among plant species, embryo maturation programs have diversified between eudicots and monocots. This diversification in crop species reflects the likely effects of domestication on seed quality traits that are determined during embryo maturation, and also assures seed germination in different environmental conditions. This review describes the most important features of embryonic development in plants, and the scope and applications of genomics in plant embryo studies.
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Affiliation(s)
- Alma Armenta-Medina
- Global Institute for Food Security, University of Saskatchewan, Saskatoon, SK S7N 4J8, Canada
- Laboratorio Nacional de Genómica para la Biodiversidad (Langebio), Unidad de Genómica Avanzada, Centro de Investigación y Estudios Avanzados del IPN (CINVESTAV-IPN), Irapuato, Guanajuato, México
| | - C. Stewart Gillmor
- Laboratorio Nacional de Genómica para la Biodiversidad (Langebio), Unidad de Genómica Avanzada, Centro de Investigación y Estudios Avanzados del IPN (CINVESTAV-IPN), Irapuato, Guanajuato, México
| | - Peng Gao
- Global Institute for Food Security, University of Saskatchewan, Saskatoon, SK S7N 4J8, Canada
| | - Javier Mora-Macias
- Global Institute for Food Security, University of Saskatchewan, Saskatoon, SK S7N 4J8, Canada
| | - Leon V. Kochian
- Global Institute for Food Security, University of Saskatchewan, Saskatoon, SK S7N 4J8, Canada
| | - Daoquan Xiang
- National Research Council Canada, 110 Gymnasium Place, Saskatoon, SK S7N 0W9, Canada
| | - Raju Datla
- Global Institute for Food Security, University of Saskatchewan, Saskatoon, SK S7N 4J8, Canada
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16
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Abstract
Flow cytometry and sorting represents a valuable and mature experimental platform for the analysis of cellular populations. Applications involving higher plants started to emerge around 40 years ago and are now widely employed both to provide unique information regarding basic and applied questions in the biosciences and to advance agricultural productivity in practical ways. Further development of this platform is being actively pursued, and this promises additional progress in our understanding of the interactions of cells within complex tissues and organs. Higher plants offer unique challenges in terms of flow cytometric analysis, first since their organs and tissues are, almost without exception, three-dimensional assemblies of different cell types held together by tough cell walls, and, second, because individual plant cells are generally larger than those of mammals.This chapter, which updates work last reviewed in 2014 [Galbraith DW (2014) Flow cytometry and sorting in Arabidopsis. In: Sanchez Serrano JJ, Salinas J (eds) Arabidopsis Protocols, 3rd ed. Methods in molecular biology, vol 1062. Humana Press, Totowa, pp 509-537], describes the application of techniques of flow cytometry and sorting to the model plant species Arabidopsis thaliana, in particular emphasizing (a) fluorescence labeling in vivo of specific cell types and of subcellular components, (b) analysis using both conventional cytometers and spectral analyzers, (c) fluorescence-activated sorting of protoplasts and nuclei, and (d) transcriptome analyses using sorted protoplasts and nuclei, focusing on population analyses at the level of single protoplasts and nuclei. Since this is an update, details of new experimental methods are emphasized.
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Affiliation(s)
- David W Galbraith
- University of Arizona, School of Plant Sciences and Bio5 Institute, Tucson, AZ, USA. .,Henan University, Institute of Plant Stress Biology, School of Life Sciences, Kaifeng, China.
| | - Guiling Sun
- Henan University, Institute of Plant Stress Biology, School of Life Sciences, Kaifeng, China
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17
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Harnvanichvech Y, Gorelova V, Sprakel J, Weijers D. The Arabidopsis embryo as a quantifiable model for studying pattern formation. QUANTITATIVE PLANT BIOLOGY 2021; 2:e3. [PMID: 37077211 PMCID: PMC10095805 DOI: 10.1017/qpb.2021.3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/02/2020] [Revised: 02/15/2021] [Accepted: 02/21/2021] [Indexed: 05/03/2023]
Abstract
Phenotypic diversity of flowering plants stems from common basic features of the plant body pattern with well-defined body axes, organs and tissue organisation. Cell division and cell specification are the two processes that underlie the formation of a body pattern. As plant cells are encased into their cellulosic walls, directional cell division through precise positioning of division plane is crucial for shaping plant morphology. Since many plant cells are pluripotent, their fate establishment is influenced by their cellular environment through cell-to-cell signaling. Recent studies show that apart from biochemical regulation, these two processes are also influenced by cell and tissue morphology and operate under mechanical control. Finding a proper model system that allows dissecting the relationship between these aspects is the key to our understanding of pattern establishment. In this review, we present the Arabidopsis embryo as a simple, yet comprehensive model of pattern formation compatible with high-throughput quantitative assays.
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Affiliation(s)
- Yosapol Harnvanichvech
- Physical Chemistry and Soft Matter, Wageningen University, Wageningen, The Netherlands
- Laboratory of Biochemistry, Wageningen University, Wageningen, The Netherlands
| | - Vera Gorelova
- Laboratory of Biochemistry, Wageningen University, Wageningen, The Netherlands
| | - Joris Sprakel
- Physical Chemistry and Soft Matter, Wageningen University, Wageningen, The Netherlands
| | - Dolf Weijers
- Laboratory of Biochemistry, Wageningen University, Wageningen, The Netherlands
- Author for correspondence: Dolf Weijers, E-mail:
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18
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Slane D, Lee CH, Kolb M, Dent C, Miao Y, Franz-Wachtel M, Lau S, Maček B, Balasubramanian S, Bayer M, Jürgens G. The integral spliceosomal component CWC15 is required for development in Arabidopsis. Sci Rep 2020; 10:13336. [PMID: 32770129 PMCID: PMC7415139 DOI: 10.1038/s41598-020-70324-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2019] [Accepted: 07/27/2020] [Indexed: 01/01/2023] Open
Abstract
Efficient mRNA splicing is a prerequisite for protein biosynthesis and the eukaryotic splicing machinery is evolutionarily conserved among species of various phyla. At its catalytic core resides the activated splicing complex Bact consisting of the three small nuclear ribonucleoprotein complexes (snRNPs) U2, U5 and U6 and the so-called NineTeen complex (NTC) which is important for spliceosomal activation. CWC15 is an integral part of the NTC in humans and it is associated with the NTC in other species. Here we show the ubiquitous expression and developmental importance of the Arabidopsis ortholog of yeast CWC15. CWC15 associates with core components of the Arabidopsis NTC and its loss leads to inefficient splicing. Consistent with the central role of CWC15 in RNA splicing, cwc15 mutants are embryo lethal and additionally display strong defects in the female haploid phase. Interestingly, the haploid male gametophyte or pollen in Arabidopsis, on the other hand, can cope without functional CWC15, suggesting that developing pollen might be more tolerant to CWC15-mediated defects in splicing than either embryo or female gametophyte.
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Affiliation(s)
- Daniel Slane
- Max Planck Institute for Developmental Biology, Cell Biology, 72076, Tübingen, Germany
| | - Cameron H Lee
- Howard Hughes Medical Institute, Division of Basic Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA, 98109, USA
| | - Martina Kolb
- Max Planck Institute for Developmental Biology, Cell Biology, 72076, Tübingen, Germany
| | - Craig Dent
- School of Biological Sciences, Monash University, Clayton Campus, Clayton, VIC, 3800, Australia
| | - Yingjing Miao
- Max Planck Institute for Developmental Biology, Cell Biology, 72076, Tübingen, Germany
| | - Mirita Franz-Wachtel
- Proteome Center Tübingen, University of Tübingen, Auf der Morgenstelle 15, 72076, Tübingen, Germany
| | - Steffen Lau
- Max Planck Institute for Developmental Biology, Cell Biology, 72076, Tübingen, Germany
| | - Boris Maček
- Proteome Center Tübingen, University of Tübingen, Auf der Morgenstelle 15, 72076, Tübingen, Germany
| | | | - Martin Bayer
- Max Planck Institute for Developmental Biology, Cell Biology, 72076, Tübingen, Germany
| | - Gerd Jürgens
- Max Planck Institute for Developmental Biology, Cell Biology, 72076, Tübingen, Germany.
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19
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Ohnishi Y, Kawashima T. Plasmogamic Paternal Contributions to Early Zygotic Development in Flowering Plants. FRONTIERS IN PLANT SCIENCE 2020; 11:871. [PMID: 32636867 PMCID: PMC7317025 DOI: 10.3389/fpls.2020.00871] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/08/2020] [Accepted: 05/28/2020] [Indexed: 06/01/2023]
Abstract
Flowering plant zygotes possess complete developmental potency, and the mixture of male and female genetic and cytosolic materials in the zygote is a trigger to initiate embryo development. Plasmogamy, the fusion of the gamete cytoplasms, facilitates the cellular dynamics of the zygote. In the last decade, mutant analyses, live cell imaging-based observations, and direct observations of fertilized egg cells by in vitro fusion of isolated gametes have accelerated our understanding of the post-plasmogamic events in flowering plants including cell wall formation, gamete nuclear migration and fusion, and zygotic cell elongation and asymmetric division. Especially, it has become more evident that paternal parent-of-origin effects, via sperm cytoplasm contents, not only control canonical early zygotic development, but also activate a biparental signaling pathway critical for cell fate determination after the first cell division. Here, we summarize the plasmogamic paternal contributions via the entry of sperm contents during/after fertilization in flowering plants.
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Affiliation(s)
- Yukinosuke Ohnishi
- Kihara Institute for Biological Research, Yokohama City University, Yokohama, Japan
- Department of Plant and Soil Sciences, University of Kentucky, Lexington, KY, United States
| | - Tomokazu Kawashima
- Department of Plant and Soil Sciences, University of Kentucky, Lexington, KY, United States
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20
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Jacob D, Brian J. The short and intricate life of the suspensor. PHYSIOLOGIA PLANTARUM 2020; 169:110-121. [PMID: 31808953 DOI: 10.1111/ppl.13057] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/21/2019] [Revised: 11/04/2019] [Accepted: 12/04/2019] [Indexed: 06/10/2023]
Abstract
The suspensor is a short-lived tissue critical for proper embryonic development in many higher plants. While the tissue was initially thought to simply suspend the embryo in the endosperm, it has been found through decades of research that it serves multiple important purposes. The suspensor has been found to be vital for proper embryo patterning and numerous studies have been undertaken into the complex transcriptional cross-talk between the suspensor and the embryo proper. Indeed, many suspensor mutants also display abnormalities in the embryo. The suspensor's role as a nutrient conduit has been shown using ultrastructural and histochemical techniques. Biochemical approaches have found that the suspensor is a centre of early embryonic hormone production in several species. The suspensor has also been frequently used as a model for programmed cell death as it shows signs of termination almost immediately upon developing. This review covers the essential functions of the suspensor throughout its short existence from multiple disciplines including structural, genetic and biochemical perspectives.
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Affiliation(s)
- Downs Jacob
- Faculty of Science, University of Sydney, Sydney, NSW, 2006, Australia
| | - Jones Brian
- Faculty of Science, University of Sydney, Sydney, NSW, 2006, Australia
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21
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Smit ME, Llavata-Peris CI, Roosjen M, van Beijnum H, Novikova D, Levitsky V, Sevilem I, Roszak P, Slane D, Jürgens G, Mironova V, Brady SM, Weijers D. Specification and regulation of vascular tissue identity in the Arabidopsis embryo. Development 2020; 147:dev186130. [PMID: 32198154 DOI: 10.1242/dev.186130] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2019] [Accepted: 03/05/2020] [Indexed: 12/30/2022]
Abstract
Development of plant vascular tissues involves tissue identity specification, growth, pattern formation and cell-type differentiation. Although later developmental steps are understood in some detail, it is still largely unknown how the tissue is initially specified. We used the early Arabidopsis embryo as a simple model to study this process. Using a large collection of marker genes, we found that vascular identity was specified in the 16-cell embryo. After a transient precursor state, however, there was no persistent uniform tissue identity. Auxin is intimately connected to vascular tissue development. We found that, although an AUXIN RESPONSE FACTOR5/MONOPTEROS (ARF5/MP)-dependent auxin response was required, it was not sufficient for tissue specification. We therefore used a large-scale enhanced yeast one-hybrid assay to identify potential regulators of vascular identity. Network and functional analysis of candidate regulators suggest that vascular identity is under robust, complex control. We found that one candidate regulator, the G-class bZIP transcription factor GBF2, can modulate vascular gene expression by tuning MP output through direct interaction. Our work uncovers components of a gene regulatory network that controls the initial specification of vascular tissue identity.
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Affiliation(s)
- Margot E Smit
- Laboratory of Biochemistry, Wageningen University, Stippeneng 4, Wageningen, 6708WE, The Netherlands
| | - Cristina I Llavata-Peris
- Laboratory of Biochemistry, Wageningen University, Stippeneng 4, Wageningen, 6708WE, The Netherlands
| | - Mark Roosjen
- Laboratory of Biochemistry, Wageningen University, Stippeneng 4, Wageningen, 6708WE, The Netherlands
| | - Henriette van Beijnum
- Laboratory of Biochemistry, Wageningen University, Stippeneng 4, Wageningen, 6708WE, The Netherlands
| | - Daria Novikova
- Laboratory of Biochemistry, Wageningen University, Stippeneng 4, Wageningen, 6708WE, The Netherlands
- Novosibirsk State University, LCT&EB, Novosibirsk, 630090, Russia
- Institute of Cytology and Genetics, Novosibirsk, 630090, Russia
| | - Victor Levitsky
- Novosibirsk State University, LCT&EB, Novosibirsk, 630090, Russia
- Institute of Cytology and Genetics, Novosibirsk, 630090, Russia
| | - Iris Sevilem
- Institute of Biotechnology, HiLIFE/Organismal and Evolurionary Biology Research Programma, Faculty of Biological and Environmental Sciences, Viikki Plant Science Centre, University of Helsinki, Helsinki, 00014, Finland
| | - Pawel Roszak
- Institute of Biotechnology, HiLIFE/Organismal and Evolurionary Biology Research Programma, Faculty of Biological and Environmental Sciences, Viikki Plant Science Centre, University of Helsinki, Helsinki, 00014, Finland
- Sainsbury Laboratory, University of Cambridge, Cambridge, CB2 1LR, UK
| | - Daniel Slane
- Max Planck Institute for Developmental Biology, Cell Biology, Tübingen, 72076, Germany
| | - Gerd Jürgens
- Max Planck Institute for Developmental Biology, Cell Biology, Tübingen, 72076, Germany
| | - Victoria Mironova
- Novosibirsk State University, LCT&EB, Novosibirsk, 630090, Russia
- Institute of Cytology and Genetics, Novosibirsk, 630090, Russia
| | - Siobhan M Brady
- Department of Plant Biology and Genome Center, University of California Davis, Davis, CA 95616, USA
| | - Dolf Weijers
- Laboratory of Biochemistry, Wageningen University, Stippeneng 4, Wageningen, 6708WE, The Netherlands
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22
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McFaline-Figueroa JL, Trapnell C, Cuperus JT. The promise of single-cell genomics in plants. CURRENT OPINION IN PLANT BIOLOGY 2020; 54:114-121. [PMID: 32388018 PMCID: PMC7971421 DOI: 10.1016/j.pbi.2020.04.002] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/06/2019] [Revised: 03/01/2020] [Accepted: 04/03/2020] [Indexed: 05/20/2023]
Abstract
Single-cell genomic approaches have the potential to revolutionize the study of plant systems. Here, we highlight newly developed techniques to analyze transcriptomes at single-cell resolution. We focus on the rigorous standards necessary to generate and compare these data sets introducing analysis methods that can be applied to interpret their results. Lastly, we discuss the inherent limitations of single-cell studies and address future directions for plant single-cell genomics.
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Affiliation(s)
| | - Cole Trapnell
- Department of Genome Sciences, University of Washington, Seattle, WA, USA; Brotman Baty Institute for Precision Medicine, Seattle, WA, USA; Allen Discovery Center for Cell Lineage Tracing, Seattle, WA, USA
| | - Josh T Cuperus
- Department of Genome Sciences, University of Washington, Seattle, WA, USA.
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23
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Cell lineage-specific transcriptome analysis for interpreting cell fate specification of proembryos. Nat Commun 2020; 11:1366. [PMID: 32170064 PMCID: PMC7070050 DOI: 10.1038/s41467-020-15189-w] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2019] [Accepted: 02/24/2020] [Indexed: 12/17/2022] Open
Abstract
In Arabidopsis, a zygote undergoes asymmetrical cell division that establishes the first two distinct cell types of early proembryos, apical and basal cells. However, the genome-wide transcriptional activities that guide divergence of apical and basal cell development remain unknown. Here, we present a comprehensive transcriptome analysis of apical and basal cell lineages, uncovering distinct molecular pathways during cell lineage specification. Selective deletion of inherited transcripts and specific de novo transcription contribute to the establishment of cell lineage-specific pathways for cell fate specification. Embryo-related pathways have been specifically activated in apical cell lineage since 1-cell embryo stage, but quick transcriptome remodeling toward suspensor-specific pathways are found in basal cell lineage. Furthermore, long noncoding RNAs and alternative splicing isoforms may be involved in cell lineage specification. This work also provides a valuable lineage-specific transcriptome resource to elucidate the molecular pathways for divergence of apical and basal cell lineages at genome-wide scale. Asymmetric division of the Arabidopsis zygote produces apical and basal cells that mainly develop into embryo and suspensor, respectively. Here, Zhou et al. show that de novo transcription and selective RNA turnover establish distinct apical and basal transcriptomes as early as the 1-cell stage of embryo development.
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24
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Abstract
Transcriptomic studies have proven powerful and effective as a tool to study the molecular underpinnings of plant development. Still, it remains challenging to disentangle cell- or tissue-specific transcriptomes in complex structures like the plant seed. In particular, the embryo of flowering plants is embedded in the endosperm, a nurturing tissue, which, in turn, is enclosed by the maternal seed coat. Here, we describe laser-assisted microdissection (LAM) to isolate highly pure embryo tissue from whole seeds. This technique is applicable to virtually any plant seed, and we illustrate the use of LAM to isolate embryos from species of the Boechera and Solanum genera. LAM is a tool that will greatly help to increase the repertoires of tissue-specific transcriptomes, including those of embryos and parts thereof, in nonmodel plants.
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25
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Siles L, Eastmond P, Kurup S. Big data from small tissues: extraction of high-quality RNA for RNA-sequencing from different oilseed Brassica seed tissues during seed development. PLANT METHODS 2020; 16:80. [PMID: 32518582 PMCID: PMC7275424 DOI: 10.1186/s13007-020-00626-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/16/2020] [Accepted: 05/28/2020] [Indexed: 05/03/2023]
Abstract
BACKGROUND Obtaining high-quality RNA for gene expression analyses from different seed tissues is challenging due to the presence of various contaminants, such as polyphenols, polysaccharides and lipids which interfere with RNA extraction methods. At present, the available protocols for extracting RNA from seeds require high amounts of tissue and are mainly focused on extracting RNA from whole seeds. However, extracting RNA at the tissue level enables more detailed studies regarding tissue specific transcriptomes during seed development. RESULTS Seeds from heart stage embryo to mature developmental stages of Brassica napus and B. oleracea were sampled for isolation of the embryo, endosperm and seed coat tissues. Ovules and ovary wall tissue were also collected from pre-fertilized buds. Subsequent to testing several RNA extraction methods, modifications applied to E.Z.N.A. Plant RNA and Picopure RNA Isolation kit extraction methods resulted in RNA with high yield and quality. Furthermore, the use of polyvinylpolypyrrolidone for seed coats and endosperm at green stages resulted in high-quality RNA. As a result of the introduced modifications to established RNA extraction methods, the RNA from all the above-mentioned tissues presented clear 28S and 18S bands and high RIN values, ranging from 7.0 to 10.0. The protocols reported in this study are not only suitable for different and challenging seed tissue types, but also enable the extraction of high-quality RNA using only 2 to 3 mg of starting tissue. CONCLUSIONS Here, we present efficient, reproducible and reliable high-quality RNA extraction methods for diverse oilseed Brassica spp reproductive tissue types including pre-fertilization and developing seed tissues for diploid and polyploid species. The high-quality RNA obtained is suitable for RNA-Sequencing and subsequent gene expression analysis.
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Affiliation(s)
- Laura Siles
- Department of Plant Sciences, Rothamsted Research, Harpenden, Hertfordshire AL5 2JQ UK
| | - Peter Eastmond
- Department of Plant Sciences, Rothamsted Research, Harpenden, Hertfordshire AL5 2JQ UK
| | - Smita Kurup
- Department of Plant Sciences, Rothamsted Research, Harpenden, Hertfordshire AL5 2JQ UK
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26
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Palovaara J, Weijers D. Cell Type-Specific Transcriptomics in the Plant Embryo Using an Adapted INTACT Protocol. Methods Mol Biol 2020; 2122:141-150. [PMID: 31975301 DOI: 10.1007/978-1-0716-0342-0_11] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Cells differentiate from undifferentiated precursors in order to establish the tissues of vascular plants. The different cell types and stem cells are first specified in the early embryo. How cell type specification is instructed by transcriptional control on a genome-wide level is poorly understood. A major hurdle has been the technical challenge associated with obtaining cellular transcriptomes in this inaccessible tissue. Recently, we adapted a two-component genetic labeling system called INTACT to isolate nuclei and generate a microarray-based expression atlas of the cell types in the early Arabidopsis thaliana embryo. Here we present a step-by-step description of the adapted INTACT protocol, as well as the approach to generate transcriptomic profiles. This protocol has been adapted to account for using seeds with embryos of various developmental stages as a starting material, and the relatively few cell type-specific nuclei that can be isolated from embryos.
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Affiliation(s)
| | - Dolf Weijers
- Laboratory of Biochemistry, Wageningen University, Wageningen, The Netherlands
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Chen M, Bui AQ, Goldberg RB. Using Giant Scarlet Runner Bean (Phaseolus coccineus) Embryos to Dissect the Early Events in Plant Embryogenesis. Methods Mol Biol 2020; 2122:205-222. [PMID: 31975305 DOI: 10.1007/978-1-0716-0342-0_15] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
The giant embryo of the scarlet runner bean (Phaseolus coccineus) has been used historically to investigate the molecular and developmental processes that control the early events of plant embryo development. In more recent years, our laboratory has been using scarlet runner bean embryos to uncover the genes and regulatory events that control embryo proper and suspensor region differentiation shortly after fertilization. In this chapter we describe methods that we have developed to isolate scarlet runner bean embryos at the globular stage of development, and capture embryo proper and suspensor regions by either hand dissection or laser capture microdissection (LCM) for use in downstream genomic analysis. These methods are also applicable for use in investigating the early events of common bean (Phaseolus vulgaris) embryo development, a close relative of scarlet runner bean, which also has a giant embryo in addition to a sequenced genome.
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Affiliation(s)
- Min Chen
- Department of Molecular, Cell, and Developmental Biology, University of California, Los Angeles, CA, USA
| | - Anhthu Q Bui
- Department of Molecular, Cell, and Developmental Biology, University of California, Los Angeles, CA, USA.,Inviata Ltd., Research Triangle Park, Morrisville, NC, USA
| | - Robert B Goldberg
- Department of Molecular, Cell, and Developmental Biology, University of California, Los Angeles, CA, USA.
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Evolution, Initiation, and Diversity in Early Plant Embryogenesis. Dev Cell 2019; 50:533-543. [DOI: 10.1016/j.devcel.2019.07.011] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2019] [Revised: 06/07/2019] [Accepted: 07/07/2019] [Indexed: 11/22/2022]
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Constitutive signaling activity of a receptor-associated protein links fertilization with embryonic patterning in Arabidopsis thaliana. Proc Natl Acad Sci U S A 2019; 116:5795-5804. [PMID: 30833400 DOI: 10.1073/pnas.1815866116] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
In flowering plants, the asymmetrical division of the zygote is the first hallmark of apical-basal polarity of the embryo and is controlled by a MAP kinase pathway that includes the MAPKKK YODA (YDA). In Arabidopsis, YDA is activated by the membrane-associated pseudokinase SHORT SUSPENSOR (SSP) through an unusual parent-of-origin effect: SSP transcripts accumulate specifically in sperm cells but are translationally silent. Only after fertilization is SSP protein transiently produced in the zygote, presumably from paternally inherited transcripts. SSP is a recently diverged, Brassicaceae-specific member of the BRASSINOSTEROID SIGNALING KINASE (BSK) family. BSK proteins typically play broadly overlapping roles as receptor-associated signaling partners in various receptor kinase pathways involved in growth and innate immunity. This raises two questions: How did a protein with generic function involved in signal relay acquire the property of a signal-like patterning cue, and how is the early patterning process activated in plants outside the Brassicaceae family, where SSP orthologs are absent? Here, we show that Arabidopsis BSK1 and BSK2, two close paralogs of SSP that are conserved in flowering plants, are involved in several YDA-dependent signaling events, including embryogenesis. However, the contribution of SSP to YDA activation in the early embryo does not overlap with the contributions of BSK1 and BSK2. The loss of an intramolecular regulatory interaction enables SSP to constitutively activate the YDA signaling pathway, and thus initiates apical-basal patterning as soon as SSP protein is translated after fertilization and without the necessity of invoking canonical receptor activation.
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Zhou X, Shi C, Zhao P, Sun M. Isolation of living apical and basal cell lineages of early proembryos for transcriptome analysis. PLANT REPRODUCTION 2019; 32:105-111. [PMID: 30547251 DOI: 10.1007/s00497-018-00353-6] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/26/2018] [Accepted: 11/24/2018] [Indexed: 06/09/2023]
Abstract
Plant zygotes usually undergo asymmetrical cell division, giving rise to the formation of two daughter cells with distinct developmental cell fate. The small apical cell will develop into the major part of embryo proper, whereas the larger basal cell will divide to form a transient suspensor. Thus, the apical and basal cell lineages are an excellent model to study cell fate determination in relation to zygote polarity. However, the molecular mechanism underlying the differentiation of two distinct cell lineages is not yet understood, possibly due to the technique limitations. Previously, we have established a protocol for isolating apical cell and basal cell for cDNA library construction in tobacco. However, the method for isolating tiny Arabidopsis embryos has long been considered much more difficult. Here, we present a detailed protocol for isolating early Arabidopsis proembryos and separating apical and basal cell lineages of proembryos, which allow us to establish cell lineage-specific transcriptomes of early proembryos.
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Affiliation(s)
- Xuemei Zhou
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, 430072, China
| | - Ce Shi
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, 430072, China
| | - Peng Zhao
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, 430072, China.
| | - Mengxiang Sun
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, 430072, China.
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Gao P, Xiang D, Quilichini TD, Venglat P, Pandey PK, Wang E, Gillmor CS, Datla R. Gene expression atlas of embryo development in Arabidopsis. PLANT REPRODUCTION 2019; 32:93-104. [PMID: 30762127 DOI: 10.1007/s00497-019-00364-x] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/16/2018] [Accepted: 02/01/2019] [Indexed: 05/24/2023]
Abstract
Embryogenesis represents a critical phase in the life cycle of flowering plants. Here, we characterize transcriptome landscapes associated with key stages of embryogenesis by combining an optimized method for the isolation of developing Arabidopsis embryos with high-throughput RNA-seq. The resulting RNA-seq datasets identify distinct overlapping patterns of gene expression, as well as temporal shifts in gene activity across embryogenesis. Network analysis revealed stage-specific and multi-stage gene expression clusters and biological functions associated with key stages of embryo development. Methylation-related gene expression was associated with early- and middle-stage embryos, initiation of photosynthesis components with the late embryogenesis stage, and storage/energy-related protein activation with late and mature embryos. These results provide a comprehensive understanding of transcriptome programming in Arabidopsis embryogenesis and identify modules of gene expression corresponding to key stages of embryo development. This dataset and analysis are a unique resource to advance functional genetic analysis of embryo development in plants.
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Affiliation(s)
- Peng Gao
- Aquatic and Crop Resource Development, National Research Council Canada, 110 Gymnasium Place, Saskatoon, SK, S7N 0W9, Canada
- Global Institute for Food Security, University of Saskatchewan, Saskatoon, SK, S7N 4J8, Canada
| | - Daoquan Xiang
- Aquatic and Crop Resource Development, National Research Council Canada, 110 Gymnasium Place, Saskatoon, SK, S7N 0W9, Canada
| | - Teagen D Quilichini
- Aquatic and Crop Resource Development, National Research Council Canada, 110 Gymnasium Place, Saskatoon, SK, S7N 0W9, Canada
| | - Prakash Venglat
- Aquatic and Crop Resource Development, National Research Council Canada, 110 Gymnasium Place, Saskatoon, SK, S7N 0W9, Canada
- Department of Plant Sciences and Crop Development Centre, University of Saskatchewan, 51 Campus Drive, Saskatoon, SK, S7N 5A8, Canada
| | - Prashant K Pandey
- Aquatic and Crop Resource Development, National Research Council Canada, 110 Gymnasium Place, Saskatoon, SK, S7N 0W9, Canada
| | - Edwin Wang
- Center for Health Genomics and Informatics, University of Calgary Cumming School of Medicine, Calgary, AB, T2N 4N1, Canada
| | - C Stewart Gillmor
- Laboratorio Nacional de Genómica para la Biodiversidad (Langebio), Unidad de Genómica Avanzada, Centro de Investigación y de Estudios Avanzados del IPN (CINVESTAV-IPN), Irapuato, Guanajuato, México
| | - Raju Datla
- Aquatic and Crop Resource Development, National Research Council Canada, 110 Gymnasium Place, Saskatoon, SK, S7N 0W9, Canada.
- Global Institute for Food Security, University of Saskatchewan, Saskatoon, SK, S7N 4J8, Canada.
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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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Armenta-Medina A, Gillmor CS. Genetic, molecular and parent-of-origin regulation of early embryogenesis in flowering plants. Curr Top Dev Biol 2019; 131:497-543. [DOI: 10.1016/bs.ctdb.2018.11.008] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/05/2022]
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Albert E, Duboscq R, Latreille M, Santoni S, Beukers M, Bouchet JP, Bitton F, Gricourt J, Poncet C, Gautier V, Jiménez-Gómez JM, Rigaill G, Causse M. Allele-specific expression and genetic determinants of transcriptomic variations in response to mild water deficit in tomato. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2018; 96:635-650. [PMID: 30079488 DOI: 10.1111/tpj.14057] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/01/2018] [Revised: 07/31/2018] [Accepted: 08/02/2018] [Indexed: 06/08/2023]
Abstract
Characterizing the natural diversity of gene expression across environments is an important step in understanding how genotype-by-environment interactions shape phenotypes. Here, we analyzed the impact of water deficit onto gene expression levels in tomato at the genome-wide scale. We sequenced the transcriptome of growing leaves and fruit pericarps at cell expansion stage in a cherry and a large fruited accession and their F1 hybrid grown under two watering regimes. Gene expression levels were steadily affected by the genotype and the watering regime. Whereas phenotypes showed mostly additive inheritance, ~80% of the genes displayed non-additive inheritance. By comparing allele-specific expression (ASE) in the F1 hybrid to the allelic expression in both parental lines, respectively, 3005 genes in leaf and 2857 genes in fruit deviated from 1:1 ratio independently of the watering regime. Among these genes, ~55% were controlled by cis factors, ~25% by trans factors and ~20% by a combination of both types of factors. A total of 328 genes in leaf and 113 in fruit exhibited significant ASE-by-watering regime interaction, among which ~80% presented trans-by-watering regime interaction, suggesting a response to water deficit mediated through a majority of trans-acting loci in tomato. We cross-validated the expression levels of 274 transcripts in fruit and leaves of 124 recombinant inbred lines (RILs) and identified 163 expression quantitative trait loci (eQTLs) mostly confirming the divergences identified by ASE. Combining phenotypic and expression data, we observed a complex network of variation between genes encoding enzymes involved in the sugar metabolism.
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Affiliation(s)
- Elise Albert
- INRA, UR1052, Centre de Recherche PACA, Génétique et Amélioration des Fruits et Légumes, 67 Allée des Chênes, Domaine Saint Maurice, CS60094, Montfavet, 84143, France
| | - Renaud Duboscq
- INRA, UR1052, Centre de Recherche PACA, Génétique et Amélioration des Fruits et Légumes, 67 Allée des Chênes, Domaine Saint Maurice, CS60094, Montfavet, 84143, France
| | - Muriel Latreille
- INRA, UMR1334, Amélioration génétique et Adaptation des Plantes, Montpellier SupAgro-INRA-IRD-UMII, 2 Place Pierre Viala, Montpellier, 34060, France
| | - Sylvain Santoni
- INRA, UMR1334, Amélioration génétique et Adaptation des Plantes, Montpellier SupAgro-INRA-IRD-UMII, 2 Place Pierre Viala, Montpellier, 34060, France
| | - Matthieu Beukers
- INRA, UR1052, Centre de Recherche PACA, Génétique et Amélioration des Fruits et Légumes, 67 Allée des Chênes, Domaine Saint Maurice, CS60094, Montfavet, 84143, France
| | - Jean-Paul Bouchet
- INRA, UR1052, Centre de Recherche PACA, Génétique et Amélioration des Fruits et Légumes, 67 Allée des Chênes, Domaine Saint Maurice, CS60094, Montfavet, 84143, France
| | - Fréderique Bitton
- INRA, UR1052, Centre de Recherche PACA, Génétique et Amélioration des Fruits et Légumes, 67 Allée des Chênes, Domaine Saint Maurice, CS60094, Montfavet, 84143, France
| | - Justine Gricourt
- INRA, UR1052, Centre de Recherche PACA, Génétique et Amélioration des Fruits et Légumes, 67 Allée des Chênes, Domaine Saint Maurice, CS60094, Montfavet, 84143, France
| | - Charles Poncet
- INRA, UMR1095, Génétique Diversité et Ecophysiologie des Céréales, 5 Chemin de Beaulieu, Clermont-Ferrand, 63039, France
| | - Véronique Gautier
- INRA, UMR1095, Génétique Diversité et Ecophysiologie des Céréales, 5 Chemin de Beaulieu, Clermont-Ferrand, 63039, France
| | - José M Jiménez-Gómez
- INRA, UMR1318, Institut Jean-Pierre Bourgin, AgroParisTech-INRA-CNRS, Route de Saint Cyr, Versailles, 78026, France
| | - Guillem Rigaill
- INRA, UMR8071, Laboratoire de Mathématiques et Modélisation d'Evry, Université d'Evry Val d'Essonne, ENSIIE-INRA-CNRS, Évry, 91037, France
| | - Mathilde Causse
- INRA, UR1052, Centre de Recherche PACA, Génétique et Amélioration des Fruits et Légumes, 67 Allée des Chênes, Domaine Saint Maurice, CS60094, Montfavet, 84143, France
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Robinson AJ, Tamiru M, Salby R, Bolitho C, Williams A, Huggard S, Fisch E, Unsworth K, Whelan J, Lewsey MG. AgriSeqDB: an online RNA-Seq database for functional studies of agriculturally relevant plant species. BMC PLANT BIOLOGY 2018; 18:200. [PMID: 30231853 PMCID: PMC6146512 DOI: 10.1186/s12870-018-1406-2] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/24/2018] [Accepted: 08/30/2018] [Indexed: 05/12/2023]
Abstract
BACKGROUND The genome-wide expression profile of genes in different tissues/cell types and developmental stages is a vital component of many functional genomic studies. Transcriptome data obtained by RNA-sequencing (RNA-Seq) is often deposited in public databases that are made available via data portals. Data visualization is one of the first steps in assessment and hypothesis generation. However, these databases do not typically include visualization tools and establishing one is not trivial for users who are not computational experts. This, as well as the various formats in which data is commonly deposited, makes the processes of data access, sharing and utility more difficult. Our goal was to provide a simple and user-friendly repository that meets these needs for data-sets from major agricultural crops. DESCRIPTION AgriSeqDB ( https://expression.latrobe.edu.au/agriseqdb ) is a database for viewing, analysing and interpreting developmental and tissue/cell-specific transcriptome data from several species, including major agricultural crops such as wheat, rice, maize, barley and tomato. The disparate manner in which public transcriptome data is often warehoused and the challenge of visualizing raw data are both major hurdles to data reuse. The popular eFP browser does an excellent job of presenting transcriptome data in an easily interpretable view, but previous implementation has been mostly on a case-by-case basis. Here we present an integrated visualisation database of transcriptome data-sets from six species that did not previously have public-facing visualisations. We combine the eFP browser, for gene-by-gene investigation, with the Degust browser, which enables visualisation of all transcripts across multiple samples. The two visualisation interfaces launch from the same point, enabling users to easily switch between analysis modes. The tools allow users, even those without bioinformatics expertise, to mine into data-sets and understand the behaviour of transcripts of interest across samples and time. We have also incorporated an additional graphic download option to simplify incorporation into presentations or publications. CONCLUSION Powered by eFP and Degust browsers, AgriSeqDB is a quick and easy-to-use platform for data analysis and visualization in five crops and Arabidopsis. Furthermore, it provides a tool that makes it easy for researchers to share their data-sets, promoting research collaborations and data-set reuse.
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Affiliation(s)
| | - Muluneh Tamiru
- Department of Animal, Plant and Soil Sciences, School of Life Sciences, La Trobe University, Melbourne, Australia
| | - Rachel Salby
- Library, La Trobe University, Melbourne, Australia
| | | | | | | | - Eva Fisch
- Library, La Trobe University, Melbourne, Australia
| | | | - James Whelan
- Department of Animal, Plant and Soil Sciences, School of Life Sciences, La Trobe University, Melbourne, Australia
| | - Mathew G. Lewsey
- Department of Animal, Plant and Soil Sciences, School of Life Sciences, La Trobe University, Melbourne, Australia
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Pierre-Jerome E, Drapek C, Benfey PN. Regulation of Division and Differentiation of Plant Stem Cells. Annu Rev Cell Dev Biol 2018; 34:289-310. [PMID: 30134119 DOI: 10.1146/annurev-cellbio-100617-062459] [Citation(s) in RCA: 52] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
A major challenge in developmental biology is unraveling the precise regulation of plant stem cell maintenance and the transition to a fully differentiated cell. In this review, we highlight major themes coordinating the acquisition of cell identity and subsequent differentiation in plants. Plant cells are immobile and establish position-dependent cell lineages that rely heavily on external cues. Central players are the hormones auxin and cytokinin, which balance cell division and differentiation during organogenesis. Transcription factors and miRNAs, many of which are mobile in plants, establish gene regulatory networks that communicate cell position and fate. Small peptide signaling also provides positional cues as new cell types emerge from stem cell division and progress through differentiation. These pathways recruit similar players for patterning different organs, emphasizing the modular nature of gene regulatory networks. Finally, we speculate on the outstanding questions in the field and discuss how they may be addressed by emerging technologies.
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Affiliation(s)
- Edith Pierre-Jerome
- Department of Biology and Howard Hughes Medical Institute, Duke University, Durham, North Carolina 27708, USA;
| | - Colleen Drapek
- Department of Biology and Howard Hughes Medical Institute, Duke University, Durham, North Carolina 27708, USA;
| | - Philip N Benfey
- Department of Biology and Howard Hughes Medical Institute, Duke University, Durham, North Carolina 27708, USA;
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37
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Golz JF, Allen PJ, Li SF, Parish RW, Jayawardana NU, Bacic A, Doblin MS. Layers of regulation - Insights into the role of transcription factors controlling mucilage production in the Arabidopsis seed coat. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2018; 272:179-192. [PMID: 29807590 DOI: 10.1016/j.plantsci.2018.04.021] [Citation(s) in RCA: 41] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/18/2018] [Revised: 04/22/2018] [Accepted: 04/24/2018] [Indexed: 05/12/2023]
Abstract
A polysaccharide-rich mucilage is released from the seed coat epidermis of numerous plant species and has been intensively studied in the model plant Arabidopsis. This has led to the identification of a large number of genes involved in the synthesis, secretion and modification of cell wall polysaccharides such as pectin, hemicellulose and cellulose being identified. These genes include a small network of transcription factors (TFs) and transcriptional co-regulators, that not only regulate mucilage production, but epidermal cell differentiation and in some cases flavonoid biosynthesis in the internal endothelial layer of the seed coat. Here we focus on the function of these regulators and propose a simplified model where they are assigned to a hierarchical gene network with three regulatory levels (tiers) as a means of assisting in the interpretation of the complexity. We discuss limitations of current methodologies and highlight some of the problems associated with defining the function of TFs, particularly those that perform different functions in adjacent layers of the seed coat. We suggest approaches that should provide a more accurate picture of the function of transcription factors involved with mucilage production and release.
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Affiliation(s)
- John F Golz
- School of BioSciences, University of Melbourne, Royal Parade, Parkville, VIC 3010, Australia.
| | - Patrick J Allen
- Department of Animal, Plant and Soil Sciences, AgriBio Centre, School of Life Sciences, La Trobe University, Bundoora, VIC 3086, Australia
| | - Song F Li
- Department of Animal, Plant and Soil Sciences, AgriBio Centre, School of Life Sciences, La Trobe University, Bundoora, VIC 3086, Australia
| | - Roger W Parish
- Department of Animal, Plant and Soil Sciences, AgriBio Centre, School of Life Sciences, La Trobe University, Bundoora, VIC 3086, Australia
| | - Nadeeka U Jayawardana
- ARC Centre of Excellence in Plant Cell Walls, School of BioSciences, The University of Melbourne, Parkville, VIC 3010, Australia
| | - Antony Bacic
- ARC Centre of Excellence in Plant Cell Walls, School of BioSciences, The University of Melbourne, Parkville, VIC 3010, Australia
| | - Monika S Doblin
- ARC Centre of Excellence in Plant Cell Walls, School of BioSciences, The University of Melbourne, Parkville, VIC 3010, Australia
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Henry KF, Bui AQ, Kawashima T, Goldberg RB. A shared cis-regulatory module activates transcription in the suspensor of plant embryos. Proc Natl Acad Sci U S A 2018; 115:E5824-E5833. [PMID: 29866850 PMCID: PMC6016821 DOI: 10.1073/pnas.1805802115] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
The mechanisms controlling the transcription of gene sets in specific regions of a plant embryo shortly after fertilization remain unknown. Previously, we showed that G564 mRNA, encoding a protein of unknown function, accumulates to high levels in the giant suspensor of both Scarlet Runner Bean (SRB) and Common Bean embryos, and a cis-regulatory module containing three unique DNA sequences, designated as the 10-bp, Region 2, and Fifth motifs, is required for G564 suspensor-specific transcription [Henry KF, et al. (2015) Plant Mol Biol 88:207-217; Kawashima T, et al. (2009) Proc Natl Acad Sci USA 106:3627-3632]. We tested the hypothesis that these motifs are also required for transcription of the SRB GA 20-oxidase gene, which encodes a gibberellic acid hormone biosynthesis enzyme and is coexpressed with G564 at a high level in giant bean suspensors. We used deletion and gain-of-function experiments in transgenic tobacco embryos to show that two GA 20-oxidase DNA regions are required for suspensor-specific transcription, one in the 5' UTR (+119 to +205) and another in the 5' upstream region (-341 to -316). Mutagenesis of sequences in these two regions determined that the cis-regulatory motifs required for G564 suspensor transcription are also required for GA 20-oxidase transcription within the suspensor, although the motif arrangement differs. Our results demonstrate the flexibility of motif positioning within a cis-regulatory module that activates gene transcription within giant bean suspensors and suggest that G564 and GA 20-oxidase comprise part of a suspensor gene regulatory network.
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Affiliation(s)
- Kelli F Henry
- Department of Molecular, Cell, and Developmental Biology, University of California, Los Angeles, CA 90095
| | - Anhthu Q Bui
- Department of Molecular, Cell, and Developmental Biology, University of California, Los Angeles, CA 90095
| | - Tomokazu Kawashima
- Department of Molecular, Cell, and Developmental Biology, University of California, Los Angeles, CA 90095
| | - Robert B Goldberg
- Department of Molecular, Cell, and Developmental Biology, University of California, Los Angeles, CA 90095
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39
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Sakai K, Taconnat L, Borrega N, Yansouni J, Brunaud V, Paysant-Le Roux C, Delannoy E, Martin Magniette ML, Lepiniec L, Faure JD, Balzergue S, Dubreucq B. Combining laser-assisted microdissection (LAM) and RNA-seq allows to perform a comprehensive transcriptomic analysis of epidermal cells of Arabidopsis embryo. PLANT METHODS 2018; 14:10. [PMID: 29434651 PMCID: PMC5797369 DOI: 10.1186/s13007-018-0275-x] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/14/2017] [Accepted: 01/15/2018] [Indexed: 05/11/2023]
Abstract
BACKGROUND Genome-wide characterization of tissue- or cell-specific gene expression is a recurrent bottleneck in biology. We have developed a sensitive approach based on ultra-low RNA sequencing coupled to laser assisted microdissection for analyzing different tissues of the small Arabidopsis embryo. METHODS AND RESULTS We first characterized the number of genes detected according to the quantity of tissue yield and total RNA extracted. Our results revealed that as low as 0.02 mm2 of tissue and 50 pg of total RNA can be used without compromising the number of genes detected. The optimised protocol was used to compare the epidermal versus mesophyll cell transcriptomes of cotyledons at the torpedo-shaped stage of embryo development. The approach was validated by the recovery of well-known epidermal genes such AtML1 or AtPDF2 and genes involved in flavonoid and cuticular waxes pathways. Moreover, the interest and sensitivity of this approach were highlighted by the characterization of several transcription factors preferentially expressed in epidermal cells. CONCLUSION This technical advance unlocks some current limitations of transcriptomic analyses and allows to investigate further and efficiently new biological questions for which only a very small amounts of cells need to be isolated. For instance, it paves the way to increasing the spatial accuracy of regulatory networks in developing small embryo of Arabidopsis or other plant tissues.
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Affiliation(s)
- Kaori Sakai
- Institut Jean-Pierre Bourgin (IJPB), INRA, AgroParisTech, CNRS, Université Paris-Saclay, RD10, 78026 Versailles Cedex, France
| | - Ludivine Taconnat
- Institute of Plant Sciences Paris Saclay IPS2, CNRS, INRA, Université Paris-Sud, Université Evry, Université Paris-Saclay, Bâtiment 630, 91405 Orsay, France
- Institute of Plant Sciences Paris-Saclay IPS2, Paris Diderot, Sorbonne Paris-Cité, Bâtiment 630, 91405 Orsay, France
| | - Nero Borrega
- Institut Jean-Pierre Bourgin (IJPB), INRA, AgroParisTech, CNRS, Université Paris-Saclay, RD10, 78026 Versailles Cedex, France
| | - Jennifer Yansouni
- Institute of Plant Sciences Paris Saclay IPS2, CNRS, INRA, Université Paris-Sud, Université Evry, Université Paris-Saclay, Bâtiment 630, 91405 Orsay, France
- Institute of Plant Sciences Paris-Saclay IPS2, Paris Diderot, Sorbonne Paris-Cité, Bâtiment 630, 91405 Orsay, France
| | - Véronique Brunaud
- Institute of Plant Sciences Paris Saclay IPS2, CNRS, INRA, Université Paris-Sud, Université Evry, Université Paris-Saclay, Bâtiment 630, 91405 Orsay, France
- Institute of Plant Sciences Paris-Saclay IPS2, Paris Diderot, Sorbonne Paris-Cité, Bâtiment 630, 91405 Orsay, France
| | - Christine Paysant-Le Roux
- Institute of Plant Sciences Paris Saclay IPS2, CNRS, INRA, Université Paris-Sud, Université Evry, Université Paris-Saclay, Bâtiment 630, 91405 Orsay, France
- Institute of Plant Sciences Paris-Saclay IPS2, Paris Diderot, Sorbonne Paris-Cité, Bâtiment 630, 91405 Orsay, France
| | - Etienne Delannoy
- Institute of Plant Sciences Paris Saclay IPS2, CNRS, INRA, Université Paris-Sud, Université Evry, Université Paris-Saclay, Bâtiment 630, 91405 Orsay, France
- Institute of Plant Sciences Paris-Saclay IPS2, Paris Diderot, Sorbonne Paris-Cité, Bâtiment 630, 91405 Orsay, France
| | - Marie-Laure Martin Magniette
- Institute of Plant Sciences Paris Saclay IPS2, CNRS, INRA, Université Paris-Sud, Université Evry, Université Paris-Saclay, Bâtiment 630, 91405 Orsay, France
- Institute of Plant Sciences Paris-Saclay IPS2, Paris Diderot, Sorbonne Paris-Cité, Bâtiment 630, 91405 Orsay, France
- UMR MIA-Paris, AgroParisTech, INRA, Université Paris-Saclay, 75005 Paris, France
| | - Loïc Lepiniec
- Institut Jean-Pierre Bourgin (IJPB), INRA, AgroParisTech, CNRS, Université Paris-Saclay, RD10, 78026 Versailles Cedex, France
| | - Jean Denis Faure
- Institut Jean-Pierre Bourgin (IJPB), INRA, AgroParisTech, CNRS, Université Paris-Saclay, RD10, 78026 Versailles Cedex, France
| | - Sandrine Balzergue
- Institute of Plant Sciences Paris Saclay IPS2, CNRS, INRA, Université Paris-Sud, Université Evry, Université Paris-Saclay, Bâtiment 630, 91405 Orsay, France
- Institute of Plant Sciences Paris-Saclay IPS2, Paris Diderot, Sorbonne Paris-Cité, Bâtiment 630, 91405 Orsay, France
- Present Address: IRHS, Université d’Angers, INRA, AGROCAMPUS-Ouest, SFR4207 QUASAV, Université Bretagne Loire, 49045 Angers, France
| | - Bertrand Dubreucq
- Institut Jean-Pierre Bourgin (IJPB), INRA, AgroParisTech, CNRS, Université Paris-Saclay, RD10, 78026 Versailles Cedex, France
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40
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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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41
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Slane D, Reichardt I, El Kasmi F, Bayer M, Jürgens G. Evolutionarily diverse SYP1 Qa-SNAREs jointly sustain pollen tube growth in Arabidopsis. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2017; 92:375-385. [PMID: 28792633 DOI: 10.1111/tpj.13659] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/24/2017] [Revised: 08/01/2017] [Accepted: 08/03/2017] [Indexed: 05/08/2023]
Abstract
Intracellular membrane fusion is effected by SNARE proteins that reside on adjacent membranes and form bridging trans-SNARE complexes. Qa-SNARE members of the Arabidopsis SYP1 family are involved in membrane fusion at the plasma membrane or during cell plate formation. Three SYP1 family members have been classified as pollen-specific as inferred from gene expression profiling studies, and two of them, SYP124 and SYP125, are confined to angiosperms. The SYP124 gene appears genetically unstable, whereas its sister gene SYP125 shows essentially no variation among Arabidopsis accessions. The third pollen-specific member SYP131 is sister to SYP132, which appears evolutionarily conserved in the plant lineage. Although evolutionarily diverse, the three SYP1 proteins are functionally overlapping in that only the triple mutant syp124 syp125 syp131 shows a specific and severe male gametophytic defect. While pollen development and germination appear normal, pollen tube growth is arrested during passage through the style. Our results suggest that angiosperm pollen tubes employ a combination of ancient and modern Qa-SNARE proteins to sustain their growth-promoting membrane dynamics during the reproductive process.
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Affiliation(s)
- Daniel Slane
- Max Planck Institute for Developmental Biology, Cell Biology, 72076, Tübingen, Germany
| | - Ilka Reichardt
- ZMBP, Developmental Genetics, University of Tübingen, 72076, Tübingen, Germany
| | - Farid El Kasmi
- ZMBP, Developmental Genetics, University of Tübingen, 72076, Tübingen, Germany
| | - Martin Bayer
- Max Planck Institute for Developmental Biology, Cell Biology, 72076, Tübingen, Germany
| | - Gerd Jürgens
- Max Planck Institute for Developmental Biology, Cell Biology, 72076, Tübingen, Germany
- ZMBP, Developmental Genetics, University of Tübingen, 72076, Tübingen, Germany
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42
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Bayer M, Slane D, Jürgens G. Early plant embryogenesis-dark ages or dark matter? CURRENT OPINION IN PLANT BIOLOGY 2017; 35:30-36. [PMID: 27810634 DOI: 10.1016/j.pbi.2016.10.004] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/17/2016] [Revised: 10/11/2016] [Accepted: 10/13/2016] [Indexed: 05/11/2023]
Abstract
In nearly all flowering plants, the basic body plan is laid down during embryogenesis. In Arabidopsis, the crucial cell types are established extremely early as reflected in the stereotypic sequence of oriented cell divisions in the developing young embryo. Research into early embryogenesis was especially focused on the role of the infamous tryptophan derivative auxin in establishing embryo polarity and generating the main body axis. However, it is becoming obvious that the mere link to auxin does not provide any mechanistic understanding of early embryo patterning. Taking recent research into account, we discuss mechanisms underlying early embryonic patterning from an evolutionary perspective.
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Affiliation(s)
- Martin Bayer
- Department of Cell Biology, Max Planck Institute for Developmental Biology, 72076 Tübingen, Germany
| | - Daniel Slane
- Department of Cell Biology, Max Planck Institute for Developmental Biology, 72076 Tübingen, Germany
| | - Gerd Jürgens
- Department of Cell Biology, Max Planck Institute for Developmental Biology, 72076 Tübingen, Germany; Department of Developmental Genetics, Center for Plant Molecular Biology, University of Tübingen, 72076 Tübingen, Germany.
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43
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Abstract
Fluorescence-activated cell sorting (FACS) is a powerful method for the analysis of cell type-specific transcriptome profiles, DNA or histone modifications, and chemical compounds. In plants, it has been employed mainly with root and shoot tissue in combination with cell wall digestion on cellular and nuclear content. However, many tissues are recalcitrant to cell separation and are therefore not readily accessible for FACS analysis. Here, we lay out a detailed protocol for the generation of transcriptional profiles from fluorescently labeled nuclei. The protocol described in this chapter has been used successfully to generate a transcriptional map of the early Arabidopsis thaliana embryo.
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44
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Slane D, Bürgel P, Bayer M. Staining and Clearing of Arabidopsis Reproductive Tissue for Imaging of Fluorescent Proteins. Methods Mol Biol 2017; 1669:87-94. [PMID: 28936652 DOI: 10.1007/978-1-4939-7286-9_8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Imaging of fluorescent proteins in whole-mount tissue is a powerful tool to understand growth and developmental processes, not only in plants. With the advent of genetically encoded fluorescent reporters, which specifically label reproductive cells in Arabidopsis, deep tissue imaging has become increasingly important for the study of plant reproduction. To penetrate the surrounding layers of maternal tissue, however, the tissue has to be cleared by homogenizing the refractive index of the sample, often leading to inactivation of fluorescent proteins. 2,2'-thiodiethanol (TDE) has recently been introduced as a clearing agent that allows the imaging of fluorescent proteins in a cleared plant tissue. Here, we describe a simple protocol that combines TDE-based tissue clearing with cell wall staining to outline cells that enable deep tissue imaging in reproductive structures of Arabidopsis thaliana.
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Affiliation(s)
- Daniel Slane
- Department of Cell Biology, Max Planck Institute for Developmental Biology, Spemannstrasse 35, 72076, Tuebingen, Germany
| | - Patrick Bürgel
- Department of Cell Biology, Max Planck Institute for Developmental Biology, Spemannstrasse 35, 72076, Tuebingen, Germany
| | - Martin Bayer
- Department of Cell Biology, Max Planck Institute for Developmental Biology, Spemannstrasse 35, 72076, Tuebingen, Germany.
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45
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Palovaara J, de Zeeuw T, Weijers D. Tissue and Organ Initiation in the Plant Embryo: A First Time for Everything. Annu Rev Cell Dev Biol 2016; 32:47-75. [PMID: 27576120 DOI: 10.1146/annurev-cellbio-111315-124929] [Citation(s) in RCA: 63] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Land plants can grow to tremendous body sizes, yet even the most complex architectures are the result of iterations of the same developmental processes: organ initiation, growth, and pattern formation. A central question in plant biology is how these processes are regulated and coordinated to allow for the formation of ordered, 3D structures. All these elementary processes first occur in early embryogenesis, during which, from a fertilized egg cell, precursors for all major tissues and stem cells are initiated, followed by tissue growth and patterning. Here we discuss recent progress in our understanding of this phase of plant life. We consider the cellular basis for multicellular development in 3D and focus on the genetic regulatory mechanisms that direct specific steps during early embryogenesis.
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Affiliation(s)
- Joakim Palovaara
- Laboratory of Biochemistry, Wageningen University, 6703 HA Wageningen, The Netherlands;
| | - Thijs de Zeeuw
- Laboratory of Biochemistry, Wageningen University, 6703 HA Wageningen, The Netherlands;
| | - Dolf Weijers
- Laboratory of Biochemistry, Wageningen University, 6703 HA Wageningen, The Netherlands;
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46
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Musielak TJ, Slane D, Liebig C, Bayer M. A Versatile Optical Clearing Protocol for Deep Tissue Imaging of Fluorescent Proteins in Arabidopsis thaliana. PLoS One 2016; 11:e0161107. [PMID: 27517463 PMCID: PMC4982668 DOI: 10.1371/journal.pone.0161107] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2016] [Accepted: 07/29/2016] [Indexed: 11/19/2022] Open
Abstract
Confocal microscopy is widely used to visualize gene expression patterns and developmental processes in plants. However, the imaging of plant tissue can be challenging due to its opacity, which often makes previous immersion in a clearing agent necessary. Many commonly-used chemicals suffer either from their incompatibility with fluorescent proteins or their complex and lengthy application. 2,2'-thiodiethanol (TDE) has recently been described as a clearing agent with an emphasis on high resolution microscopy due to its potential to adjust the refractive index. Here, we evaluate the use of TDE-based clearing for confocal as well as two-photon microscopy in various Arabidopsis thaliana tissue types. We demonstrate that tissue fixation is a mandatory prerequisite for the use of TDE, in order to preserve tissue integrity and fluorescent protein activity. TDE concentrations between 50-70% are a good compromise for imaging of technically challenging tissue to achieve good clearing without affecting fluorescent protein activity. TDE-based clearing is simple and rapid to use and allows for a flexible experimental setup while facilitating high quality imaging.
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Affiliation(s)
- Thomas J. Musielak
- Max Planck Institute for Developmental Biology, Department of Cell Biology, Spemannstrasse 35, 72076 Tuebingen, Germany
| | - Daniel Slane
- Max Planck Institute for Developmental Biology, Department of Cell Biology, Spemannstrasse 35, 72076 Tuebingen, Germany
| | - Christian Liebig
- Max Planck Institute for Developmental Biology, Light Microscopy Facility, Spemannstrasse 35, 72076 Tuebingen, Germany
| | - Martin Bayer
- Max Planck Institute for Developmental Biology, Department of Cell Biology, Spemannstrasse 35, 72076 Tuebingen, Germany
- * E-mail:
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47
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Murphy E, Vu LD, Van den Broeck L, Lin Z, Ramakrishna P, van de Cotte B, Gaudinier A, Goh T, Slane D, Beeckman T, Inzé D, Brady SM, Fukaki H, De Smet I. RALFL34 regulates formative cell divisions in Arabidopsis pericycle during lateral root initiation. JOURNAL OF EXPERIMENTAL BOTANY 2016; 67:4863-75. [PMID: 27521602 PMCID: PMC4983113 DOI: 10.1093/jxb/erw281] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
In plants, many signalling molecules, such as phytohormones, miRNAs, transcription factors, and small signalling peptides, drive growth and development. However, very few small signalling peptides have been shown to be necessary for lateral root development. Here, we describe the role of the peptide RALFL34 during early events in lateral root development, and demonstrate its specific importance in orchestrating formative cell divisions in the pericycle. Our results further suggest that this small signalling peptide acts on the transcriptional cascade leading to a new lateral root upstream of GATA23, an important player in lateral root formation. In addition, we describe a role for ETHYLENE RESPONSE FACTORs (ERFs) in regulating RALFL34 expression. Taken together, we put forward RALFL34 as a new, important player in lateral root initiation.
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Affiliation(s)
- Evan Murphy
- Division of Plant and Crop Sciences, School of Biosciences, University of Nottingham, Loughborough LE12 5RD, UK
| | - Lam Dai Vu
- Department of Plant Systems Biology, VIB, B-9052 Ghent, Belgium Department of Plant Biotechnology and Bioinformatics, Ghent University, B-9052 Ghent, Belgium Department of Medical Protein Research, VIB, 9000 Ghent, Belgium Department of Biochemistry, Ghent University, 9000 Ghent, Belgium
| | - Lisa Van den Broeck
- Department of Plant Systems Biology, VIB, B-9052 Ghent, Belgium Department of Plant Biotechnology and Bioinformatics, Ghent University, B-9052 Ghent, Belgium
| | - Zhefeng Lin
- Division of Plant and Crop Sciences, School of Biosciences, University of Nottingham, Loughborough LE12 5RD, UK
| | - Priya Ramakrishna
- Division of Plant and Crop Sciences, School of Biosciences, University of Nottingham, Loughborough LE12 5RD, UK
| | - Brigitte van de Cotte
- Division of Plant and Crop Sciences, School of Biosciences, University of Nottingham, Loughborough LE12 5RD, UK Department of Plant Systems Biology, VIB, B-9052 Ghent, Belgium
| | - Allison Gaudinier
- Department of Plant Biology and Genome Center, University of California Davis, One Shields Avenue, Davis, CA 95616, USA
| | - Tatsuaki Goh
- Department of Biology, Graduate School of Science, Kobe University, Kobe 657-8501, Japan
| | - Daniel Slane
- Department of Cell Biology, Max Planck Institute for Developmental Biology, D- 72076 Tübingen, Germany
| | - Tom Beeckman
- Department of Plant Systems Biology, VIB, B-9052 Ghent, Belgium Department of Plant Biotechnology and Bioinformatics, Ghent University, B-9052 Ghent, Belgium
| | - Dirk Inzé
- Department of Plant Systems Biology, VIB, B-9052 Ghent, Belgium Department of Plant Biotechnology and Bioinformatics, Ghent University, B-9052 Ghent, Belgium
| | - Siobhan M Brady
- Department of Plant Biology and Genome Center, University of California Davis, One Shields Avenue, Davis, CA 95616, USA
| | - Hidehiro Fukaki
- Department of Biology, Graduate School of Science, Kobe University, Kobe 657-8501, Japan
| | - Ive De Smet
- Division of Plant and Crop Sciences, School of Biosciences, University of Nottingham, Loughborough LE12 5RD, UK Department of Plant Systems Biology, VIB, B-9052 Ghent, Belgium Department of Plant Biotechnology and Bioinformatics, Ghent University, B-9052 Ghent, Belgium Centre for Plant Integrative Biology, University of Nottingham, Loughborough LE12 5RD, UK
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48
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Jeong S, Eilbert E, Bolbol A, Lukowitz W. Going mainstream: How is the body axis of plants first initiated in the embryo? Dev Biol 2016; 419:78-84. [PMID: 27207388 DOI: 10.1016/j.ydbio.2016.05.002] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2016] [Revised: 04/30/2016] [Accepted: 05/02/2016] [Indexed: 10/21/2022]
Abstract
Vascular plants have an open body plan and continuously generate new axes of growth, such as shoot or root branches. Apical-to-basal transport of the hormone auxin is a hallmark of every axis, and the resulting pattern of auxin distribution affects plant development across scales, from overall architecture to cellular differentiation. How the first axis is initiated in the early embryo is a long-standing question. While our knowledge is still sparse, some of the key players of axialization have emerged, and recent work points to specific models for connecting cellular polarity to the asymmetric division of the zygote and domain specific gene expression to the organization of basipetal auxin flux.
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Affiliation(s)
- Sangho Jeong
- Department of Plant Biology, University of Georgia, 120 Carlton Street, Athens, GA 30602-7271, United States.
| | - Emily Eilbert
- Department of Plant Biology, University of Georgia, 120 Carlton Street, Athens, GA 30602-7271, United States.
| | - Ahmed Bolbol
- Botany Department, Faculty of Science, Zagazig University, 44519 Sharkira, Egypt.
| | - Wolfgang Lukowitz
- Department of Plant Biology, University of Georgia, 120 Carlton Street, Athens, GA 30602-7271, United States.
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49
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Samadder P, Weng N, Doetschman T, Heimark RL, Galbraith DW. Flow cytometry and single nucleus sorting for Cre-based analysis of changes in transcriptional states. Cytometry A 2016; 89:430-42. [PMID: 27003621 DOI: 10.1002/cyto.a.22847] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2015] [Revised: 02/23/2016] [Accepted: 02/29/2016] [Indexed: 12/13/2022]
Abstract
The organs of eukaryotic organisms comprise complex interspersions of cell types, whose different molecular activities, and corresponding cellular states, cooperate during development to produce the final, functional organ. Dysfunction of organs in disease, particularly oncogenesis, initiates with changes of state of a minor subset of cells. It therefore is hard to detect early molecular indicators of disease within an overwhelming background of normal cells. Flow cytometry and sorting provides a convenient way to purify minority subpopulations, if a specific fluorophore can be unambiguously and exclusively associated with this subpopulation. We have generated a number of transgenic mouse lines expressing a nuclear-localized version of the Green Fluorescent Protein (GFP), within which the production of a chimeric histone 2B-GFP protein occurs under the control of a constitutively-active, actin-derived promoter, separated by a Floxed-STOP sequence. In the presence of Cre recombinase, within F1 progeny of these mouse lines, excision of the STOP sequence activates transcription which results in the emergence of cells containing green fluorescent nuclei. We describe the characterization of these lines using a combination of microscopic imaging, flow cytometry and sorting, and Reverse-Transcription polymerase chain reaction of transcripts within single sorted nuclei isolated from tissue homogenates. These lines should be particularly useful for analysis of transcriptional changes in oncogenesis. © 2016 International Society for Advancement of Cytometry.
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Affiliation(s)
| | - Ning Weng
- BIO5 Institute, University of Arizona, Tucson, Arizona
| | - Thomas Doetschman
- BIO5 Institute, University of Arizona, Tucson, Arizona
- Department of Cellular and Molecular Medicine, University of Arizona, Tucson, Arizona
- University of Arizona Cancer Center, Tucson, Arizona
| | - Ronald L Heimark
- Department of Cellular and Molecular Medicine, University of Arizona, Tucson, Arizona
- University of Arizona Cancer Center, Tucson, Arizona
- Department of Surgery, University of Arizona, Tucson, Arizona
| | - David W Galbraith
- BIO5 Institute, University of Arizona, Tucson, Arizona
- University of Arizona Cancer Center, Tucson, Arizona
- School of Plant Sciences, University of Arizona, Tucson, Arizona
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50
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Herud O, Weijers D, Lau S, Jürgens G. Auxin responsiveness of the MONOPTEROS-BODENLOS module in primary root initiation critically depends on the nuclear import kinetics of the Aux/IAA inhibitor BODENLOS. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2016; 85:269-77. [PMID: 26714008 DOI: 10.1111/tpj.13108] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/27/2015] [Revised: 12/07/2015] [Accepted: 12/14/2015] [Indexed: 05/28/2023]
Abstract
Primary root formation in early embryogenesis of Arabidopsis thaliana is initiated with the specification of a single cell called hypophysis. This initial step requires the auxin-dependent release of the transcription factor MONOPTEROS (MP, also known as ARF5) from its inhibition by the Aux/IAA protein BODENLOS (BDL, also known as IAA12). Auxin-insensitive bdl mutant embryos and mp loss-of-function embryos fail to specify the hypophysis, giving rise to rootless seedlings. A suppressor screen of rootless bdl mutant seedlings yielded a mutation in the nuclear import receptor IMPORTIN-ALPHA 6 (IMPα6) that promoted primary root formation through rescue of the embryonic hypophysis defects, without causing additional phenotypic changes. Aux/IAA proteins are continually synthesized and degraded, which is essential for rapid transcriptional responses to changing auxin concentrations. Nuclear translocation of bdl:3×GFP was slowed down in impα6 mutants as measured by fluorescence recovery after photobleaching (FRAP) analysis, which correlated with the reduced inhibition of MP by bdl in transient expression assays in impα6 knock-down protoplasts. The MP-BDL module acts like an auxin-triggered genetic switch because MP activates its own expression as well as the expression of its inhibitor BDL. Using an established simulation model, we determined that the reduced nuclear translocation rate of BDL in impα6 mutant embryos rendered the auxin-triggered switch unstable, impairing the fast response to changes in auxin concentration. Our results suggest that the instability of the inhibitor BDL necessitates a fast nuclear uptake in order to reach the critical threshold level required for auxin responsiveness of the MP-BDL module in primary root initiation.
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Affiliation(s)
- Ole Herud
- Department of Cell Biology, Max Planck Institute for Developmental Biology, Tübingen, 72076, Germany
| | - Dolf Weijers
- Department of Developmental Genetics, Center for Plant Molecular Biology, University of Tübingen, Tübingen, 72076, Germany
| | - Steffen Lau
- Department of Cell Biology, Max Planck Institute for Developmental Biology, Tübingen, 72076, Germany
| | - Gerd Jürgens
- Department of Cell Biology, Max Planck Institute for Developmental Biology, Tübingen, 72076, Germany
- Department of Developmental Genetics, Center for Plant Molecular Biology, University of Tübingen, Tübingen, 72076, Germany
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