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Huang Y, Zhou L, Hou C, Guo D. The dynamic proteome in Arabidopsis thaliana early embryogenesis. Development 2022; 149:276287. [DOI: 10.1242/dev.200715] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2022] [Accepted: 07/26/2022] [Indexed: 11/20/2022]
Abstract
ABSTRACT
The morphology of the flowering plant is established during early embryogenesis. In recent years, many studies have focused on transcriptional profiling in plant embryogenesis, but the dynamic landscape of the Arabidopsis thaliana proteome remains elusive. In this study, Arabidopsis embryos at 2/4-cell, 8-cell, 16-cell, 32-cell, globular and heart stages were collected for nanoproteomic analysis. In total, 5386 proteins were identified. Of these, 1051 proteins were universally identified in all developmental stages and a range of 27 to 2154 proteins was found to be stage specific. These proteins could be grouped into eight clusters according to their expression levels. Gene Ontology enrichment analysis showed that genes involved in ribosome biogenesis and auxin-activated signalling were enriched during early embryogenesis, indicating that active translation and auxin signalling are important events in Arabidopsis embryo development. Combining RNA-sequencing data with the proteomics analysis, the correlation between mRNA and protein was evaluated. An overall positive correlation was found between mRNA and protein. This work provides a comprehensive landscape of the Arabidopsis proteome in early embryogenesis. Some important proteins/transcription factors identified through network analysis may serve as potential targets for future investigation.
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Affiliation(s)
- Yingzhang Huang
- State Key Laboratory of Agrobiotechnology and School of Life Science, The Chinese University of Hong Kong 1 , 999077 Hong Kong , China
| | - Limeng Zhou
- State Key Laboratory of Agrobiotechnology and School of Life Science, The Chinese University of Hong Kong 1 , 999077 Hong Kong , China
| | - Chunhui Hou
- Southern University of Science and Technology 2 Department of Biology , , Shenzhen 518055 , China
| | - Dianjing Guo
- State Key Laboratory of Agrobiotechnology and School of Life Science, The Chinese University of Hong Kong 1 , 999077 Hong Kong , China
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Tiscareño-Andrade M, Oktaba K, Vielle-Calzada JP. Isolation of Boechera stricta Developing Embryos for Hi-C. Methods Mol Biol 2022; 2512:249-257. [PMID: 35818009 DOI: 10.1007/978-1-0716-2429-6_14] [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: 06/15/2023]
Abstract
The possibility of analyzing chromatin topology in developing plant embryos is hampered by inaccessibility of the embryo sac, deeply embedded in the maternal seed tissue, following double fertilization. Here we describe a protocol to isolate, purify, and prepare developing Boechera stricta embryos for chromosome conformation capture-based methods as in situ Hi-C experiments. Early globular embryos can be isolated by air-pressure microaspiration, and subsequently washed to eliminate residual cells from the endosperm and maternal seed coat, allowing for pure sampling of selected stages of embryogenesis. This protocol allows for the possibility of comparing genome topology during plant embryonic differentiation since early until late embryo development stages.
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Affiliation(s)
- Mariana Tiscareño-Andrade
- Unidad Irapuato, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional (Cinvestav), Irapuato, Mexico
- Grupo de Desarrollo Reproductivo y Apomixis, Unidad de Genómica Avanzada Laboratorio Nacional de Genómica para la Biodiversidad (LANGEBIO), Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional (Cinvestav), Irapuato, Mexico
| | - Katarzyna Oktaba
- Unidad Irapuato, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional (Cinvestav), Irapuato, Guanajuato, Mexico
| | - Jean-Philippe Vielle-Calzada
- Grupo de Desarrollo Reproductivo y Apomixis, Unidad de Genómica Avanzada Laboratorio Nacional de Genómica para la Biodiversidad (LANGEBIO), Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional (Cinvestav), Irapuato, Mexico.
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3
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Vaddepalli P, de Zeeuw T, Strauss S, Bürstenbinder K, Liao CY, Ramalho JJ, Smith RS, Weijers D. Auxin-dependent control of cytoskeleton and cell shape regulates division orientation in the Arabidopsis embryo. Curr Biol 2021; 31:4946-4955.e4. [PMID: 34610273 PMCID: PMC8612740 DOI: 10.1016/j.cub.2021.09.019] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2021] [Revised: 07/22/2021] [Accepted: 09/07/2021] [Indexed: 11/25/2022]
Abstract
Premitotic control of cell division orientation is critical for plant development, as cell walls prevent extensive cell remodeling or migration. While many divisions are proliferative and add cells to existing tissues, some divisions are formative and generate new tissue layers or growth axes. Such formative divisions are often asymmetric in nature, producing daughters with different fates. We have previously shown that, in the Arabidopsis thaliana embryo, developmental asymmetry is correlated with geometric asymmetry, creating daughter cells of unequal volume. Such divisions are generated by division planes that deviate from a default “minimal surface area” rule. Inhibition of auxin response leads to reversal to this default, yet the mechanisms underlying division plane choice in the embryo have been unclear. Here, we show that auxin-dependent division plane control involves alterations in cell geometry, but not in cell polarity axis or nuclear position. Through transcriptome profiling, we find that auxin regulates genes controlling cell wall and cytoskeleton properties. We confirm the involvement of microtubule (MT)-binding proteins in embryo division control. Organization of both MT and actin cytoskeleton depends on auxin response, and genetically controlled MT or actin depolymerization in embryos leads to disruption of asymmetric divisions, including reversion to the default. Our work shows how auxin-dependent control of MT and actin cytoskeleton properties interacts with cell geometry to generate asymmetric divisions during the earliest steps in plant development. Auxin responses regulate directional cell expansion in Arabidopsis embryos Cell shape and division orientation are tightly coupled Transcriptome analysis identifies MT-associated IQD proteins in division control Cytoskeletal dynamics control division orientation
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Affiliation(s)
- Prasad Vaddepalli
- Laboratory of Biochemistry, Wageningen University, Stippeneng 4, 6708 Wageningen, the Netherlands.
| | - Thijs de Zeeuw
- Laboratory of Biochemistry, Wageningen University, Stippeneng 4, 6708 Wageningen, the Netherlands
| | - Sören Strauss
- Department of Comparative Development and Genetics, Max Planck Institute for Plant Breeding Research, Carl-von-Linne-Weg 10, Cologne, Germany
| | - Katharina Bürstenbinder
- Department of Molecular Signal Processing, Leibniz Institute of Plant Biochemistry, Weinberg 3, Halle (Saale), Germany
| | - Che-Yang Liao
- Laboratory of Biochemistry, Wageningen University, Stippeneng 4, 6708 Wageningen, the Netherlands
| | - João Jacob Ramalho
- Laboratory of Biochemistry, Wageningen University, Stippeneng 4, 6708 Wageningen, the Netherlands
| | - Richard S Smith
- Department of Comparative Development and Genetics, Max Planck Institute for Plant Breeding Research, Carl-von-Linne-Weg 10, Cologne, Germany; John Innes Centre, Norwich Research Park, Norwich NR4 7UH, UK
| | - Dolf Weijers
- Laboratory of Biochemistry, Wageningen University, Stippeneng 4, 6708 Wageningen, the Netherlands.
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Yoo H, Park K, Lee J, Lee S, Choi Y. An Optimized Method for the Construction of a DNA Methylome from Small Quantities of Tissue or Purified DNA from Arabidopsis Embryo. Mol Cells 2021; 44:602-612. [PMID: 34462399 PMCID: PMC8424141 DOI: 10.14348/molcells.2021.0084] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2021] [Revised: 05/25/2021] [Accepted: 06/08/2021] [Indexed: 12/29/2022] Open
Abstract
DNA methylation is an important epigenetic mechanism affecting genome structure, gene regulation, and the silencing of transposable elements. Cell- and tissue-specific methylation patterns are critical for differentiation and development in eukaryotes. Dynamic spatiotemporal methylation data in these cells or tissues is, therefore, of great interest. However, the construction of bisulfite sequencing libraries can be challenging if the starting material is limited or the genome size is small, such as in Arabidopsis. Here, we describe detailed methods for the purification of Arabidopsis embryos at all stages, and the construction of comprehensive bisulfite libraries from small quantities of input. We constructed bisulfite libraries by releasing embryos from intact seeds, using a different approach for each developmental stage, and manually picking single-embryo with microcapillaries. From these libraries, reliable Arabidopsis methylome data were collected allowing, on average, 11-fold coverage of the genome using as few as five globular, heart, and torpedo embryos as raw input material without the need for DNA purification step. On the other hand, purified DNA from as few as eight bending torpedo embryos or a single mature embryo is sufficient for library construction when RNase A is treated before DNA extraction. This method can be broadly applied to cells from different tissues or cells from other model organisms. Methylome construction can be achieved using a minimal amount of input material using our method; thereby, it has the potential to increase our understanding of dynamic spatiotemporal methylation patterns in model organisms.
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Affiliation(s)
- Hyunjin Yoo
- Department of Biological Sciences, Seoul National University, Seoul 08826, Korea
| | - Kyunghyuk Park
- Department of Biological Sciences, Seoul National University, Seoul 08826, Korea
| | - Jaehoon Lee
- Department of Biological Sciences, Seoul National University, Seoul 08826, Korea
| | - Seunga Lee
- Department of Biological Sciences, Seoul National University, Seoul 08826, Korea
| | - Yeonhee Choi
- Department of Biological Sciences, Seoul National University, Seoul 08826, Korea
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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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Abstract
Genome-wide characterization of RNA populations in early flowering plant embryos can yield insights into the gene regulatory processes functioning during this formative phase of development. However, early embryonic transcriptomes are technically challenging to profile because of the low amount of RNA obtainable and potential RNA contamination from surrounding nonembryonic tissues. Here we provide a detailed protocol for collecting early Arabidopsis thaliana (Arabidopsis) embryos, generating mRNA sequencing (mRNA-seq) libraries, and basic data processing and quality controls of the resulting mRNA-seq data.
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Affiliation(s)
- Ping Kao
- Gregor Mendel Institute (GMI), Austrian Academy of Sciences, Vienna Biocenter (VBC), Vienna, Austria
| | - Michael D Nodine
- Gregor Mendel Institute (GMI), Austrian Academy of Sciences, Vienna Biocenter (VBC), Vienna, Austria.
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Abstract
The long linear chromosomes of eukaryotic organisms are tightly packed into the nucleus of the cell. Beyond a first organization into nucleosomes and higher-order chromatin fibers, the positioning of nuclear DNA within the three-dimensional space of the nucleus plays a critical role in genome function and gene expression. Different techniques have been developed to assess nanoscale chromatin organization, nuclear position of genomic regions or specific chromatin features and binding proteins as well as higher-order chromatin organization. Here, I present an overview of imaging and molecular techniques applied to study nuclear architecture in plants, with special attention to the related protocols published in the "Plant Chromatin Dynamics" edition from Methods in Molecular Biology.
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Affiliation(s)
- Aline V Probst
- GReD, Université Clermont Auvergne, CNRS, INSERM, 63001, Clermont-Ferrand, France.
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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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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 DOI: 10.1038/s41477-017-0035-33] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Subscribe] [Scholar Register] [Received: 05/15/2017] [Accepted: 09/19/2017] [Indexed: 05/22/2023]
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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She W, Baroux C. Chromatin dynamics during plant sexual reproduction. FRONTIERS IN PLANT SCIENCE 2014; 5:354. [PMID: 25104954 PMCID: PMC4109563 DOI: 10.3389/fpls.2014.00354] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/06/2014] [Accepted: 07/03/2014] [Indexed: 05/19/2023]
Abstract
Plants have the remarkable ability to establish new cell fates throughout their life cycle, in contrast to most animals that define all cell lineages during embryogenesis. This ability is exemplified during sexual reproduction in flowering plants where novel cell types are generated in floral tissues of the adult plant during sporogenesis, gametogenesis, and embryogenesis. While the molecular and genetic basis of cell specification during sexual reproduction is being studied for a long time, recent works disclosed an unsuspected role of global chromatin organization and its dynamics. In this review, we describe the events of chromatin dynamics during the different phases of sexual reproduction and discuss their possible significance particularly in cell fate establishment.
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Affiliation(s)
| | - Célia Baroux
- *Correspondence: Célia Baroux, Institute of Plant Biology – Zürich-Basel Plant Science Center, University of Zürich, Zollikerstrasse 107, 8008 Zürich, Switzerland e-mail:
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Baroux C, Autran D, Raissig MT, Grimanelli D, Grossniklaus U. Parental contributions to the transcriptome of early plant embryos. Curr Opin Genet Dev 2013; 23:72-4. [DOI: 10.1016/j.gde.2013.01.006] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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