1
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Tsuji H, Sato M. The Function of Florigen in the Vegetative-to-Reproductive Phase Transition in and around the Shoot Apical Meristem. PLANT & CELL PHYSIOLOGY 2024; 65:322-337. [PMID: 38179836 PMCID: PMC11020210 DOI: 10.1093/pcp/pcae001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/10/2023] [Revised: 11/30/2023] [Accepted: 01/03/2024] [Indexed: 01/06/2024]
Abstract
Plants undergo a series of developmental phases throughout their life-cycle, each characterized by specific processes. Three critical features distinguish these phases: the arrangement of primordia (phyllotaxis), the timing of their differentiation (plastochron) and the characteristics of the lateral organs and axillary meristems. Identifying the unique molecular features of each phase, determining the molecular triggers that cause transitions and understanding the molecular mechanisms underlying these transitions are keys to gleaning a complete understanding of plant development. During the vegetative phase, the shoot apical meristem (SAM) facilitates continuous leaf and stem formation, with leaf development as the hallmark. The transition to the reproductive phase induces significant changes in these processes, driven mainly by the protein FT (FLOWERING LOCUS T) in Arabidopsis and proteins encoded by FT orthologs, which are specified as 'florigen'. These proteins are synthesized in leaves and transported to the SAM, and act as the primary flowering signal, although its impact varies among species. Within the SAM, florigen integrates with other signals, culminating in developmental changes. This review explores the central question of how florigen induces developmental phase transition in the SAM. Future research may combine phase transition studies, potentially revealing the florigen-induced developmental phase transition in the SAM.
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Affiliation(s)
- Hiroyuki Tsuji
- Bioscience and Biotechnology Center, Nagoya University, Furocho, Chikusa, Nagoya, Japan
- Kihara Institute for Biological Research, Yokohama City University, Yokohama, Japan
| | - Moeko Sato
- Kihara Institute for Biological Research, Yokohama City University, Yokohama, Japan
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2
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Santhanagopalan I, Netzl A, Mathur T, Smith A, Griffiths H, Holzer A. Protocol to isolate nuclei from Chlamydomonas reinhardtii for ATAC sequencing. STAR Protoc 2024; 5:102764. [PMID: 38236771 PMCID: PMC10828896 DOI: 10.1016/j.xpro.2023.102764] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2023] [Revised: 10/13/2023] [Accepted: 11/21/2023] [Indexed: 02/03/2024] Open
Abstract
The isolation of sufficient amounts of intact nuclei is essential to obtain high-resolution maps of chromatin accessibility via assay for transposase-accessible chromatin using sequencing (ATAC-seq). Here, we present a protocol for tag-free isolation of nuclei from both cell walled and cell wall-deficient strains of the green model alga Chlamydomonas reinhardtii at a suitable quality for ATAC-seq. We describe steps for nuclei isolation, quantification, and downstream ATAC-seq. This protocol is optimized to shorten the time of isolation and quantification of nuclei.
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Affiliation(s)
- Indu Santhanagopalan
- Department of Plant Sciences, University of Cambridge, Downing Street, Cambridge CB2 3EA, UK.
| | - Antonia Netzl
- Department of Plant Sciences, University of Cambridge, Downing Street, Cambridge CB2 3EA, UK; Department of Zoology, University of Cambridge, Cambridge CB2 3EJ, UK
| | - Tanya Mathur
- Department of Plant Sciences, University of Cambridge, Downing Street, Cambridge CB2 3EA, UK; Institute of Molecular Plant Sciences, University of Edinburgh, Edinburgh EH9 3BF, UK
| | - Alison Smith
- Department of Plant Sciences, University of Cambridge, Downing Street, Cambridge CB2 3EA, UK
| | - Howard Griffiths
- Department of Plant Sciences, University of Cambridge, Downing Street, Cambridge CB2 3EA, UK
| | - Andre Holzer
- Department of Plant Sciences, University of Cambridge, Downing Street, Cambridge CB2 3EA, UK; Center for Bioinformatics and Department of Computer Science, Saarland University, 66123 Saarbrücken, Germany.
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3
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Huang R, Irish VF. An epigenetic timer regulates the transition from cell division to cell expansion during Arabidopsis petal organogenesis. PLoS Genet 2024; 20:e1011203. [PMID: 38442104 PMCID: PMC10942257 DOI: 10.1371/journal.pgen.1011203] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2023] [Revised: 03/15/2024] [Accepted: 02/28/2024] [Indexed: 03/07/2024] Open
Abstract
A number of studies have demonstrated that epigenetic factors regulate plant developmental timing in response to environmental changes. However, we still have an incomplete view of how epigenetic factors can regulate developmental events such as organogenesis, and the transition from cell division to cell expansion, in plants. The small number of cell types and the relatively simple developmental progression required to form the Arabidopsis petal makes it a good model to investigate the molecular mechanisms driving plant organogenesis. In this study, we investigated how the RABBIT EARS (RBE) transcriptional repressor maintains the downregulation of its downstream direct target, TCP5, long after RBE expression dissipates. We showed that RBE recruits the Groucho/Tup1-like corepressor TOPLESS (TPL) to repress TCP5 transcription in petal primordia. This process involves multiple layers of changes such as remodeling of chromatin accessibility, alteration of RNA polymerase activity, and histone modifications, resulting in an epigenetic memory that is maintained through multiple cell divisions. This memory functions to maintain cell divisions during the early phase of petal development, and its attenuation in a cell division-dependent fashion later in development enables the transition from cell division to cell expansion. Overall, this study unveils a novel mechanism by which the memory of an epigenetic state, and its cell-cycle regulated decay, acts as a timer to precisely control organogenesis.
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Affiliation(s)
- Ruirui Huang
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, Connecticut, United States of America
| | - Vivian F. Irish
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, Connecticut, United States of America
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, Connecticut, United States of America
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4
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Lei Y, Yu Y, Fu W, Zhu T, Wu C, Zhang Z, Yu Z, Song X, Xu J, Liang Z, Lü P, Li C. BCL7A and BCL7B potentiate SWI/SNF-complex-mediated chromatin accessibility to regulate gene expression and vegetative phase transition in plants. Nat Commun 2024; 15:935. [PMID: 38296999 PMCID: PMC10830565 DOI: 10.1038/s41467-024-45250-x] [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: 06/29/2023] [Accepted: 01/19/2024] [Indexed: 02/02/2024] Open
Abstract
Switch defective/sucrose non-fermentable (SWI/SNF) chromatin remodeling complexes are multi-subunit machineries that establish and maintain chromatin accessibility and gene expression by regulating chromatin structure. However, how the remodeling activities of SWI/SNF complexes are regulated in eukaryotes remains elusive. B-cell lymphoma/leukemia protein 7 A/B/C (BCL7A/B/C) have been reported as subunits of SWI/SNF complexes for decades in animals and recently in plants; however, the role of BCL7 subunits in SWI/SNF function remains undefined. Here, we identify a unique role for plant BCL7A and BCL7B homologous subunits in potentiating the genome-wide chromatin remodeling activities of SWI/SNF complexes in plants. BCL7A/B require the catalytic ATPase BRAHMA (BRM) to assemble with the signature subunits of the BRM-Associated SWI/SNF complexes (BAS) and for genomic binding at a subset of target genes. Loss of BCL7A and BCL7B diminishes BAS-mediated genome-wide chromatin accessibility without changing the stability and genomic targeting of the BAS complex, highlighting the specialized role of BCL7A/B in regulating remodeling activity. We further show that BCL7A/B fine-tune the remodeling activity of BAS complexes to generate accessible chromatin at the juvenility resetting region (JRR) of the microRNAs MIR156A/C for plant juvenile identity maintenance. In summary, our work uncovers the function of previously elusive SWI/SNF subunits in multicellular eukaryotes and provides insights into the mechanisms whereby plants memorize the juvenile identity through SWI/SNF-mediated control of chromatin accessibility.
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Affiliation(s)
- Yawen Lei
- State Key Laboratory of Biocontrol and Guangdong Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, Guangzhou, 510275, China
| | - Yaoguang Yu
- State Key Laboratory of Biocontrol and Guangdong Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, Guangzhou, 510275, China
| | - Wei Fu
- State Key Laboratory of Biocontrol and Guangdong Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, Guangzhou, 510275, China
| | - Tao Zhu
- State Key Laboratory of Biocontrol and Guangdong Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, Guangzhou, 510275, China
| | - Caihong Wu
- State Key Laboratory of Biocontrol and Guangdong Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, Guangzhou, 510275, China
| | - Zhihao Zhang
- State Key Laboratory of Biocontrol and Guangdong Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, Guangzhou, 510275, China
| | - Zewang Yu
- State Key Laboratory of Biocontrol and Guangdong Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, Guangzhou, 510275, China
| | - Xin Song
- State Key Laboratory of Biocontrol and Guangdong Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, Guangzhou, 510275, China
| | - Jianqu Xu
- State Key Laboratory of Biocontrol and Guangdong Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, Guangzhou, 510275, China
| | - Zhenwei Liang
- State Key Laboratory of Biocontrol and Guangdong Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, Guangzhou, 510275, China
| | - Peitao Lü
- College of Horticulture, FAFU-UCR Joint Center for Horticultural Biology and Metabolomics, Haixia Institute of Science and Technology, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Chenlong Li
- State Key Laboratory of Biocontrol and Guangdong Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, Guangzhou, 510275, China.
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5
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Lu C, Wei Y, Abbas M, Agula H, Wang E, Meng Z, Zhang R. Application of Single-Cell Assay for Transposase-Accessible Chromatin with High Throughput Sequencing in Plant Science: Advances, Technical Challenges, and Prospects. Int J Mol Sci 2024; 25:1479. [PMID: 38338756 PMCID: PMC10855595 DOI: 10.3390/ijms25031479] [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: 11/28/2023] [Revised: 01/16/2024] [Accepted: 01/23/2024] [Indexed: 02/12/2024] Open
Abstract
The Single-cell Assay for Transposase-Accessible Chromatin with high throughput sequencing (scATAC-seq) has gained increasing popularity in recent years, allowing for chromatin accessibility to be deciphered and gene regulatory networks (GRNs) to be inferred at single-cell resolution. This cutting-edge technology now enables the genome-wide profiling of chromatin accessibility at the cellular level and the capturing of cell-type-specific cis-regulatory elements (CREs) that are masked by cellular heterogeneity in bulk assays. Additionally, it can also facilitate the identification of rare and new cell types based on differences in chromatin accessibility and the charting of cellular developmental trajectories within lineage-related cell clusters. Due to technical challenges and limitations, the data generated from scATAC-seq exhibit unique features, often characterized by high sparsity and noise, even within the same cell type. To address these challenges, various bioinformatic tools have been developed. Furthermore, the application of scATAC-seq in plant science is still in its infancy, with most research focusing on root tissues and model plant species. In this review, we provide an overview of recent progress in scATAC-seq and its application across various fields. We first conduct scATAC-seq in plant science. Next, we highlight the current challenges of scATAC-seq in plant science and major strategies for cell type annotation. Finally, we outline several future directions to exploit scATAC-seq technologies to address critical challenges in plant science, ranging from plant ENCODE(The Encyclopedia of DNA Elements) project construction to GRN inference, to deepen our understanding of the roles of CREs in plant biology.
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Affiliation(s)
- Chao Lu
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China; (C.L.); (Y.W.)
- Key Laboratory of Herbage & Endemic Crop Biology, Ministry of Education, School of Life Sciences, Inner Mongolia University, Hohhot 010070, China
| | - Yunxiao Wei
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China; (C.L.); (Y.W.)
| | - Mubashir Abbas
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China; (C.L.); (Y.W.)
| | - Hasi Agula
- Key Laboratory of Herbage & Endemic Crop Biology, Ministry of Education, School of Life Sciences, Inner Mongolia University, Hohhot 010070, China
| | - Edwin Wang
- Cumming School of Medicine, University of Calgary, Calgary, AB T2N 4N1, Canada
| | - Zhigang Meng
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China; (C.L.); (Y.W.)
| | - Rui Zhang
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China; (C.L.); (Y.W.)
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6
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Manosalva Pérez N, Ferrari C, Engelhorn J, Depuydt T, Nelissen H, Hartwig T, Vandepoele K. MINI-AC: inference of plant gene regulatory networks using bulk or single-cell accessible chromatin profiles. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2024; 117:280-301. [PMID: 37788349 DOI: 10.1111/tpj.16483] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/23/2023] [Revised: 09/13/2023] [Accepted: 09/16/2023] [Indexed: 10/05/2023]
Abstract
Gene regulatory networks (GRNs) represent the interactions between transcription factors (TF) and their target genes. Plant GRNs control transcriptional programs involved in growth, development, and stress responses, ultimately affecting diverse agricultural traits. While recent developments in accessible chromatin (AC) profiling technologies make it possible to identify context-specific regulatory DNA, learning the underlying GRNs remains a major challenge. We developed MINI-AC (Motif-Informed Network Inference based on Accessible Chromatin), a method that combines AC data from bulk or single-cell experiments with TF binding site (TFBS) information to learn GRNs in plants. We benchmarked MINI-AC using bulk AC datasets from different Arabidopsis thaliana tissues and showed that it outperforms other methods to identify correct TFBS. In maize, a crop with a complex genome and abundant distal AC regions, MINI-AC successfully inferred leaf GRNs with experimentally confirmed, both proximal and distal, TF-target gene interactions. Furthermore, we showed that both AC regions and footprints are valid alternatives to infer AC-based GRNs with MINI-AC. Finally, we combined MINI-AC predictions from bulk and single-cell AC datasets to identify general and cell-type specific maize leaf regulators. Focusing on C4 metabolism, we identified diverse regulatory interactions in specialized cell types for this photosynthetic pathway. MINI-AC represents a powerful tool for inferring accurate AC-derived GRNs in plants and identifying known and novel candidate regulators, improving our understanding of gene regulation in plants.
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Affiliation(s)
- Nicolás Manosalva Pérez
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052, Ghent, Belgium
- Center for Plant Systems Biology, VIB, 9052, Ghent, Belgium
| | - Camilla Ferrari
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052, Ghent, Belgium
- Center for Plant Systems Biology, VIB, 9052, Ghent, Belgium
| | - Julia Engelhorn
- Molecular Physiology Department, Heinrich-Heine University, 40225, Düsseldorf, Germany
- Max Planck Institute for Plant Breeding Research, 50829, Cologne, Germany
| | - Thomas Depuydt
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052, Ghent, Belgium
- Center for Plant Systems Biology, VIB, 9052, Ghent, Belgium
| | - Hilde Nelissen
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052, Ghent, Belgium
- Center for Plant Systems Biology, VIB, 9052, Ghent, Belgium
| | - Thomas Hartwig
- Molecular Physiology Department, Heinrich-Heine University, 40225, Düsseldorf, Germany
- Max Planck Institute for Plant Breeding Research, 50829, Cologne, Germany
- Cluster of Excellence on Plant Sciences, Düsseldorf, Germany
| | - Klaas Vandepoele
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052, Ghent, Belgium
- Center for Plant Systems Biology, VIB, 9052, Ghent, Belgium
- Bioinformatics Institute Ghent, Ghent University, 9052, Ghent, Belgium
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7
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Yu G, Sun B, Zhu Z, Mehareb EM, Teng A, Han J, Zhang H, Liu J, Liu X, Raza G, Zhang B, Zhang Y, Wang K. Genome-wide DNase I-hypersensitive site assay reveals distinct genomic distributions and functional features of open chromatin in autopolyploid sugarcane. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2024; 117:573-589. [PMID: 37897092 DOI: 10.1111/tpj.16513] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/06/2023] [Revised: 09/15/2023] [Accepted: 10/09/2023] [Indexed: 10/29/2023]
Abstract
The characterization of cis-regulatory DNA elements (CREs) is essential for deciphering the regulation of gene expression in eukaryotes. Although there have been endeavors to identify CREs in plants, the properties of CREs in polyploid genomes are still largely unknown. Here, we conducted the genome-wide identification of DNase I-hypersensitive sites (DHSs) in leaf and stem tissues of the auto-octoploid species Saccharum officinarum. We revealed that DHSs showed highly similar distributions in the genomes of these two S. officinarum tissues. Notably, we observed that approximately 74% of DHSs were located in distal intergenic regions, suggesting considerable differences in the abundance of distal CREs between S. officinarum and other plants. Leaf- and stem-dependent transcriptional regulatory networks were also developed by mining the binding motifs of transcription factors (TFs) from tissue-specific DHSs. Four TEOSINTE BRANCHED 1, CYCLOIDEA, and PCF1 (TCP) TFs (TCP2, TCP4, TCP7, and TCP14) and two ethylene-responsive factors (ERFs) (ERF109 and ERF03) showed strong causal connections with short binding distances from each other, pointing to their possible roles in the regulatory networks of leaf and stem development. Through functional validation in transiently transgenic protoplasts, we isolate a set of tissue-specific promoters. Overall, the DHS maps presented here offer a global view of the potential transcriptional regulatory elements in polyploid sugarcane and can be expected to serve as a valuable resource for both transcriptional network elucidation and genome editing in sugarcane breeding.
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Affiliation(s)
- Guangrun Yu
- School of Life Sciences, Nantong University, Nantong, 226019, China
| | - Bo Sun
- School of Life Sciences, Nantong University, Nantong, 226019, China
- College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Zhiying Zhu
- School of Life Sciences, Nantong University, Nantong, 226019, China
- College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Eid M Mehareb
- Sugar Crops Research Institute (SRCI), Agricultural Research Center (ARC), Giza, 12619, Egypt
| | - Ailing Teng
- School of Life Sciences, Nantong University, Nantong, 226019, China
| | - Jinlei Han
- School of Life Sciences, Nantong University, Nantong, 226019, China
| | - Hui Zhang
- School of Life Sciences, Nantong University, Nantong, 226019, China
| | - Jiayong Liu
- Sugarcane Institute, Yunnan Academy of Agricultural Sciences, Kaiyuan, 661699, China
| | - Xinlong Liu
- Sugarcane Institute, Yunnan Academy of Agricultural Sciences, Kaiyuan, 661699, China
| | - Ghulam Raza
- National Institute for Biotechnology and Genetic Engineering (NIBGE), Faisalabad, 38000, Pakistan
| | - Baohong Zhang
- Department of Biology, East Carolina University, Greenville, North Carolina, 27858, USA
| | - Yuebin Zhang
- Sugarcane Institute, Yunnan Academy of Agricultural Sciences, Kaiyuan, 661699, China
| | - Kai Wang
- School of Life Sciences, Nantong University, Nantong, 226019, China
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8
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Seller CA, Schroeder JI. Distinct guard cell-specific remodeling of chromatin accessibility during abscisic acid- and CO 2-dependent stomatal regulation. Proc Natl Acad Sci U S A 2023; 120:e2310670120. [PMID: 38113262 PMCID: PMC10756262 DOI: 10.1073/pnas.2310670120] [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: 06/29/2023] [Accepted: 11/07/2023] [Indexed: 12/21/2023] Open
Abstract
In plants, epidermal guard cells integrate and respond to numerous environmental signals to control stomatal pore apertures, thereby regulating gas exchange. Chromatin structure controls transcription factor (TF) access to the genome, but whether large-scale chromatin remodeling occurs in guard cells during stomatal movements, and in response to the hormone abscisic acid (ABA) in general, remains unknown. Here, we isolate guard cell nuclei from Arabidopsis thaliana plants to examine whether the physiological signals, ABA and CO2 (carbon dioxide), regulate guard cell chromatin during stomatal movements. Our cell type-specific analyses uncover patterns of chromatin accessibility specific to guard cells and define cis-regulatory sequences supporting guard cell-specific gene expression. We find that ABA triggers extensive and dynamic chromatin remodeling in guard cells, roots, and mesophyll cells with clear patterns of cell type specificity. DNA motif analyses uncover binding sites for distinct TFs enriched in ABA-induced and ABA-repressed chromatin. We identify the Abscisic Acid Response Element (ABRE) Binding Factor (ABF) bZIP-type TFs that are required for ABA-triggered chromatin opening in guard cells and roots and implicate the inhibition of a clade of bHLH-type TFs in controlling ABA-repressed chromatin. Moreover, we demonstrate that ABA and CO2 induce distinct programs of chromatin remodeling, whereby elevated atmospheric CO2 had only minimal impact on chromatin dynamics. We provide insight into the control of guard cell chromatin dynamics and propose that ABA-induced chromatin remodeling primes the genome for abiotic stress resistance.
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Affiliation(s)
- Charles A. Seller
- School of Biological Sciences, Cell and Developmental Biology Department, University of California San Diego, La Jolla, CA92093-0116
| | - Julian I. Schroeder
- School of Biological Sciences, Cell and Developmental Biology Department, University of California San Diego, La Jolla, CA92093-0116
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9
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You Y, Jiang Z. The eINTACT method for studying nuclear changes in host plant cells targeted by bacterial effectors in native infection contexts. Nat Protoc 2023; 18:3173-3193. [PMID: 37697105 DOI: 10.1038/s41596-023-00879-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2022] [Accepted: 06/23/2023] [Indexed: 09/13/2023]
Abstract
Type-III effector proteins are major virulence determinants that most gram-negative bacteria inject into host cells to manipulate cellular processes for infection. Because effector-targeted cells are embedded and underrepresented in infected plant tissues, it is technically challenging to isolate them for focused studies of effector-induced cellular changes. This protocol describes a novel technique, effector-inducible isolation of nuclei tagged in specific cell types (eINTACT), for isolating biotin-labeled nuclei from Arabidopsis plant cells that have received Xanthomonas bacterial effectors by using streptavidin-coated magnetic beads. This protocol is an extension of the existing Nature Protocols Protocol of the INTACT method for the affinity-based purification of nuclei of specific cell types in the context of developmental biology. In a phytopathology scenario, our protocol addresses how to obtain eINTACT transgenic lines and compatible bacterial mutants, verify the eINTACT system and purify nuclei of bacterial effector-recipient cells from infected tissues. Differential analyses of purified nuclei from plants infected by bacteria expressing the effector of interest and those from plants infected by effector-deletion bacterial mutants will reveal the effector-dependent nuclear changes in targeted host cells. Provided that the eINTACT system is available, the infection experiment takes 5 d, and the procedures, from collecting bacteria-infected leaves to obtaining nuclei of effector-targeted cells, can be completed in 4 h. eINTACT is a unique method for isolating high-quality nuclei from bacterial effector-targeted host cells in native infection contexts. This method is adaptable to study the functions of type-III effectors from numerous gram-negative bacteria in host plants that are amenable to transformation.
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Affiliation(s)
- Yuan You
- Department of Molecular Life Sciences, Technical University of Munich, Freising, Germany.
- Department of General Genetics, Center for Plant Molecular Biology, Eberhard-Karls-University Tübingen, Tübingen, Germany.
| | - Zhihao Jiang
- Department of Plant Biochemistry, Center for Plant Molecular Biology, Eberhard-Karls-University Tübingen, Tübingen, Germany
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10
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Fernie AR, Yan J, Aharoni A, Ma J. Editorial: The past, present and future of The Plant Journal Resource Articles. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2023; 116:967-973. [PMID: 37943112 DOI: 10.1111/tpj.16515] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/10/2023]
Affiliation(s)
- Alisdair R Fernie
- Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476, Potsdam-Golm, Germany
| | - Jianbing Yan
- National Key Laboratory of Crop Genetics, Huazhong Agricultural District, Wuhan, China
| | - Asaph Aharoni
- Department of Plant Sciences, Weizmann Institute of Science, Rehovot, Israel
| | - Jianxian Ma
- Purdue University, 915 S. University St, West Lafayette, IN, USA
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11
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Seller CA, Schroeder JI. Distinct guard cell specific remodeling of chromatin accessibility during abscisic acid and CO 2 dependent stomatal regulation. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.05.11.540345. [PMID: 37215031 PMCID: PMC10197618 DOI: 10.1101/2023.05.11.540345] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
In plants, epidermal guard cells integrate and respond to numerous environmental signals to control stomatal pore apertures thereby regulating gas exchange. Chromatin structure controls transcription factor access to the genome, but whether large-scale chromatin remodeling occurs in guard cells during stomatal movements, and in response to the hormone abscisic acid (ABA) in general, remain unknown. Here we isolate guard cell nuclei from Arabidopsis thaliana plants to examine whether the physiological signals, ABA and CO2, regulate guard cell chromatin during stomatal movements. Our cell type specific analyses uncover patterns of chromatin accessibility specific to guard cells and define novel cis-regulatory sequences supporting guard cell specific gene expression. We find that ABA triggers extensive and dynamic chromatin remodeling in guard cells, roots, and mesophyll cells with clear patterns of cell-type specificity. DNA motif analyses uncover binding sites for distinct transcription factors enriched in ABA-induced and ABA-repressed chromatin. We identify the ABF/AREB bZIP-type transcription factors that are required for ABA-triggered chromatin opening in guard cells and implicate the inhibition of a set of bHLH-type transcription factors in controlling ABA-repressed chromatin. Moreover, we demonstrate that ABA and CO2 induce distinct programs of chromatin remodeling. We provide insight into the control of guard cell chromatin dynamics and propose that ABA-induced chromatin remodeling primes the genome for abiotic stress resistance.
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Affiliation(s)
- Charles A. Seller
- School of Biological Sciences, Cell and Developmental Biology Department University of California San Diego, La Jolla, CA 92093-0116
| | - Julian I. Schroeder
- School of Biological Sciences, Cell and Developmental Biology Department University of California San Diego, La Jolla, CA 92093-0116
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12
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Zhang SY, Zhao BG, Shen Z, Mei YC, Li G, Dong FQ, Zhang J, Chao Q, Wang BC. Integrating ATAC-seq and RNA-seq to identify differentially expressed genes with chromatin-accessible changes during photosynthetic establishment in Populus leaves. PLANT MOLECULAR BIOLOGY 2023; 113:59-74. [PMID: 37634200 DOI: 10.1007/s11103-023-01375-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/16/2023] [Accepted: 08/03/2023] [Indexed: 08/29/2023]
Abstract
Leaves are the primary photosynthetic organs, providing essential substances for tree growth. It is important to obtain an anatomical understanding and regulatory network analysis of leaf development. Here, we studied leaf development in Populus Nanlin895 along a development gradient from the newly emerged leaf from the shoot apex to the sixth leaf (L1 to L6) using anatomical observations and RNA-seq analysis. It indicated that mesophyll cells possess obvious vascular, palisade, and spongy tissue with distinct intercellular spaces after L3. Additionally, vacuoles fuse while epidermal cells expand to form pavement cells. RNA-seq analysis indicated that genes highly expressed in L1 and L2 were related to cell division and differentiation, while those highly expressed in L3 were enriched in photosynthesis. Therefore, we selected L1 and L3 to integrate ATAC-seq and RNA-seq and identified 735 differentially expressed genes (DEGs) with changes in chromatin accessibility regions within their promoters, of which 87 were transcription factors (TFs), such as ABI3VP1, AP-EREBP, MYB, NAC, and GRF. Motif enrichment analysis revealed potential regulatory functions for the DEGs through upstream TFs including TCP, bZIP, HD-ZIP, Dof, BBR-BPC, and MYB. Overall, our research provides a potential molecular foundation for regulatory network exploration in leaf development during photosynthesis establishment.
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Affiliation(s)
- Sheng-Ying Zhang
- Photosynthesis Research Center, Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Biligen-Gaowa Zhao
- Photosynthesis Research Center, Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Zhuo Shen
- Guangdong Key Laboratory for New Technology Research of Vegetables, Vegetable Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640, China
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, 150040, China
| | - Ying-Chang Mei
- Photosynthesis Research Center, Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Guo Li
- Photosynthesis Research Center, Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Feng-Qin Dong
- University of Chinese Academy of Sciences, Beijing, 100049, China
- The Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing, China
| | - Jiao Zhang
- Photosynthesis Research Center, Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Qing Chao
- Photosynthesis Research Center, Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China.
- University of Chinese Academy of Sciences, Beijing, 100049, China.
| | - Bai-Chen Wang
- Photosynthesis Research Center, Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China.
- University of Chinese Academy of Sciences, Beijing, 100049, China.
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13
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Xu C, Song LY, Zhou Y, Ma DN, Ding QS, Guo ZJ, Li J, Song SW, Zhang LD, Zheng HL. Integration of eQTL and GWAS analysis uncovers a genetic regulation of natural ionomic variation in Arabidopsis. PLANT CELL REPORTS 2023; 42:1473-1485. [PMID: 37516984 DOI: 10.1007/s00299-023-03042-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/27/2022] [Accepted: 06/12/2023] [Indexed: 08/01/2023]
Abstract
KEY MESSAGE This study provided important insights into the genetic architecture of variations in A. thaliana leaf ionome in a cell-type-specific manner. The functional interpretation of traits associated variants by expression quantitative trait loci (eQTL) analysis is usually performed in bulk tissue samples. While the regulation of gene expression is context-dependent, such as cell-type-specific manner. In this study, we estimated cell-type abundances from 728 bulk tissue samples using single-cell RNA-sequencing dataset, and performed cis-eQTL mapping to identify cell-type-interaction eQTL (cis-eQTLs(ci)) in A. thaliana. Also, we performed Genome-wide association studies (GWAS) analyses for 999 accessions to identify the genetic basis of variations in A. thaliana leaf ionome. As a result, a total of 5,664 unique eQTL genes and 15,038 unique cis-eQTLs(ci) were significant. The majority (62.83%) of cis-eQTLs(ci) were cell-type-specific eQTLs. Using colocalization, we uncovered one interested gene AT2G25590 in Phloem cell, encoding a kind of plant Tudor-like protein with possible chromatin-associated functions, which colocalized with the most significant cis-eQTL(ci) of a Mo-related locus (Chr2:10,908,806:A:C; P = 3.27 × 10-27). Furthermore, we prioritized eight target genes associated with AT2G25590, which were previously reported in regulating the concentration of Mo element in A. thaliana. This study revealed the genetic regulation of ionomic variations and provided a foundation for further studies on molecular mechanisms of genetic variants controlling the A. thaliana ionome.
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Affiliation(s)
- Chaoqun Xu
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, College of the Environment and Ecology, Xiamen University, Xiamen, 361104, China
| | - Ling-Yu Song
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, College of the Environment and Ecology, Xiamen University, Xiamen, 361104, China
| | - Ying Zhou
- School of Medicine, National Institute for Data Science in Health and Medicine, Xiamen University, Xiamen, 361102, China
| | - Dong-Na Ma
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, College of the Environment and Ecology, Xiamen University, Xiamen, 361104, China
- National Engineering Research Center of Cereal Fermentation and Food Biomanufacturing, School of Food Science and Technology, Jiangnan University, Wuxi, 214122, Jiangsu, China
| | - Qian-Su Ding
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, College of the Environment and Ecology, Xiamen University, Xiamen, 361104, China
| | - Ze-Jun Guo
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, College of the Environment and Ecology, Xiamen University, Xiamen, 361104, China
| | - Jing Li
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, College of the Environment and Ecology, Xiamen University, Xiamen, 361104, China
| | - Shi-Wei Song
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, College of the Environment and Ecology, Xiamen University, Xiamen, 361104, China
| | - Lu-Dan Zhang
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, College of the Environment and Ecology, Xiamen University, Xiamen, 361104, China
| | - Hai-Lei Zheng
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, College of the Environment and Ecology, Xiamen University, Xiamen, 361104, China.
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14
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Ouyang K, Liang Q, Miao L, Zhang Z, Li Z. Genome-wide mapping of DNase I hypersensitive sites in pineapple leaves. Front Genet 2023; 14:1086554. [PMID: 37470036 PMCID: PMC10352800 DOI: 10.3389/fgene.2023.1086554] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2022] [Accepted: 06/21/2023] [Indexed: 07/21/2023] Open
Abstract
Pineapple [Ananas comosus (L.) Merr.] is the most economically important crop possessing crassulacean acid metabolism (CAM) photosynthesis which has a higher water use efficiency by control of nocturnal opening and diurnal closure of stomata. To provide novel insights into the diel regulatory landscape in pineapple leaves, we performed genome-wide mapping of DNase I hypersensitive sites (DHSs) in pineapple leaves at day (2a.m.) and night (10a.m.) using a simplified DNase-seq method. As a result, totally 33340 and 28753 DHSs were found in green-tip tissue, and 29597 and 40068 were identified in white-base tissue at 2a.m. and 10a.m., respectively. We observed that majority of the pineapple genes occupied less than two DHSs with length shorter than 1 kb, and the promotor DHSs showed a proximal trend to the transcription start site (>77% promotor DHSs within 1 kb). In addition, more intergenic DHSs were identified around transcription factors or transcription co-regulators (TFs/TCs) than other functional genes, indicating complex regulatory contexts around TFs/TCs. Through combined analysis of tissue preferential DHSs and genes, we respectively found 839 and 888 coordinately changed genes in green-tip at 2a.m. and 10a.m. (AcG2 and AcG10). Furthermore, AcG2-specific, AcG10-specific and common accessible DHSs were dissected from the total photosynthetic preferential DHSs, and the regulatory networks indicated dynamic regulations with multiple cis-regulatory elements occurred to genes preferentially expressed in photosynthetic tissues. Interestingly, binding motifs of several cycling TFs were identified in the DHSs of key CAM genes, revealing a circadian regulation to CAM coordinately diurnal expression. Our results provide a chromatin regulatory landscape in pineapple leaves during the day and night. This will provide important information to assist with deciphering the circadian regulation of CAM photosynthesis.
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Affiliation(s)
- Kai Ouyang
- Key Laboratory of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education, Key Laboratory of Biological Breeding for Fujian and Taiwan Crops, Ministry of Agriculture and Rural Affairs, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Center for Genomics and Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Qifu Liang
- Fujian Key Laboratory of Agro-Products Quality and Safety, Institute of Quality Standards and Testing Technology for Agro-Products, Fujian Academy of Agricultural Sciences, Fuzhou, Fujian, China
| | - Li Miao
- Key Laboratory of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education, Key Laboratory of Biological Breeding for Fujian and Taiwan Crops, Ministry of Agriculture and Rural Affairs, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Center for Genomics and Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Zhiliang Zhang
- Key Laboratory of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education, Key Laboratory of Biological Breeding for Fujian and Taiwan Crops, Ministry of Agriculture and Rural Affairs, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Center for Genomics and Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, China
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Innovative Academy for Seed Design, Chinese Academy of Sciences, Beijing, China
| | - Zhanjie Li
- Key Laboratory of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education, Key Laboratory of Biological Breeding for Fujian and Taiwan Crops, Ministry of Agriculture and Rural Affairs, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Center for Genomics and Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, China
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15
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Chen G, Liu Z, Li S, Liu L, Lu L, Wang Z, Mendu V, Li F, Yang Z. Characterization of chromatin accessibility and gene expression reveal the key genes involved in cotton fiber elongation. PHYSIOLOGIA PLANTARUM 2023; 175:e13972. [PMID: 37405386 DOI: 10.1111/ppl.13972] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/12/2023] [Revised: 06/05/2023] [Accepted: 06/29/2023] [Indexed: 07/06/2023]
Abstract
Cotton (Gossypium hirsutum L.) is an important economic crop, and cotton fiber is one of the longest plant cells, which provides an ideal model for the study of cell elongation and secondary cell wall synthesis. Cotton fiber length is regulated by a variety of transcription factors (TF) and their target genes; however, the mechanism of fiber elongation mediated by transcriptional regulatory networks is still unclear to a large extent. Here, we used a comparative assay for transposase-accessible chromatin with high-throughput sequencing (ATAC-seq) assay and RNA-seq analysis to identify fiber elongation transcription factors and genes using the short-fiber mutant ligon linless-2 (Li2 ) and wild type (WT). A total of 499 differential target genes were identified and GO analysis shows that differential genes are mainly involved in plant secondary wall synthesis and microtubule-binding processes. Analysis of the genomic regions preferentially accessible (Peak) has identified a number of overrepresented TF-binding motifs, highlighting sets of TFs that are important for cotton fiber development. Using ATAC-seq and RNA-seq data, we have constructed a functional regulatory network of each TF regulatory target gene and also the network pattern of TF regulating differential target genes. Further, to obtain the genes related to fiber length, the differential target genes were combined with FLGWAS data to identify the genes highly related to fiber length. Our work provides new insights into cotton fiber elongation.
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Affiliation(s)
- Guoquan Chen
- Zhengzhou Research Base, National Key Laboratory of Cotton Bio-breeding and Integrated Utilization, School of Agricultural Sciences, Zhengzhou University, Zhengzhou, Henan, China
| | - Zhao Liu
- Zhengzhou Research Base, National Key Laboratory of Cotton Bio-breeding and Integrated Utilization, School of Agricultural Sciences, Zhengzhou University, Zhengzhou, Henan, China
| | - Shengdong Li
- Zhengzhou Research Base, National Key Laboratory of Cotton Bio-breeding and Integrated Utilization, School of Agricultural Sciences, Zhengzhou University, Zhengzhou, Henan, China
| | - Le Liu
- Zhengzhou Research Base, National Key Laboratory of Cotton Bio-breeding and Integrated Utilization, School of Agricultural Sciences, Zhengzhou University, Zhengzhou, Henan, China
| | - Lili Lu
- National Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, Henan, China
| | - Zhi Wang
- Zhengzhou Research Base, National Key Laboratory of Cotton Bio-breeding and Integrated Utilization, School of Agricultural Sciences, Zhengzhou University, Zhengzhou, Henan, China
- Hainan Yazhou Bay Seed Lab, Sanya, Hainan, China
| | - Venugopal Mendu
- Department of Plant Sciences and Plant Pathology, Montana State University, Bozeman, Montana, USA
| | - Fuguang Li
- Zhengzhou Research Base, National Key Laboratory of Cotton Bio-breeding and Integrated Utilization, School of Agricultural Sciences, Zhengzhou University, Zhengzhou, Henan, China
- National Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, Henan, China
| | - Zuoren Yang
- Zhengzhou Research Base, National Key Laboratory of Cotton Bio-breeding and Integrated Utilization, School of Agricultural Sciences, Zhengzhou University, Zhengzhou, Henan, China
- National Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, Henan, China
- Xinjiang Production and Construction Group Key Laboratory of Crop Germplasm Enhancement and Gene Resources Utilization, Biotechnology Research Institute of Xinjiang Academy of Agricultural and Reclamation Science, Xinjiang, China
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16
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Smith GD, Ching WH, Cornejo-Páramo P, Wong ES. Decoding enhancer complexity with machine learning and high-throughput discovery. Genome Biol 2023; 24:116. [PMID: 37173718 PMCID: PMC10176946 DOI: 10.1186/s13059-023-02955-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2022] [Accepted: 04/28/2023] [Indexed: 05/15/2023] Open
Abstract
Enhancers are genomic DNA elements controlling spatiotemporal gene expression. Their flexible organization and functional redundancies make deciphering their sequence-function relationships challenging. This article provides an overview of the current understanding of enhancer organization and evolution, with an emphasis on factors that influence these relationships. Technological advancements, particularly in machine learning and synthetic biology, are discussed in light of how they provide new ways to understand this complexity. Exciting opportunities lie ahead as we continue to unravel the intricacies of enhancer function.
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Affiliation(s)
- Gabrielle D Smith
- Victor Chang Cardiac Research Institute, 405 Liverpool Street, Darlinghurst, NSW, Australia
- School of Biotechnology and Biomolecular Sciences, UNSW Sydney, Kensington, NSW, Australia
| | - Wan Hern Ching
- Victor Chang Cardiac Research Institute, 405 Liverpool Street, Darlinghurst, NSW, Australia
| | - Paola Cornejo-Páramo
- Victor Chang Cardiac Research Institute, 405 Liverpool Street, Darlinghurst, NSW, Australia
- School of Biotechnology and Biomolecular Sciences, UNSW Sydney, Kensington, NSW, Australia
| | - Emily S Wong
- Victor Chang Cardiac Research Institute, 405 Liverpool Street, Darlinghurst, NSW, Australia.
- School of Biotechnology and Biomolecular Sciences, UNSW Sydney, Kensington, NSW, Australia.
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17
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Integrated ATAC-Seq and RNA-Seq Data Analysis to Reveal OsbZIP14 Function in Rice in Response to Heat Stress. Int J Mol Sci 2023; 24:ijms24065619. [PMID: 36982696 PMCID: PMC10057503 DOI: 10.3390/ijms24065619] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2023] [Revised: 03/08/2023] [Accepted: 03/14/2023] [Indexed: 03/17/2023] Open
Abstract
Transcription factors (TFs) play critical roles in mediating the plant response to various abiotic stresses, particularly heat stress. Plants respond to elevated temperatures by modulating the expression of genes involved in diverse metabolic pathways, a regulatory process primarily governed by multiple TFs in a networked configuration. Many TFs, such as WRKY, MYB, NAC, bZIP, zinc finger protein, AP2/ERF, DREB, ERF, bHLH, and brassinosteroids, are associated with heat shock factor (Hsf) families, and are involved in heat stress tolerance. These TFs hold the potential to control multiple genes, which makes them ideal targets for enhancing the heat stress tolerance of crop plants. Despite their immense importance, only a small number of heat-stress-responsive TFs have been identified in rice. The molecular mechanisms underpinning the role of TFs in rice adaptation to heat stress still need to be researched. This study identified three TF genes, including OsbZIP14, OsMYB2, and OsHSF7, by integrating transcriptomic and epigenetic sequencing data analysis of rice in response to heat stress. Through comprehensive bioinformatics analysis, we demonstrated that OsbZIP14, one of the key heat-responsive TF genes, contained a basic-leucine zipper domain and primarily functioned as a nuclear TF with transcriptional activation capability. By knocking out the OsbZIP14 gene in the rice cultivar Zhonghua 11, we observed that the knockout mutant OsbZIP14 exhibited dwarfism with reduced tiller during the grain-filling stage. Under high-temperature treatment, it was also demonstrated that in the OsbZIP14 mutant, the expression of the OsbZIP58 gene, a key regulator of rice seed storage protein (SSP) accumulation, was upregulated. Furthermore, bimolecular fluorescence complementation (BiFC) experiments uncovered a direct interaction between OsbZIP14 and OsbZIP58. Our results suggested that OsbZIP14 acts as a key TF gene through the concerted action of OsbZIP58 and OsbZIP14 during rice filling under heat stress. These findings provide good candidate genes for genetic improvement of rice but also offer valuable scientific insights into the mechanism of heat tolerance stress in rice.
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18
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Jia Y, Xu Y, Wang B, Guo L, Guo M, Che X, Ye K. The tissue-specific chromatin accessibility landscape of Papaver somniferum. Front Genet 2023; 14:1136736. [PMID: 37007951 PMCID: PMC10050356 DOI: 10.3389/fgene.2023.1136736] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2023] [Accepted: 03/03/2023] [Indexed: 03/17/2023] Open
Affiliation(s)
- Yanyan Jia
- School of Automation Science and Engineering, Faculty of Electronic and Information Engineering, Xi’an Jiaotong University, Xi’an, Shaanxi, China
| | - Yu Xu
- School of Life Science and Technology, Xi’an Jiaotong University, Xi’an, Shaanxi, China
| | - Bo Wang
- School of Automation Science and Engineering, Faculty of Electronic and Information Engineering, Xi’an Jiaotong University, Xi’an, Shaanxi, China
- MOE Key Lab for Intelligent Networks & Networks Security, Faculty of Electronic and Information Engineering, Xi’an Jiaotong University, Xi’an, Shaanxi, China
| | - Li Guo
- School of Automation Science and Engineering, Faculty of Electronic and Information Engineering, Xi’an Jiaotong University, Xi’an, Shaanxi, China
| | - Mengyao Guo
- School of Life Science and Technology, Xi’an Jiaotong University, Xi’an, Shaanxi, China
| | - Xiaofei Che
- School of Automation Science and Engineering, Faculty of Electronic and Information Engineering, Xi’an Jiaotong University, Xi’an, Shaanxi, China
| | - Kai Ye
- School of Automation Science and Engineering, Faculty of Electronic and Information Engineering, Xi’an Jiaotong University, Xi’an, Shaanxi, China
- School of Life Science and Technology, Xi’an Jiaotong University, Xi’an, Shaanxi, China
- MOE Key Lab for Intelligent Networks & Networks Security, Faculty of Electronic and Information Engineering, Xi’an Jiaotong University, Xi’an, Shaanxi, China
- Genome Institute, the First Affiliated Hospital of Xi’an Jiaotong University, Xi’an, Shaanxi, China
- Faculty of Science, Leiden University, Leiden, Netherlands
- *Correspondence: Kai Ye,
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19
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Guo S, Ji Y, Zheng Y, Watkins CB, Ma L, Wang Q, Liang H, Bai C, Fu A, Li L, Meng D, Liu M, Zuo J. Transcriptomic, metabolomic, and ATAC-seq analysis reveal the regulatory mechanism of senescence of post-harvest tomato fruit. FRONTIERS IN PLANT SCIENCE 2023; 14:1142913. [PMID: 36968400 PMCID: PMC10032333 DOI: 10.3389/fpls.2023.1142913] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/12/2023] [Accepted: 02/13/2023] [Indexed: 06/18/2023]
Abstract
Several physiological changes occur during fruit storage, which include the regulation of genes, metabolisms and transcription factors. In this study, we compared 'JF308' (a normal tomato cultivar) and 'YS006' (a storable tomato cultivar) to determine the difference in accumulated metabolites, gene expression, and accessible chromatin regions through metabolome, transcriptome, and ATAC-seq analysis. A total of 1006 metabolites were identified in two cultivars. During storage time, sugars, alcohols and flavonoids were found to be more abundant in 'YS006' compared to 'JF308' on day 7, 14, and 21, respectively. Differentially expressed genes, which involved in starch and sucrose biosynthesis were observed higher in 'YS006'. 'YS006' had lower expression levels of CesA (cellulose synthase), PL (pectate lyase), EXPA (expansin) and XTH (xyglucan endoglutransglucosylase/hydrolase) than 'JF308'. The results showed that phenylpropanoid pathway, carbohydrate metabolism and cell wall metabolism play important roles in prolonging the shelf life of tomato (Solanum lycopersicum) fruit. The ATAC-seq analysis revealed that the most significantly up-regulated transcription factors during storage were TCP 2,3,4,5, and 24 in 'YS006' compared to 'JF308' on day 21. This information on the molecular regulatory mechanisms and metabolic pathways of post-harvest quality changes in tomato fruit provides a theoretical foundation for slowing post-harvest decay and loss, and has theoretical importance and application value in breeding for longer shelf life cultivars.
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Affiliation(s)
- Susu Guo
- State Key Laboratory of Food Nutrition and Safety, College of Food Science and Engineering, Tianjin University of Science & Technology, Tianjin, China
- Key Laboratory of Vegetable Postharvest Processing, Ministry of Agriculture, Institute of Agri-Products Processing and Food Nutrition, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
- Beijing Key Laboratory of Fruits and Vegetable Storage and Processing, Institute of Agri-Products Processing and Food Nutrition, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China) of Ministry of Agriculture, Institute of Agri-Products Processing and Food Nutrition, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
- Key Laboratory of Urban Agriculture (North) of Ministry of Agriculture, Beijing Vegetable Research Center, Institute of Agri-Products Processing and Food Nutrition, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
| | - Yanhai Ji
- Key Laboratory of Vegetable Postharvest Processing, Ministry of Agriculture, Institute of Agri-Products Processing and Food Nutrition, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
- Beijing Key Laboratory of Fruits and Vegetable Storage and Processing, Institute of Agri-Products Processing and Food Nutrition, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China) of Ministry of Agriculture, Institute of Agri-Products Processing and Food Nutrition, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
- Key Laboratory of Urban Agriculture (North) of Ministry of Agriculture, Beijing Vegetable Research Center, Institute of Agri-Products Processing and Food Nutrition, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
| | - Yanyan Zheng
- Key Laboratory of Vegetable Postharvest Processing, Ministry of Agriculture, Institute of Agri-Products Processing and Food Nutrition, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
- Beijing Key Laboratory of Fruits and Vegetable Storage and Processing, Institute of Agri-Products Processing and Food Nutrition, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China) of Ministry of Agriculture, Institute of Agri-Products Processing and Food Nutrition, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
- Key Laboratory of Urban Agriculture (North) of Ministry of Agriculture, Beijing Vegetable Research Center, Institute of Agri-Products Processing and Food Nutrition, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
| | - Christopher B. Watkins
- School of Integrative Plant Science, Horticulture Section, College of Agriculture and Life Science, Cornell University, NY, Ithaca, United States
| | - Lili Ma
- College of Food Science and Biotechnology, Tianjin Agricultural University, Tianjin, China
| | - Qing Wang
- Key Laboratory of Vegetable Postharvest Processing, Ministry of Agriculture, Institute of Agri-Products Processing and Food Nutrition, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
- Beijing Key Laboratory of Fruits and Vegetable Storage and Processing, Institute of Agri-Products Processing and Food Nutrition, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China) of Ministry of Agriculture, Institute of Agri-Products Processing and Food Nutrition, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
- Key Laboratory of Urban Agriculture (North) of Ministry of Agriculture, Beijing Vegetable Research Center, Institute of Agri-Products Processing and Food Nutrition, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
| | - Hao Liang
- Key Laboratory of Vegetable Postharvest Processing, Ministry of Agriculture, Institute of Agri-Products Processing and Food Nutrition, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
- Beijing Key Laboratory of Fruits and Vegetable Storage and Processing, Institute of Agri-Products Processing and Food Nutrition, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China) of Ministry of Agriculture, Institute of Agri-Products Processing and Food Nutrition, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
- Key Laboratory of Urban Agriculture (North) of Ministry of Agriculture, Beijing Vegetable Research Center, Institute of Agri-Products Processing and Food Nutrition, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
| | - Chunmei Bai
- Key Laboratory of Vegetable Postharvest Processing, Ministry of Agriculture, Institute of Agri-Products Processing and Food Nutrition, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
- Beijing Key Laboratory of Fruits and Vegetable Storage and Processing, Institute of Agri-Products Processing and Food Nutrition, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China) of Ministry of Agriculture, Institute of Agri-Products Processing and Food Nutrition, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
- Key Laboratory of Urban Agriculture (North) of Ministry of Agriculture, Beijing Vegetable Research Center, Institute of Agri-Products Processing and Food Nutrition, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
| | - Anzhen Fu
- Key Laboratory of Vegetable Postharvest Processing, Ministry of Agriculture, Institute of Agri-Products Processing and Food Nutrition, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
- Beijing Key Laboratory of Fruits and Vegetable Storage and Processing, Institute of Agri-Products Processing and Food Nutrition, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China) of Ministry of Agriculture, Institute of Agri-Products Processing and Food Nutrition, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
- Key Laboratory of Urban Agriculture (North) of Ministry of Agriculture, Beijing Vegetable Research Center, Institute of Agri-Products Processing and Food Nutrition, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
| | - Ling Li
- College of Food Science and Biotechnology, Tianjin Agricultural University, Tianjin, China
| | - Demei Meng
- State Key Laboratory of Food Nutrition and Safety, College of Food Science and Engineering, Tianjin University of Science & Technology, Tianjin, China
| | - Mingchi Liu
- Key Laboratory of Vegetable Postharvest Processing, Ministry of Agriculture, Institute of Agri-Products Processing and Food Nutrition, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
- Beijing Key Laboratory of Fruits and Vegetable Storage and Processing, Institute of Agri-Products Processing and Food Nutrition, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China) of Ministry of Agriculture, Institute of Agri-Products Processing and Food Nutrition, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
- Key Laboratory of Urban Agriculture (North) of Ministry of Agriculture, Beijing Vegetable Research Center, Institute of Agri-Products Processing and Food Nutrition, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
| | - Jinhua Zuo
- Key Laboratory of Vegetable Postharvest Processing, Ministry of Agriculture, Institute of Agri-Products Processing and Food Nutrition, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
- Beijing Key Laboratory of Fruits and Vegetable Storage and Processing, Institute of Agri-Products Processing and Food Nutrition, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China) of Ministry of Agriculture, Institute of Agri-Products Processing and Food Nutrition, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
- Key Laboratory of Urban Agriculture (North) of Ministry of Agriculture, Beijing Vegetable Research Center, Institute of Agri-Products Processing and Food Nutrition, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
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20
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Benstein RM, Schmid M, You Y. Isolation of Nuclei Tagged in Specific Cell Types (INTACT) in Arabidopsis. Methods Mol Biol 2023; 2686:313-328. [PMID: 37540367 DOI: 10.1007/978-1-0716-3299-4_16] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/05/2023]
Abstract
Many functionally distinct plant tissues have relatively low numbers of cells that are embedded within complex tissues. For example, the shoot apical meristem (SAM) consists of a small population of pluripotent stem cells surrounded by developing leaves and/or flowers at the growing tip of the plant. It is technically challenging to collect enough high-quality SAM samples for molecular analyses. Isolation of Nuclei Tagged in specific Cell Types (INTACT) is an easily reproducible method that allows the enrichment of biotin-tagged cell-type-specific nuclei from the total nuclei pool using biotin-streptavidin affinity purification. Here, we provide a detailed INTACT protocol for isolating nuclei from the Arabidopsis SAM. One can also adapt this protocol to isolate nuclei from other tissues and cell types for investigating tissue/cell-type-specific transcriptome and epigenome and their changes during developmental programs at a high spatiotemporal resolution. Furthermore, due to its low cost and simple procedures, INTACT can be conducted in any standard molecular laboratory.
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Affiliation(s)
- Ruben M Benstein
- Umeå Plant Science Centre, Department of Plant Physiology, Umeå University, Umeå, Sweden
| | - Markus Schmid
- Umeå Plant Science Centre, Department of Plant Physiology, Umeå University, Umeå, Sweden
- Department of Plant Biology, Linnean Centre for Plant Biology, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Yuan You
- Center for Plant Molecular Biology (ZMBP), Department of General Genetics, Eberhard Karls University of Tübingen, Tübingen, Germany.
- Department of Molecular Life Sciences, Technical University of Munich, Freising, Germany.
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21
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Wang P, Gu M, Yu X, Shao S, Du J, Wang Y, Wang F, Chen S, Liao Z, Ye N, Zhang X. Allele-specific expression and chromatin accessibility contribute to heterosis in tea plants (Camellia sinensis). THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2022; 112:1194-1211. [PMID: 36219505 DOI: 10.1111/tpj.16004] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/20/2022] [Revised: 10/05/2022] [Accepted: 10/07/2022] [Indexed: 06/16/2023]
Abstract
Heterosis is extensively used to improve crop productivity, yet its allelic and chromatin regulation remains unclear. Based on our resolved genomes of the maternal TGY and paternal HD, we analyzed the contribution of allele-specific expression (ASE) and chromatin accessibility of JGY and HGY, the artificial hybrids of oolong tea with the largest cultivated area in China. The ASE genes (ASEGs) of tea hybrids with maternal-biased were mainly related to the energy and terpenoid metabolism pathways, whereas the ASEGs with paternal-biased tend to be enriched in glutathione metabolism, and these parental bias of hybrids may coordinate and lead to the acquisition of heterosis in more biological pathways. ATAC-seq results showed that hybrids have significantly higher accessible chromatin regions (ACRs) compared with their parents, which may confer broader and stronger transcriptional activity of genes in hybrids. The number of ACRs with significantly increased accessibility in hybrids was much greater than decreased, and the associated alleles were also affected by differential ACRs across different parents, suggesting enhanced positive chromatin regulation and potential genetic effects in hybrids. Core ASEGs of terpene and purine alkaloid metabolism pathways with significant positive heterosis have greater chromatin accessibility in hybrids, and were potentially regulated by several members of the MYB, DOF and TRB families. The binding motif of CsMYB85 in the promoter ACR of the rate-limiting enzyme CsDXS was verified by DAP-seq. These results suggest that higher numbers and more accessible ACRs in hybrids contribute to the regulation of ASEGs, thereby affecting the formation of heterotic metabolites.
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Affiliation(s)
- Pengjie Wang
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518120, China
- College of Horticulture, Fujian Agriculture and Forestry University/Key Laboratory of Tea Science in Universities of Fujian Province, Fuzhou, 350002, China
| | - Mengya Gu
- College of Horticulture, Fujian Agriculture and Forestry University/Key Laboratory of Tea Science in Universities of Fujian Province, Fuzhou, 350002, China
| | - Xikai Yu
- College of Agriculture, Guangxi University, Nanning, 530004, China
| | - Shuxian Shao
- College of Horticulture, Fujian Agriculture and Forestry University/Key Laboratory of Tea Science in Universities of Fujian Province, Fuzhou, 350002, China
| | - Jiayin Du
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518120, China
| | - Yibin Wang
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518120, China
| | - Feiquan Wang
- College of Tea and Food Science, Wuyi University, Wuyishan, Fujian, 354300, China
| | - Shuai Chen
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518120, China
| | - Zhenyang Liao
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518120, China
| | - Naixing Ye
- College of Horticulture, Fujian Agriculture and Forestry University/Key Laboratory of Tea Science in Universities of Fujian Province, Fuzhou, 350002, China
| | - Xingtan Zhang
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518120, China
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22
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Nguyen V, Gutzat R. Epigenetic regulation in the shoot apical meristem. CURRENT OPINION IN PLANT BIOLOGY 2022; 69:102267. [PMID: 35985107 DOI: 10.1016/j.pbi.2022.102267] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/21/2022] [Revised: 06/09/2022] [Accepted: 06/17/2022] [Indexed: 06/15/2023]
Abstract
Epigenetic mechanisms form the basis of cellular memory, developmental decisions, and the cellular immune system that defends against transposons and viruses. Organs develop from the shoot apical meristem (SAM) to shape the plant's areal phenotype, and stem cells in the SAM serve as a functional germline. While many details on the regulation of stem cell pool size, organ initiation, and patterning at the meristem periphery are known, we know surprisingly little about the molecular characteristics of SAM cells, including their epigenome and how it changes during development. Here, we summarize information on epigenetic regulation of selected genes necessary for stem cell maintenance. As recent evidence suggests that SAM stem cells might be a hotspot of transposon activation, we discuss this aspect of epigenetic control in the meristem and speculate on mechanisms that maintain the flexibility of SAM stem cells in response to developmental or environmental cues.
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Affiliation(s)
- Vu Nguyen
- Gregor Mendel Institute of Molecular Plant Biology, Austrian Academy of Sciences, Vienna Biocenter (VBC), Vienna, 1030, Austria
| | - Ruben Gutzat
- Gregor Mendel Institute of Molecular Plant Biology, Austrian Academy of Sciences, Vienna Biocenter (VBC), Vienna, 1030, Austria.
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23
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Wang S, He J, Deng M, Wang C, Wang R, Yan J, Luo M, Ma F, Guan Q, Xu J. Integrating ATAC-seq and RNA-seq Reveals the Dynamics of Chromatin Accessibility and Gene Expression in Apple Response to Drought. Int J Mol Sci 2022; 23:ijms231911191. [PMID: 36232500 PMCID: PMC9570298 DOI: 10.3390/ijms231911191] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2022] [Revised: 09/19/2022] [Accepted: 09/21/2022] [Indexed: 11/16/2022] Open
Abstract
Drought resistance in plants is influenced by multiple signaling pathways that involve various transcription factors, many target genes, and multiple types of epigenetic modifications. Studies on epigenetic modifications of drought focus on DNA methylation and histone modifications, with fewer on chromatin remodeling. Changes in chromatin accessibility can play an important role in abiotic stress in plants by affecting RNA polymerase binding and various regulatory factors. However, the changes in chromatin accessibility during drought in apples are not well understood. In this study, the landscape of chromatin accessibility associated with the gene expression of apple (GL3) under drought conditions was analyzed by Assay for Transposase Accessible Chromatin with high-throughput sequencing (ATAC-seq) and RNA-seq. Differential analysis between drought treatment and control identified 23,466 peaks of upregulated chromatin accessibility and 2447 peaks of downregulated accessibility. The drought-induced chromatin accessibility changed genes were mainly enriched in metabolism, stimulus, and binding pathways. By combining results from differential analysis of RNA-seq and ATAC-seq, we identified 240 genes with higher chromatin accessibility and increased gene expression under drought conditions that may play important functions in the drought response process. Among them, a total of nine transcription factor genes were identified, including ATHB7, HAT5, and WRKY26. These transcription factor genes are differentially expressed with different chromatin accessibility motif binding loci that may participate in apple response to drought by regulating downstream genes. Our study provides a reference for chromatin accessibility under drought stress in apples and the results will facilitate subsequent studies on chromatin remodelers and transcription factors.
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Affiliation(s)
- Shicong Wang
- State Key Laboratory of Crop Stress Biology for Arid Areas/Shaanxi Key Laboratory of Apple, College of Horticulture, Northwest Agricultural and Forestry University, Yangling, Xianyang 712100, China
| | - Jieqiang He
- State Key Laboratory of Crop Stress Biology for Arid Areas/Shaanxi Key Laboratory of Apple, College of Horticulture, Northwest Agricultural and Forestry University, Yangling, Xianyang 712100, China
| | - Mengting Deng
- State Key Laboratory of Crop Stress Biology for Arid Areas/Shaanxi Key Laboratory of Apple, College of Horticulture, Northwest Agricultural and Forestry University, Yangling, Xianyang 712100, China
| | - Caixia Wang
- State Key Laboratory of Crop Stress Biology for Arid Areas/Shaanxi Key Laboratory of Apple, College of Horticulture, Northwest Agricultural and Forestry University, Yangling, Xianyang 712100, China
| | - Ruifeng Wang
- State Key Laboratory of Crop Stress Biology for Arid Areas/Shaanxi Key Laboratory of Apple, College of Horticulture, Northwest Agricultural and Forestry University, Yangling, Xianyang 712100, China
| | - Jinjiao Yan
- College of Forestry, Northwest Agricultural and Forestry University, Yangling, Xianyang 712100, China
| | - Minrong Luo
- State Key Laboratory of Crop Stress Biology for Arid Areas/Shaanxi Key Laboratory of Apple, College of Horticulture, Northwest Agricultural and Forestry University, Yangling, Xianyang 712100, China
| | - Fengwang Ma
- State Key Laboratory of Crop Stress Biology for Arid Areas/Shaanxi Key Laboratory of Apple, College of Horticulture, Northwest Agricultural and Forestry University, Yangling, Xianyang 712100, China
| | - Qingmei Guan
- State Key Laboratory of Crop Stress Biology for Arid Areas/Shaanxi Key Laboratory of Apple, College of Horticulture, Northwest Agricultural and Forestry University, Yangling, Xianyang 712100, China
| | - Jidi Xu
- State Key Laboratory of Crop Stress Biology for Arid Areas/Shaanxi Key Laboratory of Apple, College of Horticulture, Northwest Agricultural and Forestry University, Yangling, Xianyang 712100, China
- Correspondence:
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24
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Yi R, Cho K, Bonneau R. NetTIME: a Multitask and Base-pair Resolution Framework for Improved Transcription Factor Binding Site Prediction. Bioinformatics 2022; 38:4762-4770. [PMID: 35997560 PMCID: PMC9563695 DOI: 10.1093/bioinformatics/btac569] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2021] [Revised: 08/16/2022] [Accepted: 08/20/2022] [Indexed: 12/05/2022] Open
Abstract
Motivation Machine learning models for predicting cell-type-specific transcription factor (TF) binding sites have become increasingly more accurate thanks to the increased availability of next-generation sequencing data and more standardized model evaluation criteria. However, knowledge transfer from data-rich to data-limited TFs and cell types remains crucial for improving TF binding prediction models because available binding labels are highly skewed towards a small collection of TFs and cell types. Transfer prediction of TF binding sites can potentially benefit from a multitask learning approach; however, existing methods typically use shallow single-task models to generate low-resolution predictions. Here, we propose NetTIME, a multitask learning framework for predicting cell-type-specific TF binding sites with base-pair resolution. Results We show that the multitask learning strategy for TF binding prediction is more efficient than the single-task approach due to the increased data availability. NetTIME trains high-dimensional embedding vectors to distinguish TF and cell-type identities. We show that this approach is critical for the success of the multitask learning strategy and allows our model to make accurate transfer predictions within and beyond the training panels of TFs and cell types. We additionally train a linear-chain conditional random field (CRF) to classify binding predictions and show that this CRF eliminates the need for setting a probability threshold and reduces classification noise. We compare our method’s predictive performance with two state-of-the-art methods, Catchitt and Leopard, and show that our method outperforms previous methods under both supervised and transfer learning settings. Availability and implementation NetTIME is freely available at https://github.com/ryi06/NetTIME and the code is also archived at https://doi.org/10.5281/zenodo.6994897. Supplementary information Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Ren Yi
- Department of Computer Science, New York University, New York, NY, 10011, USA
| | - Kyunghyun Cho
- Department of Computer Science, New York University, New York, NY, 10011, USA.,Center for Data Science, New York University, New York, NY, 10011, USA.,Prescient Design, a Genentech accelerator, New York, NY, 10010, USA
| | - Richard Bonneau
- Department of Computer Science, New York University, New York, NY, 10011, USA.,Center for Data Science, New York University, New York, NY, 10011, USA.,Department of Biology, New York University, New York, NY, 10003, USA.,Prescient Design, a Genentech accelerator, New York, NY, 10010, USA
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25
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Li Z, Li M, Wang J. Asymmetric subgenomic chromatin architecture impacts on gene expression in resynthesized and natural allopolyploid Brassica napus. Commun Biol 2022; 5:762. [PMID: 35906482 PMCID: PMC9338098 DOI: 10.1038/s42003-022-03729-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2022] [Accepted: 07/15/2022] [Indexed: 11/26/2022] Open
Abstract
Although asymmetric subgenomic epigenetic modification and gene expression have been revealed in the successful establishment of allopolyploids, the changes in chromatin accessibility and their relationship with epigenetic modifications and gene expression are poorly understood. Here, we synthetically analyzed chromatin accessibility, four epigenetic modifications and gene expression in natural allopolyploid Brassica napus, resynthesized allopolyploid B. napus, and diploid progenitors (B. rapa and B. oleracea). “Chromatin accessibility shock” occurred in both allopolyploidization and natural evolutionary processes, and genic accessible chromatin regions (ACRs) increased after allopolyploidization. ACRs associated with H3K27me3 modifications were more accessible than those with H3K27ac or H3K4me3. Although overall chromatin accessibility may be defined by H3K27me3, the enrichment of H3K4me3 and H3K27ac and depletion of DNA methylation around transcriptional start sites up-regulated gene expression. Moreover, we found that subgenome Cn exhibited higher chromatin accessibility than An, which depended on the higher chromatin accessibility of Cn-unique genes but not homologous genes. Changes in chromatin accessibility occuring during the process of allopolyploidization of Brassica napus are analysed using ATAC and ChIPseq, with differences in asymmetric chromatin accessibility between subgenomes of B. napus investigated.
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Affiliation(s)
- Zeyu Li
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, 430072, Hubei, China
| | - Mengdi Li
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, 430072, Hubei, China.,Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, Xi'an, 710069, China
| | - Jianbo Wang
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, 430072, Hubei, China.
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26
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Fu LY, Zhu T, Zhou X, Yu R, He Z, Zhang P, Wu Z, Chen M, Kaufmann K, Chen D. ChIP-Hub provides an integrative platform for exploring plant regulome. Nat Commun 2022; 13:3413. [PMID: 35701419 PMCID: PMC9197862 DOI: 10.1038/s41467-022-30770-1] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2021] [Accepted: 05/18/2022] [Indexed: 11/18/2022] Open
Abstract
Plant genomes encode a complex and evolutionary diverse regulatory grammar that forms the basis for most life on earth. A wealth of regulome and epigenome data have been generated in various plant species, but no common, standardized resource is available so far for biologists. Here, we present ChIP-Hub, an integrative web-based platform in the ENCODE standards that bundles >10,000 publicly available datasets reanalyzed from >40 plant species, allowing visualization and meta-analysis. We manually curate the datasets through assessing ~540 original publications and comprehensively evaluate their data quality. As a proof of concept, we extensively survey the co-association of different regulators and construct a hierarchical regulatory network under a broad developmental context. Furthermore, we show how our annotation allows to investigate the dynamic activity of tissue-specific regulatory elements (promoters and enhancers) and their underlying sequence grammar. Finally, we analyze the function and conservation of tissue-specific promoters, enhancers and chromatin states using comparative genomics approaches. Taken together, the ChIP-Hub platform and the analysis results provide rich resources for deep exploration of plant ENCODE. ChIP-Hub is available at https://biobigdata.nju.edu.cn/ChIPHub/. A comprehensive data portal to explore plant regulomes is still unavailable. Here, the authors develop a web-based platform ChIP-Hub in the ENCODE standards and demonstrate its applications in the identification of hierarchical regulatory network, tissue-specific chromatin dynamics, putative enhancers and chromatin states.
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Affiliation(s)
- Liang-Yu Fu
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, 210023, China.,Department for Plant Cell and Molecular Biology, Institute for Biology, Humboldt-Universität zu Berlin, 10115, Berlin, Germany
| | - Tao Zhu
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, 210023, China
| | - Xinkai Zhou
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, 210023, China
| | - Ranran Yu
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, 210023, China
| | - Zhaohui He
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, 210023, China
| | - Peijing Zhang
- Department of Bioinformatics, College of Life Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Zhigui Wu
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, 210023, China
| | - Ming Chen
- Department of Bioinformatics, College of Life Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Kerstin Kaufmann
- Department for Plant Cell and Molecular Biology, Institute for Biology, Humboldt-Universität zu Berlin, 10115, Berlin, Germany.
| | - Dijun Chen
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, 210023, China.
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27
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Mao XQ, Cheng Y, Zhang RZ, Liu YB, Li Y, Ge K, Jin HL. RNA-seq and ATAC-seq analyses of multilineage differentiating stress enduring cells: Comparison with dermal fibroblasts. Cell Biol Int 2022; 46:1480-1494. [PMID: 35673985 DOI: 10.1002/cbin.11834] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2021] [Revised: 04/20/2022] [Accepted: 04/30/2022] [Indexed: 11/09/2022]
Abstract
The aim of this study is to characterize the molecular properties of multilineage differentiating stress-enduring (Muse) cells compared with dermal fibroblasts (FBs) and to characterize differences in their transcriptomes and open chromatin regions that are involved in cellular plasticity. Assay for transposase-accessible chromatin with high-throughput sequencing (ATAC-seq) and RNA sequencing (RNA-seq) analyses was then performed on FBs and Muse cells. Subsequently, cell type-selective gene regulatory regions were identified by coalition analysis. Expression patterns of transcription factors (TFs) and signaling pathways intermediates were verified using quantitative real-time polymerase chain reaction and Western blot analyses. RNA-seq identified 2355 significantly differentially expressed genes (DEGs) that regulate the transcriptome, including 1222 upregulated and 1133 downregulated DEGs. The general panorama of RNA-seq and ATAC-seq analyses confirmed the differences in TFs and open chromatin regions between FBs and Muse cells. ATAC-seq analysis showed that Muse cells had more reproducible and meaningful peaks than FBs, and the peak signals were concentrated near promoter-transcription start site areas. In genomic regions that can be preferentially accessed in FBs and Muse cells, more than 200 TFs had binding motif sequences. Gene Ontology, Kyoto Encyclopedia of Genes and Genomes, and coalition analyses identified differences in factors involved in the cell cycle and the protein kinase B (AKT) signaling pathway of FBs and Muse cells. The results of RNA-seq and ATAC-seq analyses clarified the genetic basis of the different biological properties of Muse cells and FBs. These results suggest that the cell cycle transition and the AKT signaling pathway may affect the morphology and biological characteristics of Muse cells.
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Affiliation(s)
- Xiao-Qian Mao
- Department of Dermatology, The Third Affiliated Hospital of Soochow University, Changzhou, China.,Department of Dermatology, The First Affiliated Hospital of Bengbu Medical College, Bengbu, China
| | - Yan Cheng
- Interdisciplinary Research Center on Biology and Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai, China
| | - Ru-Zhi Zhang
- Department of Dermatology, The Third Affiliated Hospital of Soochow University, Changzhou, China
| | - Yi-Bo Liu
- Department of Plastic Surgery, Affiliated Renmin Hospital of Jiangsu University, Zhenjiang, China
| | - Yue Li
- Department of Dermatology, The Third Affiliated Hospital of Soochow University, Changzhou, China
| | - Kang Ge
- Department of Dermatology, The Third Affiliated Hospital of Soochow University, Changzhou, China.,Department of Dermatology, The First Affiliated Hospital of Bengbu Medical College, Bengbu, China
| | - Hui-Ling Jin
- Department of Dermatology, The First Affiliated Hospital of Bengbu Medical College, Bengbu, China
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28
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Roulé T, Christ A, Hussain N, Huang Y, Hartmann C, Benhamed M, Gutierrez-Marcos J, Ariel F, Crespi M, Blein T. The lncRNA MARS modulates the epigenetic reprogramming of the marneral cluster in response to ABA. MOLECULAR PLANT 2022; 15:840-856. [PMID: 35150931 DOI: 10.1016/j.molp.2022.02.007] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/25/2021] [Revised: 11/05/2021] [Accepted: 02/07/2022] [Indexed: 06/14/2023]
Abstract
Clustered organization of biosynthetic non-homologous genes is emerging as a characteristic feature of plant genomes. The co-regulation of clustered genes seems to largely depend on epigenetic reprogramming and three-dimensional chromatin conformation. In this study, we identified the long non-coding RNA (lncRNA) MARneral Silencing (MARS), localized inside the Arabidopsis marneral cluster, which controls the local epigenetic activation of its surrounding region in response to abscisic acid (ABA). MARS modulates the POLYCOMB REPRESSIVE COMPLEX 1 (PRC1) component LIKE HETEROCHROMATIN PROTEIN 1 (LHP1) binding throughout the cluster in a dose-dependent manner, determining H3K27me3 deposition and chromatin condensation. In response to ABA, MARS decoys LHP1 away from the cluster and promotes the formation of a chromatin loop bringing together the MARNERAL SYNTHASE 1 (MRN1) locus and a distal ABA-responsive enhancer. The enrichment of co-regulated lncRNAs in clustered metabolic genes in Arabidopsis suggests that the acquisition of novel non-coding transcriptional units may constitute an additional regulatory layer driving the evolution of biosynthetic pathways.
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Affiliation(s)
- Thomas Roulé
- Université Paris-Saclay, CNRS, INRAE, Université Evry, Institute of Plant Sciences Paris-Saclay (IPS2), 91190 Gif-sur-Yvette, France; Université de Paris, Institute of Plant Sciences Paris-Saclay (IPS2), 91190 Gif-sur-Yvette, France
| | - Aurelie Christ
- Université Paris-Saclay, CNRS, INRAE, Université Evry, Institute of Plant Sciences Paris-Saclay (IPS2), 91190 Gif-sur-Yvette, France; Université de Paris, Institute of Plant Sciences Paris-Saclay (IPS2), 91190 Gif-sur-Yvette, France
| | - Nosheen Hussain
- School of Life Sciences, University of Warwick, Coventry CV4 7AL, UK
| | - Ying Huang
- Université Paris-Saclay, CNRS, INRAE, Université Evry, Institute of Plant Sciences Paris-Saclay (IPS2), 91190 Gif-sur-Yvette, France; Université de Paris, Institute of Plant Sciences Paris-Saclay (IPS2), 91190 Gif-sur-Yvette, France
| | - Caroline Hartmann
- Université Paris-Saclay, CNRS, INRAE, Université Evry, Institute of Plant Sciences Paris-Saclay (IPS2), 91190 Gif-sur-Yvette, France; Université de Paris, Institute of Plant Sciences Paris-Saclay (IPS2), 91190 Gif-sur-Yvette, France
| | - Moussa Benhamed
- Université Paris-Saclay, CNRS, INRAE, Université Evry, Institute of Plant Sciences Paris-Saclay (IPS2), 91190 Gif-sur-Yvette, France; Université de Paris, Institute of Plant Sciences Paris-Saclay (IPS2), 91190 Gif-sur-Yvette, France
| | | | - Federico Ariel
- Instituto de Agrobiotecnología del Litoral, CONICET, FBCB, Universidad Nacional del Litoral, Colectora Ruta Nacional 168 km 0, 3000 Santa Fe, Argentina
| | - Martin Crespi
- Université Paris-Saclay, CNRS, INRAE, Université Evry, Institute of Plant Sciences Paris-Saclay (IPS2), 91190 Gif-sur-Yvette, France; Université de Paris, Institute of Plant Sciences Paris-Saclay (IPS2), 91190 Gif-sur-Yvette, France.
| | - Thomas Blein
- Université Paris-Saclay, CNRS, INRAE, Université Evry, Institute of Plant Sciences Paris-Saclay (IPS2), 91190 Gif-sur-Yvette, France; Université de Paris, Institute of Plant Sciences Paris-Saclay (IPS2), 91190 Gif-sur-Yvette, France.
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29
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Han Y, Lu M, Yue S, Li K, Dong M, Liu L, Wang H, Shang F. Comparative methylomics and chromatin accessibility analysis in Osmanthus fragrans uncovers regulation of genic transcription and mechanisms of key floral scent production. HORTICULTURE RESEARCH 2022; 9:uhac096. [PMID: 35795393 PMCID: PMC9250655 DOI: 10.1093/hr/uhac096] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/10/2021] [Accepted: 04/07/2022] [Indexed: 06/12/2023]
Abstract
Linalool and ionone are two important aromatic components in sweet osmanthus petals, and the regulatory mechanisms that produce these two components remain unclear. In this study, we employed whole-genome methylation sequencing and ATAC-seq technology to analyze the genomic DNA methylation status and chromatin accessibility of the sweet osmanthus cultivars 'Zaohuang' and 'Chenghong Dangui'. Results showed that the promoter region of TPS2, a key gene in the linalool synthesis pathway, was less methylated in 'Chenghong Dangui' than in 'Zaohuang'. The chromatin was more accessible in 'Chenghong Dangui' than in 'Zaohuang', which resulted in a much stronger expression of this gene in 'Chenghong Dangui' than in 'Zaohuang'. This eventually led to a high quantity of linalool and its oxides in the petals of 'Chenghong Dangui', but there were lower levels present in the petals of 'Zaohuang'. These results suggest that DNA methylation and chromatin accessibility play major roles in linalool synthesis in sweet osmanthus. The methylation level of the promoter region of CCD4, a key gene for ionone synthesis, was higher in 'Zaohuang' than in 'Chenghong Dangui'. The chromatin accessibility was lower in 'Zaohuang' than in 'Chenghong Dangui', although the expression of this gene was significantly higher in 'Zaohuang' than in 'Chenghong Dangui'. ChIP-seq analysis and a series of experiments showed that the differential expression of CCD4 and CCD1 in the two cultivars may predominantly be the result of regulation by ERF2 and other transcription factors. However, a 183-bp deletion involving the CCD4 promoter region in 'Chenghong Dangui' may be the main reason for the low expression of this gene in its petals. This study provides an important theoretical basis for improving selective breeding of key floral fragrance components in sweet osmanthus.
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Affiliation(s)
| | - Miaomiao Lu
- State Key Laboratory of Crop Stress Adaptation and Improvement, Laboratory of Plant Germplasm and Genetic Engineering, School of Life Sciences, Henan University, Kaifeng, Henan 475004, China
| | - Shumin Yue
- State Key Laboratory of Crop Stress Adaptation and Improvement, Laboratory of Plant Germplasm and Genetic Engineering, School of Life Sciences, Henan University, Kaifeng, Henan 475004, China
| | - Ke Li
- State Key Laboratory of Crop Stress Adaptation and Improvement, Laboratory of Plant Germplasm and Genetic Engineering, School of Life Sciences, Henan University, Kaifeng, Henan 475004, China
| | - Meifang Dong
- State Key Laboratory of Crop Stress Adaptation and Improvement, Laboratory of Plant Germplasm and Genetic Engineering, School of Life Sciences, Henan University, Kaifeng, Henan 475004, China
| | - Luxian Liu
- State Key Laboratory of Crop Stress Adaptation and Improvement, Laboratory of Plant Germplasm and Genetic Engineering, School of Life Sciences, Henan University, Kaifeng, Henan 475004, China
| | - Hongyun Wang
- State Key Laboratory of Crop Stress Adaptation and Improvement, Laboratory of Plant Germplasm and Genetic Engineering, School of Life Sciences, Henan University, Kaifeng, Henan 475004, China
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30
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Jamge B, Berger F. Diversification of chromatin organization in eukaryotes. Curr Opin Cell Biol 2022; 74:1-6. [PMID: 34998094 DOI: 10.1016/j.ceb.2021.12.002] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2021] [Revised: 12/03/2021] [Accepted: 12/06/2021] [Indexed: 12/24/2022]
Abstract
Our knowledge of the chromatin landscape and its regulation was originally discovered using yeast and a limited number of animals models. A wealth of studies in model plants now strongly demonstrates the conservation of certain features while illuminating the diversification of others. Here we summarize recent advances that describe specific features of chromatin organization of transcriptional units and specific regulation of heterochromatin in flowering plants. We highlight the importance of transcriptional regulation in plant chromatin organization and the need to investigate a more diverse range of species to understand the chromatin landscape in eukaryotes.
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Affiliation(s)
- Bhagyshree Jamge
- Gregor Mendel Institute (GMI), Austrian Academy of Sciences, Vienna BioCenter (VBC), Dr. Bohr Gasse 3, 1030 Vienna, Austria; Vienna BioCenter PhD Program, Doctoral School of the University of Vienna and Medical University of Vienna, A-1030, Vienna, Austria
| | - Frédéric Berger
- Gregor Mendel Institute (GMI), Austrian Academy of Sciences, Vienna BioCenter (VBC), Dr. Bohr Gasse 3, 1030 Vienna, Austria.
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31
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Epigenome guided crop improvement: current progress and future opportunities. Emerg Top Life Sci 2022; 6:141-151. [PMID: 35072210 PMCID: PMC9023013 DOI: 10.1042/etls20210258] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2021] [Revised: 12/14/2021] [Accepted: 01/04/2022] [Indexed: 12/22/2022]
Abstract
Epigenomics encompasses a broad field of study, including the investigation of chromatin states, chromatin modifications and their impact on gene regulation; as well as the phenomena of epigenetic inheritance. The epigenome is a multi-modal layer of information superimposed on DNA sequences, instructing their usage in gene expression. As such, it is an emerging focus of efforts to improve crop performance. Broadly, this might be divided into avenues that leverage chromatin information to better annotate and decode plant genomes, and into complementary strategies that aim to identify and select for heritable epialleles that control crop traits independent of underlying genotype. In this review, we focus on the first approach, which we term ‘epigenome guided’ improvement. This encompasses the use of chromatin profiles to enhance our understanding of the composition and structure of complex crop genomes. We discuss the current progress and future prospects towards integrating this epigenomic information into crop improvement strategies; in particular for CRISPR/Cas9 gene editing and precision genome engineering. We also highlight some specific opportunities and challenges for grain and horticultural crops.
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32
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Cao X, Cheng J, Huang Y, Lan X, Lei C, Chen H. Comparative Enhancer Map of Cattle Muscle Genome Annotated by ATAC-Seq. Front Vet Sci 2022; 8:782409. [PMID: 34977215 PMCID: PMC8715921 DOI: 10.3389/fvets.2021.782409] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2021] [Accepted: 11/12/2021] [Indexed: 11/13/2022] Open
Abstract
Annotating regulatory elements could benefit the interpretation of the molecular mechanism of genome-wide association study (GWAS) hits. In this work, we performed transposase-accessible chromatin with sequencing (ATAC-seq) to annotate the cattle muscle genome's functional elements. A total of 10,023 and 11,360 peaks were revealed in muscle genomes of adult and embryo cattle, respectively. The two peak sets produced 8,850 differentially accessible regions (DARs), including 2,515 promoters and 4,319 putative enhancers. These functional elements were associated with the cell cycle, muscle development, and lipid metabolism. A total of 15 putative enhancers were selected for a dual-luciferase reporter assay, and 12 of them showed enhancer activity in cattle myoblasts. Interestingly, the GeneHancer database has annotated the interactions of eight active enhancers with gene promoters, such as embryo-specific peak1053 (log2FC = 1.81, embryo/adult, E/A) with ligand-dependent nuclear receptor corepressor-like protein (LCORL) and embryo-specific peak4218 (log2FC = 1.81) with FERM domain-containing 8 (FRMD8). A total of 295 GWAS loci from the animal QTL database were mapped to 183 putative enhancers, including rs109554838 (associated with cattle body weight and average daily gain) to peak1053 and rs110294629 (associated with beef shear force and tenderness score) to peak4218. Notably, peak4218 has been found to be involved in mouse embryo development. Deleting peak4218 clearly reduced luciferase activity (P = 3.30E-04). Our comparative enhancer map is expected to benefit the area of beef cattle breeding.
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Affiliation(s)
- Xiukai Cao
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, China.,Joint International Research Laboratory of Agriculture and Agri-Product Safety of Ministry of Education of China, Yangzhou University, Yangzhou, China
| | - Jie Cheng
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Yongzhen Huang
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Xianyong Lan
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Chuzhao Lei
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Hong Chen
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, China.,College of Animal Science, Xinjiang Agricultural University, Urumqi, China
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33
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Kumar S, Kaur S, Seem K, Kumar S, Mohapatra T. Understanding 3D Genome Organization and Its Effect on Transcriptional Gene Regulation Under Environmental Stress in Plant: A Chromatin Perspective. Front Cell Dev Biol 2021; 9:774719. [PMID: 34957106 PMCID: PMC8692796 DOI: 10.3389/fcell.2021.774719] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2021] [Accepted: 11/23/2021] [Indexed: 01/17/2023] Open
Abstract
The genome of a eukaryotic organism is comprised of a supra-molecular complex of chromatin fibers and intricately folded three-dimensional (3D) structures. Chromosomal interactions and topological changes in response to the developmental and/or environmental stimuli affect gene expression. Chromatin architecture plays important roles in DNA replication, gene expression, and genome integrity. Higher-order chromatin organizations like chromosome territories (CTs), A/B compartments, topologically associating domains (TADs), and chromatin loops vary among cells, tissues, and species depending on the developmental stage and/or environmental conditions (4D genomics). Every chromosome occupies a separate territory in the interphase nucleus and forms the top layer of hierarchical structure (CTs) in most of the eukaryotes. While the A and B compartments are associated with active (euchromatic) and inactive (heterochromatic) chromatin, respectively, having well-defined genomic/epigenomic features, TADs are the structural units of chromatin. Chromatin architecture like TADs as well as the local interactions between promoter and regulatory elements correlates with the chromatin activity, which alters during environmental stresses due to relocalization of the architectural proteins. Moreover, chromatin looping brings the gene and regulatory elements in close proximity for interactions. The intricate relationship between nucleotide sequence and chromatin architecture requires a more comprehensive understanding to unravel the genome organization and genetic plasticity. During the last decade, advances in chromatin conformation capture techniques for unravelling 3D genome organizations have improved our understanding of genome biology. However, the recent advances, such as Hi-C and ChIA-PET, have substantially increased the resolution, throughput as well our interest in analysing genome organizations. The present review provides an overview of the historical and contemporary perspectives of chromosome conformation capture technologies, their applications in functional genomics, and the constraints in predicting 3D genome organization. We also discuss the future perspectives of understanding high-order chromatin organizations in deciphering transcriptional regulation of gene expression under environmental stress (4D genomics). These might help design the climate-smart crop to meet the ever-growing demands of food, feed, and fodder.
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Affiliation(s)
- Suresh Kumar
- Division of Biochemistry, ICAR-Indian Agricultural Research Institute, New Delhi, India
| | - Simardeep Kaur
- Division of Biochemistry, ICAR-Indian Agricultural Research Institute, New Delhi, India
| | - Karishma Seem
- Division of Biochemistry, ICAR-Indian Agricultural Research Institute, New Delhi, India
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Ding P, Sakai T, Krishna Shrestha R, Manosalva Perez N, Guo W, Ngou BPM, He S, Liu C, Feng X, Zhang R, Vandepoele K, MacLean D, Jones JDG. Chromatin accessibility landscapes activated by cell-surface and intracellular immune receptors. JOURNAL OF EXPERIMENTAL BOTANY 2021; 72:7927-7941. [PMID: 34387350 DOI: 10.1093/jxb/erab373] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/11/2020] [Accepted: 08/12/2021] [Indexed: 06/13/2023]
Abstract
Activation of cell-surface and intracellular receptor-mediated immunity results in rapid transcriptional reprogramming that underpins disease resistance. However, the mechanisms by which co-activation of both immune systems lead to transcriptional changes are not clear. Here, we combine RNA-seq and ATAC-seq to define changes in gene expression and chromatin accessibility. Activation of cell-surface or intracellular receptor-mediated immunity, or both, increases chromatin accessibility at induced defence genes. Analysis of ATAC-seq and RNA-seq data combined with publicly available information on transcription factor DNA-binding motifs enabled comparison of individual gene regulatory networks activated by cell-surface or intracellular receptor-mediated immunity, or by both. These results and analyses reveal overlapping and conserved transcriptional regulatory mechanisms between the two immune systems.
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Affiliation(s)
- Pingtao Ding
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, Norwich NR4 7UH, UK
- Institute of Biology Leiden, Leiden University, Sylviusweg 72, Leiden 2333 BE, The Netherlands
| | - Toshiyuki Sakai
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, Norwich NR4 7UH, UK
| | - Ram Krishna Shrestha
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, Norwich NR4 7UH, UK
| | - Nicolas Manosalva Perez
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 71, 9052 Ghent, Belgium
- VIB Center for Plant Systems Biology, Technologiepark 71, 9052 Ghent, Belgium
| | - Wenbin Guo
- Information and Computational Sciences, The James Hutton Institute, Dundee DD2 5DA, UK
| | - Bruno Pok Man Ngou
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, Norwich NR4 7UH, UK
| | - Shengbo He
- John Innes Centre, Norwich Research Park, Norwich NR4 7UH, UK
| | - Chang Liu
- Institute of Biology, University of Hohenheim, Garbenstrasse 30, 70599 Stuttgart, Germany
| | - Xiaoqi Feng
- John Innes Centre, Norwich Research Park, Norwich NR4 7UH, UK
| | - Runxuan Zhang
- Information and Computational Sciences, The James Hutton Institute, Dundee DD2 5DA, UK
| | - Klaas Vandepoele
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 71, 9052 Ghent, Belgium
- VIB Center for Plant Systems Biology, Technologiepark 71, 9052 Ghent, Belgium
| | - Dan MacLean
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, Norwich NR4 7UH, UK
| | - Jonathan D G Jones
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, Norwich NR4 7UH, UK
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35
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Ren C, Li H, Wang Z, Dai Z, Lecourieux F, Kuang Y, Xin H, Li S, Liang Z. Characterization of Chromatin Accessibility and Gene Expression upon Cold Stress Reveals that the RAV1 Transcription Factor Functions in Cold Response in Vitis Amurensis. PLANT & CELL PHYSIOLOGY 2021; 62:1615-1629. [PMID: 34279666 PMCID: PMC8643690 DOI: 10.1093/pcp/pcab115] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/02/2021] [Revised: 06/09/2021] [Accepted: 08/09/2021] [Indexed: 05/29/2023]
Abstract
Cold tolerance is regulated by a variety of transcription factors (TFs) and their target genes. Except for the well-characterized C-repeat binding factors (CBFs)-dependent transcriptional cascade, the mechanisms of cold tolerance mediated by other transcriptional regulatory networks are still largely unknown. Here, we used the assay for transposase-accessible chromatin with sequencing (ATAC-seq) and RNA-seq to identify cold responsive TFs in Vitis amurensis, a grape species with high cold hardiness. Nine TFs, including CBF4, RAV1 and ERF104, were identified after cold treatment. Weighted gene co-expression network analysis (WGCNA) and gene ontology (GO) analysis revealed that these TFs may regulate cold response through different pathways. As a prime candidate TF, overexpression of VaRAV1 in grape cells improved its cold tolerance. The transgenic cells exhibited low electrolyte leakage and malondialdehyde content and high peroxidase activity. Moreover, the TF gene TCP8 and a gene involving in homogalacturonan biosynthesis were found to be regulated by VaRAV1, suggesting that the contribution of VaRAV1 to cold tolerance may be achieved by enhancing the stability of cell membrane and regulating the expression of target genes involved in plant cell wall composition. Our work provides novel insights into plant response to cold stress and demonstrates the utility of ATAC-seq and RNA-seq for the rapid identification of TFs in response to cold stress in grapevine. VaRAV1 may play an important role in adaption to cold stress.
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Affiliation(s)
- Chong Ren
- Beijing Key Laboratory of Grape Sciences and Enology, Key Laboratory of Plant Resource, Institute of Botany, Chinese Academy of Sciences, 20 Nanxincun, Xiangshan, Beijing 100093, PR China
| | - Huayang Li
- Beijing Key Laboratory of Grape Sciences and Enology, Key Laboratory of Plant Resource, Institute of Botany, Chinese Academy of Sciences, 20 Nanxincun, Xiangshan, Beijing 100093, PR China
- University of Chinese Academy of Sciences, 19 Yuquan Rd, Beijing 100049, PR China
| | - Zemin Wang
- Beijing Key Laboratory of Grape Sciences and Enology, Key Laboratory of Plant Resource, Institute of Botany, Chinese Academy of Sciences, 20 Nanxincun, Xiangshan, Beijing 100093, PR China
| | - Zhanwu Dai
- Beijing Key Laboratory of Grape Sciences and Enology, Key Laboratory of Plant Resource, Institute of Botany, Chinese Academy of Sciences, 20 Nanxincun, Xiangshan, Beijing 100093, PR China
| | - Fatma Lecourieux
- EGFV, Bordeaux Sciences Agro, INRA, Université de Bordeaux, ISVV, 210 chemin de Leysotte, Villenave d’Ornon 33882, France
| | - Yangfu Kuang
- Beijing Key Laboratory of Grape Sciences and Enology, Key Laboratory of Plant Resource, Institute of Botany, Chinese Academy of Sciences, 20 Nanxincun, Xiangshan, Beijing 100093, PR China
- University of Chinese Academy of Sciences, 19 Yuquan Rd, Beijing 100049, PR China
| | - Haiping Xin
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, 1 Lumo Rd, Wuhan 430074, PR China
| | - Shaohua Li
- Beijing Key Laboratory of Grape Sciences and Enology, Key Laboratory of Plant Resource, Institute of Botany, Chinese Academy of Sciences, 20 Nanxincun, Xiangshan, Beijing 100093, PR China
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36
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Zhang X, Pandey MK, Wang J, Zhao K, Ma X, Li Z, Zhao K, Gong F, Guo B, Varshney RK, Yin D. Chromatin spatial organization of wild type and mutant peanuts reveals high-resolution genomic architecture and interaction alterations. Genome Biol 2021; 22:315. [PMID: 34784945 PMCID: PMC8594070 DOI: 10.1186/s13059-021-02520-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2020] [Accepted: 10/15/2021] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Three-dimensional (3D) chromatin organization provides a critical foundation to investigate gene expression regulation and cellular homeostasis. RESULTS Here, we present the first 3D genome architecture maps in wild type and mutant allotetraploid peanut lines, which illustrate A/B compartments, topologically associated domains (TADs), and widespread chromatin interactions. Most peanut chromosomal arms (52.3%) have active regions (A compartments) with relatively high gene density and high transcriptional levels. About 2.0% of chromosomal regions switch from inactive to active (B-to-A) in the mutant line, harboring 58 differentially expressed genes enriched in flavonoid biosynthesis and circadian rhythm functions. The mutant peanut line shows a higher number of genome-wide cis-interactions than its wild-type. The present study reveals a new TAD in the mutant line that generates different chromatin loops and harbors a specific upstream AP2EREBP-binding motif which might upregulate the expression of the GA2ox gene and decrease active gibberellin (GA) content, presumably making the mutant plant dwarf. CONCLUSIONS Our findings will shed new light on the relationship between 3D chromatin architecture and transcriptional regulation in plants.
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Affiliation(s)
- Xingguo Zhang
- College of Agronomy, Henan Agricultural University, Zhengzhou, China
| | - Manish K Pandey
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
| | | | - Kunkun Zhao
- College of Agronomy, Henan Agricultural University, Zhengzhou, China
| | - Xingli Ma
- College of Agronomy, Henan Agricultural University, Zhengzhou, China
| | - Zhongfeng Li
- College of Agronomy, Henan Agricultural University, Zhengzhou, China
| | - Kai Zhao
- College of Agronomy, Henan Agricultural University, Zhengzhou, China
| | - Fangping Gong
- College of Agronomy, Henan Agricultural University, Zhengzhou, China
| | - Baozhu Guo
- Crop Protection and Management Research Unit, USDA-ARS, Tifton, USA.
| | - Rajeev K Varshney
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India.
- State Agricultural Biotechnology Centre, Centre for Crop and Food Innovation, Food Futures Institute, Murdoch University, Murdoch, Western Australia, Australia.
| | - Dongmei Yin
- College of Agronomy, Henan Agricultural University, Zhengzhou, China.
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37
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Zhou C, Liu X, Li X, Zhou H, Wang S, Yuan Z, Zhang Y, Li S, You A, Zhou L, He Z. A Genome Doubling Event Reshapes Rice Morphology and Products by Modulating Chromatin Signatures and Gene Expression Profiling. RICE (NEW YORK, N.Y.) 2021; 14:72. [PMID: 34347189 PMCID: PMC8339180 DOI: 10.1186/s12284-021-00515-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/26/2021] [Accepted: 07/27/2021] [Indexed: 05/16/2023]
Abstract
Evolutionarily, polyploidy represents a smart method for adjusting agronomically important in crops through impacts on genomic abundance and chromatin condensation. Autopolyploids have a relatively concise genetic background with great diversity and provide an ideal system to understand genetic and epigenetic mechanisms attributed to the genome-dosage effect. However, whether and how genome duplication events during autopolyploidization impact chromatin signatures are less understood in crops. To address it, we generated an autotetraploid rice line from a diploid progenitor, Oryza sativa ssp. indica 93-11. Using transposase-accessible chromatin sequencing, we found that autopolyploids lead to a higher number of accessible chromatin regions (ACRs) in euchromatin, most of which encode protein-coding genes. As expected, the profiling of ACR densities supported that the effect of ACRs on transcriptional gene activities relies on their positions in the rice genome, regardless of genome doubling. However, we noticed that genome duplication favors genic ACRs as the main drivers of transcriptional changes. In addition, we probed intricate crosstalk among various kinds of epigenetic marks and expression patterns of ACR-associated gene expression in both diploid and autotetraploid rice plants by integrating multiple-omics analyses, including chromatin immunoprecipitation sequencing and RNA-seq. Our data suggested that the combination of H3K36me2 and H3K36me3 may be associated with dynamic perturbation of ACRs introduced by autopolyploidization. As a consequence, we found that numerous metabolites were stimulated by genome doubling. Collectively, our findings suggest that autotetraploids reshape rice morphology and products by modulating chromatin signatures and transcriptional profiling, resulting in a pragmatic means of crop genetic improvement.
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Affiliation(s)
- Chao Zhou
- Key Laboratory of Three Gorges Regional Plant Genetics and Germplasm Enhancement (CTGU), Biotechnology Research Center, China Three Gorges University, Yichang, 443002, China.
| | - Xiaoyun Liu
- Institute for Interdisciplinary Research, Jianghan University, Wuhan, 430056, China
| | - Xinglei Li
- Bioacme Biotechnology Co., Ltd., Wuhan, 430056, China
| | - Hanlin Zhou
- Key Laboratory of Three Gorges Regional Plant Genetics and Germplasm Enhancement (CTGU), Biotechnology Research Center, China Three Gorges University, Yichang, 443002, China
| | - Sijia Wang
- Key Laboratory of Three Gorges Regional Plant Genetics and Germplasm Enhancement (CTGU), Biotechnology Research Center, China Three Gorges University, Yichang, 443002, China
| | - Zhu Yuan
- Key Laboratory of Three Gorges Regional Plant Genetics and Germplasm Enhancement (CTGU), Biotechnology Research Center, China Three Gorges University, Yichang, 443002, China
| | - Yonghong Zhang
- Hubei Key Laboratory of Wudang Local Chinese Medicine Research, Hubei University of Medicine, Shiyan, 442000, China
| | - Sanhe Li
- Hubei Key Laboratory of Food Crop Germplasm and Genetic Improvement, Food Crops Institute, Hubei Academy of Agricultural Sciences, Wuhan, 430064, China
| | - Aiqing You
- Hubei Key Laboratory of Food Crop Germplasm and Genetic Improvement, Food Crops Institute, Hubei Academy of Agricultural Sciences, Wuhan, 430064, China
| | - Lei Zhou
- Hubei Key Laboratory of Food Crop Germplasm and Genetic Improvement, Food Crops Institute, Hubei Academy of Agricultural Sciences, Wuhan, 430064, China.
| | - Zhengquan He
- Key Laboratory of Three Gorges Regional Plant Genetics and Germplasm Enhancement (CTGU), Biotechnology Research Center, China Three Gorges University, Yichang, 443002, China.
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Zhao H, Tu Z, Liu Y, Zong Z, Li J, Liu H, Xiong F, Zhan J, Hu X, Xie W. PlantDeepSEA, a deep learning-based web service to predict the regulatory effects of genomic variants in plants. Nucleic Acids Res 2021; 49:W523-W529. [PMID: 34037796 PMCID: PMC8262748 DOI: 10.1093/nar/gkab383] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2021] [Revised: 04/09/2021] [Accepted: 04/28/2021] [Indexed: 12/13/2022] Open
Abstract
Characterizing regulatory effects of genomic variants in plants remains a challenge. Although several tools based on deep-learning models and large-scale chromatin-profiling data have been available to predict regulatory elements and variant effects, no dedicated tools or web services have been reported in plants. Here, we present PlantDeepSEA as a deep learning-based web service to predict regulatory effects of genomic variants in multiple tissues of six plant species (including four crops). PlantDeepSEA provides two main functions. One is called Variant Effector, which aims to predict the effects of sequence variants on chromatin accessibility. Another is Sequence Profiler, a utility that performs 'in silico saturated mutagenesis' analysis to discover high-impact sites (e.g., cis-regulatory elements) within a sequence. When validated on independent test sets, the area under receiver operating characteristic curve of deep learning models in PlantDeepSEA ranges from 0.93 to 0.99. We demonstrate the usability of the web service with two examples. PlantDeepSEA could help to prioritize regulatory causal variants and might improve our understanding of their mechanisms of action in different tissues in plants. PlantDeepSEA is available at http://plantdeepsea.ncpgr.cn/.
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Affiliation(s)
- Hu Zhao
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
| | - Zhuo Tu
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
| | - Yinmeng Liu
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
| | - Zhanxiang Zong
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
| | - Jiacheng Li
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
| | - Hao Liu
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
| | - Feng Xiong
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
| | - Jinling Zhan
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
| | - Xuehai Hu
- Hubei Key Laboratory of Agricultural Bioinformatics, College of Informatics, Huazhong Agricultural University, Wuhan, China
| | - Weibo Xie
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China.,Hubei Key Laboratory of Agricultural Bioinformatics, College of Informatics, Huazhong Agricultural University, Wuhan, China
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Pei L, Li G, Lindsey K, Zhang X, Wang M. Plant 3D genomics: the exploration and application of chromatin organization. THE NEW PHYTOLOGIST 2021; 230:1772-1786. [PMID: 33560539 PMCID: PMC8252774 DOI: 10.1111/nph.17262] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/14/2020] [Accepted: 02/01/2021] [Indexed: 05/29/2023]
Abstract
Eukaryotic genomes are highly folded for packing into higher-order chromatin structures in the nucleus. With the emergence of state-of-the-art chromosome conformation capture methods and microscopic imaging techniques, the spatial organization of chromatin and its functional implications have been interrogated. Our knowledge of 3D chromatin organization in plants has improved dramatically in the past few years, building on the early advances in animal systems. Here, we review recent advances in 3D genome mapping approaches, our understanding of the sophisticated organization of spatial structures, and the application of 3D genomic principles in plants. We also discuss directions for future developments in 3D genomics in plants.
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Affiliation(s)
- Liuling Pei
- National Key Laboratory of Crop Genetic ImprovementHuazhong Agricultural UniversityWuhanHubei430070China
| | - Guoliang Li
- Hubei Key Laboratory of Agricultural BioinformaticsCollege of InformaticsHuazhong Agricultural UniversityWuhanHubei430070China
| | - Keith Lindsey
- Department of BiosciencesDurham UniversitySouth RoadDurhamDH1 3LEUK
| | - Xianlong Zhang
- National Key Laboratory of Crop Genetic ImprovementHuazhong Agricultural UniversityWuhanHubei430070China
| | - Maojun Wang
- National Key Laboratory of Crop Genetic ImprovementHuazhong Agricultural UniversityWuhanHubei430070China
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40
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Jauregui-Lozano J, Bakhle K, Weake VM. In vivo tissue-specific chromatin profiling in Drosophila melanogaster using GFP-tagged nuclei. Genetics 2021; 218:6281219. [PMID: 34022041 DOI: 10.1093/genetics/iyab079] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2021] [Accepted: 05/17/2021] [Indexed: 12/23/2022] Open
Abstract
The chromatin landscape defines cellular identity in multicellular organisms with unique patterns of DNA accessibility and histone marks decorating the genome of each cell type. Thus, profiling the chromatin state of different cell types in an intact organism under disease or physiological conditions can provide insight into how chromatin regulates cell homeostasis in vivo. To overcome the many challenges associated with characterizing chromatin state in specific cell types, we developed an improved approach to isolate Drosophila melanogaster nuclei tagged with a GFPKASH protein. The perinuclear space-localized KASH domain anchors GFP to the outer nuclear membrane, and expression of UAS-GFPKASH can be controlled by tissue-specific Gal4 drivers. Using this protocol, we profiled chromatin accessibility using an improved version of Assay for Transposable Accessible Chromatin followed by sequencing (ATAC-seq), called Omni-ATAC. In addition, we examined the distribution of histone marks using Chromatin immunoprecipitation followed by sequencing (ChIP-seq) and Cleavage Under Targets and Tagmentation (CUT&Tag) in adult photoreceptor neurons. We show that the chromatin landscape of photoreceptors reflects the transcriptional state of these cells, demonstrating the quality and reproducibility of our approach for profiling the transcriptome and epigenome of specific cell types in Drosophila.
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Affiliation(s)
| | - Kimaya Bakhle
- Department of Biochemistry, Purdue University, West Lafayette, IN 47907, USA
| | - Vikki M Weake
- Department of Biochemistry, Purdue University, West Lafayette, IN 47907, USA.,Purdue University Center for Cancer Research, Purdue University, West Lafayette, IN 47907, USA
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Tian H, Li Y, Wang C, Xu X, Zhang Y, Zeb Q, Zicola J, Fu Y, Turck F, Li L, Lu Z, Liu L. Photoperiod-responsive changes in chromatin accessibility in phloem companion and epidermis cells of Arabidopsis leaves. THE PLANT CELL 2021; 33:475-491. [PMID: 33955490 PMCID: PMC8136901 DOI: 10.1093/plcell/koaa043] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/30/2020] [Accepted: 11/29/2020] [Indexed: 05/04/2023]
Abstract
Photoperiod plays a key role in controlling the phase transition from vegetative to reproductive growth in flowering plants. Leaves are the major organs perceiving day-length signals, but how specific leaf cell types respond to photoperiod remains unknown. We integrated photoperiod-responsive chromatin accessibility and transcriptome data in leaf epidermis and vascular companion cells of Arabidopsis thaliana by combining isolation of nuclei tagged in specific cell/tissue types with assay for transposase-accessible chromatin using sequencing and RNA-sequencing. Despite a large overlap, vasculature and epidermis cells responded differently. Long-day predominantly induced accessible chromatin regions (ACRs); in the vasculature, more ACRs were induced and these were located at more distal gene regions, compared with the epidermis. Vascular ACRs induced by long days were highly enriched in binding sites for flowering-related transcription factors. Among the highly ranked genes (based on chromatin and expression signatures in the vasculature), we identified TREHALOSE-PHOSPHATASE/SYNTHASE 9 (TPS9) as a flowering activator, as shown by the late flowering phenotypes of T-DNA insertion mutants and transgenic lines with phloem-specific knockdown of TPS9. Our cell-type-specific analysis sheds light on how the long-day photoperiod stimulus impacts chromatin accessibility in a tissue-specific manner to regulate plant development.
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Affiliation(s)
| | | | | | | | - Yajie Zhang
- Beijing Key Laboratory of Plant Gene Resources and Biotechnology for Carbon Reduction and Environmental Improvement, and College of Life Sciences, Capital Normal University, Beijing 100048, China
| | - Qudsia Zeb
- Beijing Key Laboratory of Plant Gene Resources and Biotechnology for Carbon Reduction and Environmental Improvement, and College of Life Sciences, Capital Normal University, Beijing 100048, China
| | - Johan Zicola
- Max Planck Institute for Plant Breeding Research, Cologne, D-50829, Germany
| | - Yongfu Fu
- National Key Facility of Crop Gene Resource and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Franziska Turck
- Max Planck Institute for Plant Breeding Research, Cologne, D-50829, Germany
| | - Legong Li
- Beijing Key Laboratory of Plant Gene Resources and Biotechnology for Carbon Reduction and Environmental Improvement, and College of Life Sciences, Capital Normal University, Beijing 100048, China
| | - Zefu Lu
- Author for correspondence: (L.L) and (Z.L.)
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Wang P, Jin S, Chen X, Wu L, Zheng Y, Yue C, Guo Y, Zhang X, Yang J, Ye N. Chromatin accessibility and translational landscapes of tea plants under chilling stress. HORTICULTURE RESEARCH 2021; 8:96. [PMID: 33931606 PMCID: PMC8087716 DOI: 10.1038/s41438-021-00529-8] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/16/2020] [Revised: 02/25/2021] [Accepted: 03/01/2021] [Indexed: 05/03/2023]
Abstract
Plants have evolved regulatory mechanisms at multiple levels to regulate gene expression in order to improve their cold adaptability. However, limited information is available regarding the stress response at the chromatin and translational levels. Here, we characterize the chromatin accessibility, transcriptional, and translational landscapes of tea plants in vivo under chilling stress for the first time. Chilling stress significantly affected both the transcription and translation levels as well as the translation efficiency of tea plants. A total of 3010 genes that underwent rapid and independent translation under chilling stress were observed, and they were significantly enriched in the photosynthesis-antenna protein and phenylpropanoid biosynthesis pathways. A set of genes that were significantly responsive to cold at the transcription and translation levels, including four (+)-neomenthol dehydrogenases (MNDs) and two (E)-nerolidol synthases (NESs) arranged in tandem on the chromosomes, were also found. We detected potential upstream open reading frames (uORFs) on 3082 genes and found that tea plants may inhibit the overall expression of genes by enhancing the translation of uORFs under chilling stress. In addition, we identified distal transposase hypersensitive sites (THSs) and proximal THSs and constructed a transcriptional regulatory network for tea plants under chilling stress. We also identified 13 high-confidence transcription factors (TFs) that may play a crucial role in cold regulation. These results provide valuable information regarding the potential transcriptional regulatory network in plants and help to clarify how plants exhibit flexible responses to chilling stress.
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Affiliation(s)
- Pengjie Wang
- College of Horticulture, Fujian Agriculture and Forestry University/Key Laboratory of Tea Science in Universities of Fujian Province, Fuzhou, 350002, China
| | - Shan Jin
- College of Horticulture, Fujian Agriculture and Forestry University/Key Laboratory of Tea Science in Universities of Fujian Province, Fuzhou, 350002, China
| | - Xuejin Chen
- College of Horticulture, Fujian Agriculture and Forestry University/Key Laboratory of Tea Science in Universities of Fujian Province, Fuzhou, 350002, China
| | - Liangyu Wu
- College of Horticulture, Fujian Agriculture and Forestry University/Key Laboratory of Tea Science in Universities of Fujian Province, Fuzhou, 350002, China
| | - Yucheng Zheng
- College of Horticulture, Fujian Agriculture and Forestry University/Key Laboratory of Tea Science in Universities of Fujian Province, Fuzhou, 350002, China
| | - Chuan Yue
- College of Horticulture, Fujian Agriculture and Forestry University/Key Laboratory of Tea Science in Universities of Fujian Province, Fuzhou, 350002, China
| | - Yongchun Guo
- College of Horticulture, Fujian Agriculture and Forestry University/Key Laboratory of Tea Science in Universities of Fujian Province, Fuzhou, 350002, China
| | - Xingtan Zhang
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518120, China
| | - Jiangfan Yang
- College of Horticulture, Fujian Agriculture and Forestry University/Key Laboratory of Tea Science in Universities of Fujian Province, Fuzhou, 350002, China.
| | - Naixing Ye
- College of Horticulture, Fujian Agriculture and Forestry University/Key Laboratory of Tea Science in Universities of Fujian Province, Fuzhou, 350002, China.
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43
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Fan T, Huang Y. Accessible chromatin reveals regulatory mechanisms underlying cell fate decisions during early embryogenesis. Sci Rep 2021; 11:7896. [PMID: 33846424 PMCID: PMC8042068 DOI: 10.1038/s41598-021-86919-3] [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: 08/17/2020] [Accepted: 03/22/2021] [Indexed: 02/01/2023] Open
Abstract
This study was conducted to investigate epigenetic landscape across multiple species and identify transcription factors (TFs) and their roles in controlling cell fate decision events during early embryogenesis. We made a comprehensively joint-research of chromatin accessibility of five species during embryogenesis by integration of ATAC-seq and RNA-seq datasets. Regulatory roles of candidate early embryonic TFs were investigated. Widespread accessible chromatin in early embryos overlapped with putative cis-regulatory sequences. Sets of cell-fate-determining TFs were identified. YOX1, a key cell cycle regulator, were found to homologous to clusters of TFs that are involved in neuron and epidermal cell-fate determination. Our research provides an intriguing insight into evolution of cell-fate decision during early embryogenesis among organisms.
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Affiliation(s)
- Tongqiang Fan
- grid.443483.c0000 0000 9152 7385State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Lin’an, Hangzhou, 311300 People’s Republic of China
| | - Youjun Huang
- grid.443483.c0000 0000 9152 7385State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Lin’an, Hangzhou, 311300 People’s Republic of China
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De Clercq I, Van de Velde J, Luo X, Liu L, Storme V, Van Bel M, Pottie R, Vaneechoutte D, Van Breusegem F, Vandepoele K. Integrative inference of transcriptional networks in Arabidopsis yields novel ROS signalling regulators. NATURE PLANTS 2021; 7:500-513. [PMID: 33846597 DOI: 10.1038/s41477-021-00894-1] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/11/2020] [Accepted: 03/04/2021] [Indexed: 05/12/2023]
Abstract
Gene regulation is a dynamic process in which transcription factors (TFs) play an important role in controlling spatiotemporal gene expression. To enhance our global understanding of regulatory interactions in Arabidopsis thaliana, different regulatory input networks capturing complementary information about DNA motifs, open chromatin, TF-binding and expression-based regulatory interactions were combined using a supervised learning approach, resulting in an integrated gene regulatory network (iGRN) covering 1,491 TFs and 31,393 target genes (1.7 million interactions). This iGRN outperforms the different input networks to predict known regulatory interactions and has a similar performance to recover functional interactions compared to state-of-the-art experimental methods. The iGRN correctly inferred known functions for 681 TFs and predicted new gene functions for hundreds of unknown TFs. For regulators predicted to be involved in reactive oxygen species (ROS) stress regulation, we confirmed in total 75% of TFs with a function in ROS and/or physiological stress responses. This includes 13 ROS regulators, previously not connected to any ROS or stress function, that were experimentally validated in our ROS-specific phenotypic assays of loss- or gain-of-function lines. In conclusion, the presented iGRN offers a high-quality starting point to enhance our understanding of gene regulation in plants by integrating different experimental data types.
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Affiliation(s)
- Inge De Clercq
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium.
- VIB Center for Plant Systems Biology, Ghent, Belgium.
| | - Jan Van de Velde
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- VIB Center for Plant Systems Biology, Ghent, Belgium
- Bioinformatics Institute Ghent, Ghent University, Ghent, Belgium
| | - Xiaopeng Luo
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- VIB Center for Plant Systems Biology, Ghent, Belgium
| | - Li Liu
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- VIB Center for Plant Systems Biology, Ghent, Belgium
- Bioinformatics Institute Ghent, Ghent University, Ghent, Belgium
| | - Veronique Storme
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- VIB Center for Plant Systems Biology, Ghent, Belgium
| | - Michiel Van Bel
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- VIB Center for Plant Systems Biology, Ghent, Belgium
| | - Robin Pottie
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- VIB Center for Plant Systems Biology, Ghent, Belgium
| | - Dries Vaneechoutte
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- VIB Center for Plant Systems Biology, Ghent, Belgium
- Bioinformatics Institute Ghent, Ghent University, Ghent, Belgium
| | - Frank Van Breusegem
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- VIB Center for Plant Systems Biology, Ghent, Belgium
| | - Klaas Vandepoele
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium.
- VIB Center for Plant Systems Biology, Ghent, Belgium.
- Bioinformatics Institute Ghent, Ghent University, Ghent, Belgium.
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Umeda M, Ikeuchi M, Ishikawa M, Ito T, Nishihama R, Kyozuka J, Torii KU, Satake A, Goshima G, Sakakibara H. Plant stem cell research is uncovering the secrets of longevity and persistent growth. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2021; 106:326-335. [PMID: 33533118 PMCID: PMC8252613 DOI: 10.1111/tpj.15184] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/08/2020] [Revised: 01/26/2021] [Accepted: 01/28/2021] [Indexed: 05/07/2023]
Abstract
Plant stem cells have several extraordinary features: they are generated de novo during development and regeneration, maintain their pluripotency, and produce another stem cell niche in an orderly manner. This enables plants to survive for an extended period and to continuously make new organs, representing a clear difference in their developmental program from animals. To uncover regulatory principles governing plant stem cell characteristics, our research project 'Principles of pluripotent stem cells underlying plant vitality' was launched in 2017, supported by a Grant-in-Aid for Scientific Research on Innovative Areas from the Japanese government. Through a collaboration involving 28 research groups, we aim to identify key factors that trigger epigenetic reprogramming and global changes in gene networks, and thereby contribute to stem cell generation. Pluripotent stem cells in the shoot apical meristem are controlled by cytokinin and auxin, which also play a crucial role in terminating stem cell activity in the floral meristem; therefore, we are focusing on biosynthesis, metabolism, transport, perception, and signaling of these hormones. Besides, we are uncovering the mechanisms of asymmetric cell division and of stem cell death and replenishment under DNA stress, which will illuminate plant-specific features in preserving stemness. Our technology support groups expand single-cell omics to describe stem cell behavior in a spatiotemporal context, and provide correlative light and electron microscopic technology to enable live imaging of cell and subcellular dynamics at high spatiotemporal resolution. In this perspective, we discuss future directions of our ongoing projects and related research fields.
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Affiliation(s)
- Masaaki Umeda
- Graduate School of Science and TechnologyNara Institute of Science and TechnologyIkoma630‐0192Japan
| | - Momoko Ikeuchi
- Department of BiologyFaculty of ScienceNiigata UniversityNiigata950‐2181Japan
| | - Masaki Ishikawa
- National Institute for Basic BiologyOkazaki444‐8585Japan
- Department of Basic BiologyThe Graduate University for Advanced Studies (SOKENDAI)Okazaki444‐8585Japan
| | - Toshiro Ito
- Graduate School of Science and TechnologyNara Institute of Science and TechnologyIkoma630‐0192Japan
| | | | - Junko Kyozuka
- Graduate School of Life SciencesTohoku UniversitySendai980‐8577Japan
| | - Keiko U. Torii
- Howard Hughes Medical Institute and Department of Molecular BiosciencesThe University of Texas at AustinAustinTX78712USA
- Institute of Transformative Biomolecules (WPI‐ITbM)Nagoya UniversityNagoya464‐8601Japan
| | - Akiko Satake
- Department of BiologyFaculty of ScienceKyushu UniversityFukuoka819‐0395Japan
| | - Gohta Goshima
- Division of Biological ScienceGraduate School of ScienceNagoya UniversityNagoya464‐8602Japan
- Sugashima Marine Biological LaboratoryGraduate School of ScienceNagoya UniversityToba517‐0004Japan
| | - Hitoshi Sakakibara
- Graduate School of Bioagricultural SciencesNagoya UniversityNagoya464‐8601Japan
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46
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Liang Z, Zhang Q, Ji C, Hu G, Zhang P, Wang Y, Yang L, Gu X. Reorganization of the 3D chromatin architecture of rice genomes during heat stress. BMC Biol 2021; 19:53. [PMID: 33740972 PMCID: PMC7977607 DOI: 10.1186/s12915-021-00996-4] [Citation(s) in RCA: 36] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2020] [Accepted: 02/26/2021] [Indexed: 01/10/2023] Open
Abstract
BACKGROUND The three-dimensional spatial organization of the genome plays important roles in chromatin accessibility and gene expression in multiple biological processes and has been reported to be altered in response to environmental stress. However, the functional changes in spatial genome organization during environmental changes in crop plants are poorly understood. RESULTS Here we perform Hi-C, ATAC-seq, and RNA-seq in two agronomically important rice cultivars, Nipponbare (Nip; Japonica) and 93-11 (Indica), to report a comprehensive profile of nuclear dynamics during heat stress (HS). We show that heat stress affects different levels of chromosome organization, including A/B compartment transition, increase in the size of topologically associated domains, and loss of short-range interactions. The chromatin architectural changes were associated with chromatin accessibility and gene expression changes. Comparative analysis revealed that 93-11 exhibited more dynamic gene expression and chromatin accessibility changes, including HS-related genes, consistent with observed higher HS tolerance in this cultivar. CONCLUSIONS Our data uncovered higher-order chromatin architecture as a new layer in understanding transcriptional regulation in response to heat stress in rice.
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Affiliation(s)
- Zhe Liang
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
- Centre for Organismal Studies, Heidelberg University, 69120, Heidelberg, Germany
| | - Qian Zhang
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Changmian Ji
- Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, 571101, China
| | - Guihua Hu
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Pingxian Zhang
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Yifan Wang
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Liwen Yang
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Xiaofeng Gu
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, 100081, China.
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Farmer A, Thibivilliers S, Ryu KH, Schiefelbein J, Libault M. Single-nucleus RNA and ATAC sequencing reveals the impact of chromatin accessibility on gene expression in Arabidopsis roots at the single-cell level. MOLECULAR PLANT 2021; 14:372-383. [PMID: 33422696 DOI: 10.1016/j.molp.2021.01.001] [Citation(s) in RCA: 118] [Impact Index Per Article: 39.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/04/2020] [Revised: 12/14/2020] [Accepted: 01/05/2021] [Indexed: 05/22/2023]
Abstract
Similar to other complex organisms, plants consist of diverse and specialized cell types. The gain of unique biological functions of these different cell types is the consequence of the establishment of cell-type-specific transcriptional programs. As a necessary step in gaining a deeper understanding of the regulatory mechanisms controlling plant gene expression, we report the use of single-nucleus RNA sequencing (sNucRNA-seq) and single-nucleus assay for transposase accessible chromatin sequencing (sNucATAC-seq) technologies on Arabidopsis roots. The comparison of our single-nucleus transcriptomes to the published protoplast transcriptomes validated the use of nuclei as biological entities to establish plant cell-type-specific transcriptomes. Furthermore, our sNucRNA-seq results uncovered the transcriptomes of additional cell subtypes not identified by single-cell RNA-seq. Similar to our transcriptomic approach, the sNucATAC-seq approach led to the distribution of the Arabidopsis nuclei into distinct clusters, suggesting the differential accessibility of chromatin between groups of cells according to their identity. To reveal the impact of chromatin accessibility on gene expression, we integrated sNucRNA-seq and sNucATAC-seq data and demonstrated that cell-type-specific marker genes display cell-type-specific patterns of chromatin accessibility. Our data suggest that the differential chromatin accessibility is a critical mechanism to regulate gene activity at the cell-type level.
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Affiliation(s)
- Andrew Farmer
- National Center for Genome Resources, Santa Fe, NM 87505, USA
| | - Sandra Thibivilliers
- Department of Agronomy and Horticulture, Center for Plant Science Innovation, University of Nebraska-Lincoln, Beadle Center, Lincoln, NE 68503, USA
| | - Kook Hui Ryu
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, MI 48109, USA
| | - John Schiefelbein
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Marc Libault
- Department of Agronomy and Horticulture, Center for Plant Science Innovation, University of Nebraska-Lincoln, Beadle Center, Lincoln, NE 68503, USA.
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Yin X, Romero-Campero FJ, de Los Reyes P, Yan P, Yang J, Tian G, Yang X, Mo X, Zhao S, Calonje M, Zhou Y. H2AK121ub in Arabidopsis associates with a less accessible chromatin state at transcriptional regulation hotspots. Nat Commun 2021; 12:315. [PMID: 33436613 PMCID: PMC7804394 DOI: 10.1038/s41467-020-20614-1] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2020] [Accepted: 12/07/2020] [Indexed: 02/02/2023] Open
Abstract
Although it is well established that the Polycomb Group (PcG) complexes maintain gene repression through the incorporation of H2AK121ub and H3K27me3, little is known about the effect of these modifications on chromatin accessibility, which is fundamental to understand PcG function. Here, by integrating chromatin accessibility, histone marks and expression analyses in different Arabidopsis PcG mutants, we show that PcG function regulates chromatin accessibility. We find that H2AK121ub is associated with a less accessible but still permissive chromatin at transcriptional regulation hotspots. Accessibility is further reduced by EMF1 acting in collaboration with PRC2 activity. Consequently, H2AK121ub/H3K27me3 marks are linked to inaccessible although responsive chromatin. In contrast, only-H3K27me3-marked chromatin is less responsive, indicating that H2AK121ub-marked hotspots are required for transcriptional responses. Nevertheless, despite the loss of PcG activities leads to increased chromatin accessibility, this is not necessarily accompanied by transcriptional activation, indicating that accessible chromatin is not always predictive of gene expression.
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Affiliation(s)
- Xiaochang Yin
- State Key Laboratory of Protein and Plant Gene Research, School of Advanced Agricultural Sciences, Peking-Tsinghua Center for Life Sciences, Peking University, 100871, Beijing, China
| | - Francisco J Romero-Campero
- Institute of Plant Biochemistry and Photosynthesis (IBVF-CSIC), Avenida Américo Vespucio 49, 41092, Seville, Spain.
- Department of Computer Science and Artificial Intelligence (University of Sevilla), Avenida Reina Mercedes s/n, 41012, Seville, Spain.
| | - Pedro de Los Reyes
- Institute of Plant Biochemistry and Photosynthesis (IBVF-CSIC), Avenida Américo Vespucio 49, 41092, Seville, Spain
| | - Peng Yan
- State Key Laboratory of Plant Physiology and Biochemistry, College of Life Science, Zhejiang University, 310058, Hangzhou, China
| | - Jing Yang
- Beijing Agro-biotechnology Research Center, Beijing Key Laboratory of Agricultural Genetic Resources and Biotechnology, Beijing Academy of Agriculture and Forestry Sciences, 100097, Beijing, China
| | - Guangmei Tian
- Academy for Advanced Interdisciplinary Studies, Peking University, 100871, Beijing, China
| | - XiaoZeng Yang
- Beijing Agro-biotechnology Research Center, Beijing Key Laboratory of Agricultural Genetic Resources and Biotechnology, Beijing Academy of Agriculture and Forestry Sciences, 100097, Beijing, China
| | - Xiaorong Mo
- State Key Laboratory of Plant Physiology and Biochemistry, College of Life Science, Zhejiang University, 310058, Hangzhou, China
| | - Shuangshuang Zhao
- Key Laboratory of Plant Stress, Life Science College, Shandong Normal University, 250014, Jinan, China
| | - Myriam Calonje
- Institute of Plant Biochemistry and Photosynthesis (IBVF-CSIC), Avenida Américo Vespucio 49, 41092, Seville, Spain.
| | - Yue Zhou
- State Key Laboratory of Protein and Plant Gene Research, School of Advanced Agricultural Sciences, Peking-Tsinghua Center for Life Sciences, Peking University, 100871, Beijing, China.
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49
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Zhou C, Yuan Z, Ma X, Yang H, Wang P, Zheng L, Zhang Y, Liu X. Accessible chromatin regions and their functional interrelations with gene transcription and epigenetic modifications in sorghum genome. PLANT COMMUNICATIONS 2021; 2:100140. [PMID: 33511349 PMCID: PMC7816095 DOI: 10.1016/j.xplc.2020.100140] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/27/2020] [Revised: 12/23/2020] [Accepted: 12/29/2020] [Indexed: 05/23/2023]
Abstract
Accessible chromatin regions (ACRs) provide physical scaffolds to recruit transcriptional co-regulators and displace their nearby nucleosomes in multiple plant species. Characterization of ACRs and investigation of their biological effects in Sorghum bicolor has lagged behind. Regulation of gene expression relies on the transcriptional co-regulators that are recruited to ACRs to affect epigenomic modifications of surrounding nucleosomes. In this study, we employed transposase-accessible chromatin sequencing to identify ACRs and decipher how the presence of ACRs affects gene expression and epigenetic signatures in the Sorghum genome. As a result, 21 077 ACRs, which are mapped to 22.9% of genes and 2.7% of repeats, were identified. The profiling of ACRs on gene structures reveals a narrow and sharp peak around the transcription start site, with relatively weak and broad signals covering the entire gene body and an explicit but wide peak from the transcription termination site to its downstream regions. We discovered that the correlations between gene expression levels and profiled ACR densities are dependent on the positions of ACRs. The occurrence of genic ACRs cumulatively enhances the transcriptional activity of intergenic ACR-associated genes. In addition, an intricate crosstalk among ACRs, gene expression, and epigenetic marks has been unveiled by integrating multiple-omics analyses of whole-genome bisulfite sequencing, 6mA immunoprecipitation followed by sequencing, RNA sequencing, chromatin immunoprecipitation sequencing, and DNase I hypersensitive sites sequencing datasets. Our study provides a genome-wide landscape of ACRs in sorghum, decrypts their interrelations with various epigenetic marks, and sheds new light on their roles in transcriptional regulation.
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Affiliation(s)
- Chao Zhou
- Key Laboratory of Three Gorges Regional Plant Genetics and Germplasm Enhancement (CTGU), Biotechnology Research Center, Yichang Key Laboratory of Omics-Based Breeding for Chinese Medicines, China Three Gorges University, Yichang 443002, China
| | - Zhu Yuan
- Key Laboratory of Three Gorges Regional Plant Genetics and Germplasm Enhancement (CTGU), Biotechnology Research Center, Yichang Key Laboratory of Omics-Based Breeding for Chinese Medicines, China Three Gorges University, Yichang 443002, China
| | - Xueping Ma
- Laboratory of Medicinal Plants, Institute of Basic Medical Sciences, School of Basic Medicine, Biomedical Research Institute, Hubei Key Laboratory of Embryonic Stem Cell Research, Hubei University of Medicine, Shiyan 442000, China
| | - Huilan Yang
- Institute for Interdisciplinary Research, Jianghan University, Wuhan 430056, China
| | - Ping Wang
- Institute for Interdisciplinary Research, Jianghan University, Wuhan 430056, China
| | - Lanlan Zheng
- Laboratory of Medicinal Plants, Institute of Basic Medical Sciences, School of Basic Medicine, Biomedical Research Institute, Hubei Key Laboratory of Embryonic Stem Cell Research, Hubei University of Medicine, Shiyan 442000, China
| | - Yonghong Zhang
- Laboratory of Medicinal Plants, Institute of Basic Medical Sciences, School of Basic Medicine, Biomedical Research Institute, Hubei Key Laboratory of Embryonic Stem Cell Research, Hubei University of Medicine, Shiyan 442000, China
- Hubei Key Laboratory of Wudang Local Chinese Medicine Research, Hubei University of Medicine, Shiyan 442000, China
| | - Xiaoyun Liu
- Institute for Interdisciplinary Research, Jianghan University, Wuhan 430056, China
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Gutzat R, Mittelsten Scheid O. Preparing Chromatin and RNA from Rare Cell Types with Fluorescence-Activated Nuclear Sorting (FANS). Methods Mol Biol 2020; 2093:95-105. [PMID: 32088891 DOI: 10.1007/978-1-0716-0179-2_7] [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: 03/03/2023]
Abstract
The application of fluorescent tags to generate cell type-specific translational and transcriptional reporter lines is routine in plants, but separation of different cell types for downstream analyses is hampered by the presence of cell walls and tight connections between cells. Enzymatic removal of cell walls induces a wound response, dedifferentiation, or reprogramming of the resulting protoplasts. Their osmotic and mechanical instability and their large size range are challenging for FACS, a flow -sorting procedure based on differential expression of fluorescent tags. In contrast, plant nuclei are relatively robust and easy to isolate. Here, we describe a protocol for fluorescence-activated nuclear sorting (FANS) that allows efficient purification of very few fluorescence-tagged nuclei from a large background of non-labeled tissue. Purified nuclei are suitable for genome, epigenome, transcriptome, or proteome analyses. We describe in detail how to analyze nuclear RNA and DNA methylation from sorted nuclei representing the limited number of stem cells in the shoot apical meristem of Arabidopsis.
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Affiliation(s)
- Ruben Gutzat
- Gregor Mendel Institute of Molecular Plant Biology, Austrian Academy of Sciences, Vienna BioCenter (VBC), Vienna, Austria
| | - Ortrun Mittelsten Scheid
- Gregor Mendel Institute of Molecular Plant Biology, Austrian Academy of Sciences, Vienna BioCenter (VBC), Vienna, Austria.
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