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Wang J, Pu Z, Zhang W, Qu M, Gao L, Pan W, Sun Y, Fu C, Zhang L, Huang M, Hu Y. Identification of the New GmJAG1 Transcription Factor Binding Motifs Using DAP-Seq. PLANTS (BASEL, SWITZERLAND) 2024; 13:1708. [PMID: 38931140 PMCID: PMC11207949 DOI: 10.3390/plants13121708] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/08/2024] [Revised: 06/12/2024] [Accepted: 06/14/2024] [Indexed: 06/28/2024]
Abstract
Interaction between transcription factors (TFs) and motifs is essential for gene regulation and the subsequent phenotype formation. Soybean (Glycine max) JAGGEED 1 (GmJAG1) is a key TF that controls leaf shape, seed number and flower size. To understand the GmJAG1 binding motifs, in this study, we performed the GmJAG1 DNA affinity purification sequencing (DAP-seq) experiment, which is a powerful tool for the de novo motif prediction method. Two new significant GmJAG1 binding motifs were predicted and the EMSA experiments further verified the ability of GmJAG1 bound to these motifs. The potential binding sites in the downstream gene promoter were identified through motif scanning and a potential regulatory network mediated by GmJAG1 was constructed. These results served as important genomic resources for further understanding the regulatory mechanism of GmJAG1.
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Affiliation(s)
- Jinxing Wang
- Suihua Branch of the Heilongjiang Academy of Agricultural Sciences, Suihua 152052, China; (J.W.); (W.Z.); (M.Q.); (L.G.); (W.P.); (Y.S.); (C.F.)
| | - Zigang Pu
- Jiangxi Provincial Key Laboratory of Plant Germplasm Innovation and Genetic Improvement, Lushan Botanical Garden, Jiangxi Province and Chinese Academy of Sciences, Jiujiang 330022, China; (Z.P.); (L.Z.)
- Heilongjiang Longke Seed Industry Group Co., Ltd., Harbin 150000, China
| | - Weiyao Zhang
- Suihua Branch of the Heilongjiang Academy of Agricultural Sciences, Suihua 152052, China; (J.W.); (W.Z.); (M.Q.); (L.G.); (W.P.); (Y.S.); (C.F.)
| | - Mengnan Qu
- Suihua Branch of the Heilongjiang Academy of Agricultural Sciences, Suihua 152052, China; (J.W.); (W.Z.); (M.Q.); (L.G.); (W.P.); (Y.S.); (C.F.)
| | - Lusi Gao
- Suihua Branch of the Heilongjiang Academy of Agricultural Sciences, Suihua 152052, China; (J.W.); (W.Z.); (M.Q.); (L.G.); (W.P.); (Y.S.); (C.F.)
| | - Wenjing Pan
- Suihua Branch of the Heilongjiang Academy of Agricultural Sciences, Suihua 152052, China; (J.W.); (W.Z.); (M.Q.); (L.G.); (W.P.); (Y.S.); (C.F.)
| | - Yanan Sun
- Suihua Branch of the Heilongjiang Academy of Agricultural Sciences, Suihua 152052, China; (J.W.); (W.Z.); (M.Q.); (L.G.); (W.P.); (Y.S.); (C.F.)
| | - Chunxu Fu
- Suihua Branch of the Heilongjiang Academy of Agricultural Sciences, Suihua 152052, China; (J.W.); (W.Z.); (M.Q.); (L.G.); (W.P.); (Y.S.); (C.F.)
| | - Ling Zhang
- Jiangxi Provincial Key Laboratory of Plant Germplasm Innovation and Genetic Improvement, Lushan Botanical Garden, Jiangxi Province and Chinese Academy of Sciences, Jiujiang 330022, China; (Z.P.); (L.Z.)
| | - Mingkun Huang
- Jiangxi Provincial Key Laboratory of Plant Germplasm Innovation and Genetic Improvement, Lushan Botanical Garden, Jiangxi Province and Chinese Academy of Sciences, Jiujiang 330022, China; (Z.P.); (L.Z.)
| | - Yufang Hu
- Jiangxi Provincial Key Laboratory of Plant Germplasm Innovation and Genetic Improvement, Lushan Botanical Garden, Jiangxi Province and Chinese Academy of Sciences, Jiujiang 330022, China; (Z.P.); (L.Z.)
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Ayyappan V, Sripathi VR, Xie S, Saha MC, Hayford R, Serba DD, Subramani M, Thimmapuram J, Todd A, Kalavacharla VK. Genome-wide profiling of histone (H3) lysine 4 (K4) tri-methylation (me3) under drought, heat, and combined stresses in switchgrass. BMC Genomics 2024; 25:223. [PMID: 38424499 PMCID: PMC10903042 DOI: 10.1186/s12864-024-10068-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2022] [Accepted: 01/30/2024] [Indexed: 03/02/2024] Open
Abstract
BACKGROUND Switchgrass (Panicum virgatum L.) is a warm-season perennial (C4) grass identified as an important biofuel crop in the United States. It is well adapted to the marginal environment where heat and moisture stresses predominantly affect crop growth. However, the underlying molecular mechanisms associated with heat and drought stress tolerance still need to be fully understood in switchgrass. The methylation of H3K4 is often associated with transcriptional activation of genes, including stress-responsive. Therefore, this study aimed to analyze genome-wide histone H3K4-tri-methylation in switchgrass under heat, drought, and combined stress. RESULTS In total, ~ 1.3 million H3K4me3 peaks were identified in this study using SICER. Among them, 7,342; 6,510; and 8,536 peaks responded under drought (DT), drought and heat (DTHT), and heat (HT) stresses, respectively. Most DT and DTHT peaks spanned 0 to + 2000 bases from the transcription start site [TSS]. By comparing differentially marked peaks with RNA-Seq data, we identified peaks associated with genes: 155 DT-responsive peaks with 118 DT-responsive genes, 121 DTHT-responsive peaks with 110 DTHT-responsive genes, and 175 HT-responsive peaks with 136 HT-responsive genes. We have identified various transcription factors involved in DT, DTHT, and HT stresses. Gene Ontology analysis using the AgriGO revealed that most genes belonged to biological processes. Most annotated peaks belonged to metabolite interconversion, RNA metabolism, transporter, protein modifying, defense/immunity, membrane traffic protein, transmembrane signal receptor, and transcriptional regulator protein families. Further, we identified significant peaks associated with TFs, hormones, signaling, fatty acid and carbohydrate metabolism, and secondary metabolites. qRT-PCR analysis revealed the relative expressions of six abiotic stress-responsive genes (transketolase, chromatin remodeling factor-CDH3, fatty-acid desaturase A, transmembrane protein 14C, beta-amylase 1, and integrase-type DNA binding protein genes) that were significantly (P < 0.05) marked during drought, heat, and combined stresses by comparing stress-induced against un-stressed and input controls. CONCLUSION Our study provides a comprehensive and reproducible epigenomic analysis of drought, heat, and combined stress responses in switchgrass. Significant enrichment of H3K4me3 peaks downstream of the TSS of protein-coding genes was observed. In addition, the cost-effective experimental design, modified ChIP-Seq approach, and analyses presented here can serve as a prototype for other non-model plant species for conducting stress studies.
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Affiliation(s)
- Vasudevan Ayyappan
- Molecular Genetics and Epigenomics Laboratory, Delaware State University, Dover, DE, 19901, USA.
| | | | - Shaojun Xie
- Bioinformatics Core, Purdue University, West Lafayette, IN, 47907, USA
| | - Malay C Saha
- Noble Research Institute, LLC, Ardmore, OK, 73401, USA
| | - Rita Hayford
- Center for Bioinformatics and Computational Biology, University of Delaware, Newark, DE, 19716, USA
| | - Desalegn D Serba
- USDA-ARS, U.S. Arid Land Agricultural Research Center, Maricopa, AZ, 85138, USA.
| | - Mayavan Subramani
- Molecular Genetics and Epigenomics Laboratory, Delaware State University, Dover, DE, 19901, USA
| | | | - Antonette Todd
- Molecular Genetics and Epigenomics Laboratory, Delaware State University, Dover, DE, 19901, USA
| | - Venu Kal Kalavacharla
- Molecular Genetics and Epigenomics Laboratory, Delaware State University, Dover, DE, 19901, USA
- Center for Integrated Biological and Environmental Research (CIBER), Delaware State University, Dover, DE, 19901, USA
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Huang M, Zhang L, Yung WS, Hu Y, Wang Z, Li MW, Lam HM. Molecular evidence for enhancer-promoter interactions in light responses of soybean seedlings. PLANT PHYSIOLOGY 2023; 193:2287-2291. [PMID: 37668345 DOI: 10.1093/plphys/kiad487] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/28/2023] [Revised: 08/18/2023] [Accepted: 08/18/2023] [Indexed: 09/06/2023]
Abstract
Interactions of enhancers with promoters and transcription factors mediate chromatin loop formation to regulate downstream gene expression in response to environmental stimuli such as light.
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Affiliation(s)
- Mingkun Huang
- Plant Functional Genomics and Bioinformatics Centre, Lushan Botanical Garden Jiangxi Province and Chinese Academy of Sciences, 332900 Jiujiang, Jiangxi, P.R. China
- School of Life Sciences and Centre for Soybean Research of the State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, P.R. China
| | - Ling Zhang
- Plant Functional Genomics and Bioinformatics Centre, Lushan Botanical Garden Jiangxi Province and Chinese Academy of Sciences, 332900 Jiujiang, Jiangxi, P.R. China
| | - Wai-Shing Yung
- School of Life Sciences and Centre for Soybean Research of the State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, P.R. China
| | - Yufang Hu
- Plant Functional Genomics and Bioinformatics Centre, Lushan Botanical Garden Jiangxi Province and Chinese Academy of Sciences, 332900 Jiujiang, Jiangxi, P.R. China
| | - Zhili Wang
- School of Life Sciences and Centre for Soybean Research of the State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, P.R. China
| | - Man-Wah Li
- School of Life Sciences and Centre for Soybean Research of the State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, P.R. China
| | - Hon-Ming Lam
- School of Life Sciences and Centre for Soybean Research of the State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, P.R. China
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4
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Ni L, Tian Z. Toward cis-regulation in soybean: a 3D genome scope. MOLECULAR BREEDING : NEW STRATEGIES IN PLANT IMPROVEMENT 2023; 43:28. [PMID: 37313524 PMCID: PMC10248674 DOI: 10.1007/s11032-023-01374-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/04/2023] [Accepted: 03/25/2023] [Indexed: 06/15/2023]
Abstract
In eukaryotic cells, 3D genome plays an important role in the regulation of gene spatiotemporal expression, which is essential for the biological and developmental processes in a life cycle. In the past decade, the development of high-throughput technologies greatly enhances our ability to map the 3D genome organization, identifies multiple 3D genome structures, and investigates the functional role of 3D genome organization in gene regulation, which facilitates our understandings of cis-regulatory landscape and biological development. Comparing with the comprehensive analyses of 3D genome in mammals and model plants, the progress in soybean is much less. Future development and application of tools to precisely manipulate 3D genome structure at different levels will significantly strengthen the functional genome study and molecular breeding in soybean. Here, we review the recent progresses in 3D genome study and discuss future directions, which may help to improve soybean 3D functional genome study and molecular breeding.
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Affiliation(s)
- Lingbin Ni
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, 100101 China
- College of Advanced Agriculture Sciences, University of Chinese Academy of Sciences, Beijing, 100049 China
| | - Zhixi Tian
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, 100101 China
- College of Advanced Agriculture Sciences, University of Chinese Academy of Sciences, Beijing, 100049 China
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5
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Wang G, Li X, Shen W, Li MW, Huang M, Zhang J, Li H. The chromatin accessibility landscape of pistils and anthers in rice. PLANT PHYSIOLOGY 2022; 190:2797-2811. [PMID: 36149297 PMCID: PMC9706442 DOI: 10.1093/plphys/kiac448] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Accepted: 09/04/2022] [Indexed: 06/16/2023]
Abstract
Transcription activation is tightly associated with the openness of chromatin and allows direct contact between transcriptional regulators and their targeted DNA for gene expression. However, there are limited studies on the annotation of open chromatin regions (OCRs) in rice (Oryza sativa), especially those in reproductive organs. Here, we characterized OCRs in rice pistils and anthers with an assay for transposase-accessible chromatin using sequencing. Despite a large overlap, we found more OCRs in pistils than in anthers. These OCRs were enriched in gene transcription start sites (TSSs) and showed tight associations with gene expression. Transcription factor (TF) binding motifs were enriched at these OCRs as validated by TF chromatin immunoprecipitation followed by sequencing. Pistil-specific OCRs provided potential regulatory networks by binding directly to the targets, indicating that pistil-specific OCRs may be indicators of cis-regulatory elements in regulating pistil development, which are absent in anthers. We also found that open chromatin of pistils and anthers responded differently to low temperature (LT). These data offer a comprehensive overview of OCRs regulating reproductive organ development and LT responses in rice.
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Affiliation(s)
- Guanqun Wang
- College of Life Sciences and Oceanography, Shenzhen University, Shenzhen 518000, China
- State Key Laboratory of Agrobiotechnology, School of Life Sciences, The Chinese University of Hong Kong, Shatin 999077, Hong Kong
| | - Xiaozheng Li
- College of Life Sciences and Oceanography, Shenzhen University, Shenzhen 518000, China
| | - Wei Shen
- State Key Laboratory of Agrobiotechnology, School of Life Sciences, The Chinese University of Hong Kong, Shatin 999077, Hong Kong
| | - Man-Wah Li
- State Key Laboratory of Agrobiotechnology, School of Life Sciences, The Chinese University of Hong Kong, Shatin 999077, Hong Kong
| | - Mingkun Huang
- Lushan Botanical Garden Jiangxi Province, Chinese Academy of Sciences, Jiujiang 332900, China
| | - Jianhua Zhang
- State Key Laboratory of Agrobiotechnology, School of Life Sciences, The Chinese University of Hong Kong, Shatin 999077, Hong Kong
- Department of Biology, Hong Kong Baptist University, Kowloon 999077, Hong Kong
| | - Haoxuan Li
- State Key Laboratory of Agrobiotechnology, School of Life Sciences, The Chinese University of Hong Kong, Shatin 999077, Hong Kong
- Department of Biology, Hong Kong Baptist University, Kowloon 999077, Hong Kong
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Characterization of Transposon-Derived Accessible Chromatin Regions in Rice (Oryza Sativa). Int J Mol Sci 2022; 23:ijms23168947. [PMID: 36012213 PMCID: PMC9408979 DOI: 10.3390/ijms23168947] [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: 07/05/2022] [Revised: 08/05/2022] [Accepted: 08/08/2022] [Indexed: 11/17/2022] Open
Abstract
Growing evidence indicates that transposons or transposable elements (TEs)-derived accessible chromatin regions (ACRs) play essential roles in multiple biological processes by interacting with trans-acting factors. However, the function of TE-derived ACRs in the regulation of gene expression in the rice genome has not been well characterized. In this study, we examined the chromatin dynamics in six types of rice tissues and found that ~8% of ACRs were derived from TEs and exhibited distinct levels of accessibility and conservation as compared to those without TEs. TEs exhibited a TE subtype-dependent impact on ACR formation, which can be mediated by changes in the underlying DNA methylation levels. Moreover, we found that tissue-specific TE-derived ACRs might function in the tissue development through the modulation of nearby gene expression. Interestingly, many genes in domestication sweeps were found to overlap with TE-derived ACRs, suggesting their potential functions in the rice domestication. In addition, we found that the expression divergence of 1070 duplicate gene pairs were associated with TE-derived ACRs and had distinct distributions of TEs and ACRs around the transcription start sites (TSSs), which may experience different selection pressures. Thus, our study provides some insights into the biological implications of TE-derived ACRs in the rice genome. Our results imply that these ACRs are likely involved in the regulation of tissue development, rice domestication and functional divergence of duplicated genes.
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Huang M, Zhang L, Zhou L, Yung WS, Wang Z, Xiao Z, Wang Q, Wang X, Li MW, Lam HM. Identification of the accessible chromatin regions in six tissues in the soybean. Genomics 2022; 114:110364. [PMID: 35421559 DOI: 10.1016/j.ygeno.2022.110364] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Revised: 02/25/2022] [Accepted: 04/06/2022] [Indexed: 01/14/2023]
Abstract
Accessible chromatin regions (ACRs) are tightly associated with gene expressions in the genome. Conserved non-coding cis-regulatory elements, such as transcription factor binding motifs, are usually found in ACRs, indicating an essential regulatory role of ACRs in the plant genome architecture. However, there have been few studies on soybean ACRs, especially those focusing on specific tissues. Hence, in this study, with the convenient ATAC-seq, we identified the ACRs in six soybean tissues, including root, leaf bud, flower, flower bud, developing seed, and pod. In total, the ACRs occupied about 3.3% of the entire soybean genome. By integrating the results from RNA-seq and transcription factor (TF) ChIP-seq, ACRs were found to be tightly associated with gene expressions and TF binding capacities in soybean. Together, these data provide a comprehensive understanding of the genomic features of ACRs in soybean. As a collection of essential genomic resources, these processed data are made available at datahub.wildsoydb.org.
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Affiliation(s)
- Mingkun Huang
- School of Life Sciences and Centre for Soybean Research of the State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, Hong Kong, SAR, PR China; Lushan Botanical Garden Jiangxi Province and Chinese Academy of Sciences, NO.9 Zhiqing Road, Lushan, Jiujiang, Jiangxi, PR China.
| | - Ling Zhang
- Lushan Botanical Garden Jiangxi Province and Chinese Academy of Sciences, NO.9 Zhiqing Road, Lushan, Jiujiang, Jiangxi, PR China
| | - Limeng Zhou
- School of Life Sciences and Centre for Soybean Research of the State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, Hong Kong, SAR, PR China
| | - Wai-Shing Yung
- School of Life Sciences and Centre for Soybean Research of the State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, Hong Kong, SAR, PR China
| | - Zhili Wang
- School of Life Sciences and Centre for Soybean Research of the State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, Hong Kong, SAR, PR China
| | - Zhixia Xiao
- School of Life Sciences and Centre for Soybean Research of the State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, Hong Kong, SAR, PR China
| | - Qianwen Wang
- School of Life Sciences and Centre for Soybean Research of the State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, Hong Kong, SAR, PR China
| | - Xin Wang
- School of Life Sciences and Centre for Soybean Research of the State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, Hong Kong, SAR, PR China
| | - Man-Wah Li
- School of Life Sciences and Centre for Soybean Research of the State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, Hong Kong, SAR, PR China.
| | - Hon-Ming Lam
- School of Life Sciences and Centre for Soybean Research of the State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, Hong Kong, SAR, PR China.
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Yung WS, Wang Q, Huang M, Wong FL, Liu A, Ng MS, Li KP, Sze CC, Li MW, Lam HM. Priming-induced alterations in histone modifications modulate transcriptional responses in soybean under salt stress. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2022; 109:1575-1590. [PMID: 34961994 DOI: 10.1111/tpj.15652] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/29/2021] [Revised: 12/01/2021] [Accepted: 12/22/2021] [Indexed: 06/14/2023]
Abstract
Plants that have experienced certain abiotic stress may gain tolerance to a similar stress in subsequent exposure. This phenomenon, called priming, was observed here in soybean (Glycine max) seedlings exposed to salt stress. Time-course transcriptomic profiles revealed distinctively different transcriptional responses in the primed seedlings from those in the non-primed seedlings under high salinity stress, indicating a stress response strategy of repressing unhelpful biotic stress responses and focusing on the promotion of those responses important for salt tolerance. To identify histone marks altered by the priming salinity treatment, a genome-wide profiling of histone 3 lysine 4 dimethylation (H3K4me2), H3K4me3, and histone 3 lysine 9 acetylation (H3K9ac) was performed. Our integrative analyses revealed that priming induced drastic alterations in these histone marks, which coordinately modified the stress response, ion homeostasis, and cell wall modification. Furthermore, transcriptional network analyses unveiled epigenetically modified networks which mediate the strategic downregulation of defense responses. Altering the histone acetylation status using a chemical inhibitor could elicit the priming-like transcriptional responses in non-primed seedlings, confirming the importance of histone marks in forming the priming response.
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Affiliation(s)
- Wai-Shing Yung
- Centre for Soybean Research of the State Key Laboratory of Agrobiotechnology and School of Life Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, China
| | - Qianwen Wang
- Centre for Soybean Research of the State Key Laboratory of Agrobiotechnology and School of Life Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, China
| | - Mingkun Huang
- Centre for Soybean Research of the State Key Laboratory of Agrobiotechnology and School of Life Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, China
- Lushan Botanical Garden, Chinese Academy of Sciences, Jiujiang, Jiangxi, 332900, China
| | - Fuk-Ling Wong
- Centre for Soybean Research of the State Key Laboratory of Agrobiotechnology and School of Life Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, China
| | - Ailin Liu
- Centre for Soybean Research of the State Key Laboratory of Agrobiotechnology and School of Life Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, China
| | - Ming-Sin Ng
- Centre for Soybean Research of the State Key Laboratory of Agrobiotechnology and School of Life Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, China
| | - Kwan-Pok Li
- Centre for Soybean Research of the State Key Laboratory of Agrobiotechnology and School of Life Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, China
| | - Ching-Ching Sze
- Centre for Soybean Research of the State Key Laboratory of Agrobiotechnology and School of Life Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, China
| | - Man-Wah Li
- Centre for Soybean Research of the State Key Laboratory of Agrobiotechnology and School of Life Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, China
| | - Hon-Ming Lam
- Centre for Soybean Research of the State Key Laboratory of Agrobiotechnology and School of Life Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, China
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Thibivilliers SB, Anderson DK, Libault MY. Isolation of Plant Nuclei Compatible with Microfluidic Single-nucleus ATAC-sequencing. Bio Protoc 2021; 11:e4240. [PMID: 35005085 DOI: 10.21769/bioprotoc.4240] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2021] [Revised: 08/29/2021] [Accepted: 09/06/2021] [Indexed: 11/02/2022] Open
Abstract
Gene expression depends on the binding of transcription factors with DNA regulatory sequences. The level of accessibility for these sequences varies between cells and cell types. Until recently, using the Tn5 assay for transposase-accessible chromatin for sequencing (ATAC-seq) technology allowed assessing the profiles of chromatin from an entire organ or, when coupled with the isolation of nuclei tagged in specific cell types (INTACT) method, from a cell-type. Recently, ATAC-seq experiments were conducted at the level of individual plant nuclei. Applying single nuclei ATAC-seq (sNucATAC-seq) technology to thousands of individual cells revealed more finely tuned profiles of chromatin accessibility. In this manuscript, we describe a method to isolate nuclei fom plant roots and green tissues, permeabilize the nuclear membrane using detergent to allow the penetration of the Tn5 transposase, and re-suspend them in a nuclei resuspension buffer compatible with the construction of sNucATAC-seq libraries using the 10× Genomic's Chromium technology. This protocol was successfully applied on Arabidopsis thaliana and Glycine max root nuclei.
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Affiliation(s)
- Sandra B Thibivilliers
- Department of Agronomy and Horticulture, Centre for Plant Science Innovation, Center for Root and Rhizobiome Innovation, University of Nebraska-Lincoln, Lincoln, NE, USA
| | - Dirk K Anderson
- Flow Cytometry Service Center, Center for Biotechnology, University of Nebraska-Lincoln, Lincoln, Nebraska, USA
| | - Marc Y Libault
- Department of Agronomy and Horticulture, Centre for Plant Science Innovation, Center for Root and Rhizobiome Innovation, University of Nebraska-Lincoln, Lincoln, NE, USA
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