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Yang Y, Xu L, Hao C, Wan M, Tao Y, Zhuang Y, Su Y, Li L. The microRNA408-plantacyanin module balances plant growth and drought resistance by regulating reactive oxygen species homeostasis in guard cells. THE PLANT CELL 2024; 36:4338-4355. [PMID: 38723161 PMCID: PMC11448907 DOI: 10.1093/plcell/koae144] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/20/2023] [Accepted: 04/20/2024] [Indexed: 10/05/2024]
Abstract
The conserved microRNA (miRNA) miR408 enhances photosynthesis and compromises stress tolerance in multiple plants, but the cellular mechanism underlying its function remains largely unclear. Here, we show that in Arabidopsis (Arabidopsis thaliana), the transcript encoding the blue copper protein PLANTACYANIN (PCY) is the primary target for miR408 in vegetative tissues. PCY is preferentially expressed in the guard cells, and PCY is associated with the endomembrane surrounding individual chloroplasts. We found that the MIR408 promoter is suppressed by multiple abscisic acid (ABA)-responsive transcription factors, thus allowing PCY to accumulate under stress conditions. Genetic analysis revealed that PCY elevates reactive oxygen species (ROS) levels in the guard cells, promotes stomatal closure, reduces photosynthetic gas exchange, and enhances drought resistance. Moreover, the miR408-PCY module is sufficient to rescue the growth and drought tolerance phenotypes caused by gain- and loss-of-function of MYB44, an established positive regulator of ABA responses, indicating that the miR408-PCY module relays ABA signaling for regulating ROS homeostasis and drought resistance. These results demonstrate that miR408 regulates stomatal movement to balance growth and drought resistance, providing a mechanistic understanding of why miR408 is selected during land plant evolution and insights into the long-pursued quest of breeding drought-tolerant and high-yielding crops.
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Affiliation(s)
- Yanzhi Yang
- Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agricultural Sciences at Weifang, Shandong 261000, China
- State Key Laboratory of Protein and Plant Gene Research, School of Advanced Agricultural Sciences and School of Life Sciences, Peking University, Beijing 100871, China
| | - Lei Xu
- Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing 100871, China
| | - Chen Hao
- State Key Laboratory of Protein and Plant Gene Research, School of Advanced Agricultural Sciences and School of Life Sciences, Peking University, Beijing 100871, China
| | - Miaomiao Wan
- State Key Laboratory of Protein and Plant Gene Research, School of Advanced Agricultural Sciences and School of Life Sciences, Peking University, Beijing 100871, China
| | - Yihan Tao
- State Key Laboratory of Protein and Plant Gene Research, School of Advanced Agricultural Sciences and School of Life Sciences, Peking University, Beijing 100871, China
| | - Yan Zhuang
- State Key Laboratory of Protein and Plant Gene Research, School of Advanced Agricultural Sciences and School of Life Sciences, Peking University, Beijing 100871, China
| | - Yanning Su
- State Key Laboratory of Protein and Plant Gene Research, School of Advanced Agricultural Sciences and School of Life Sciences, Peking University, Beijing 100871, China
| | - Lei Li
- Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agricultural Sciences at Weifang, Shandong 261000, China
- State Key Laboratory of Protein and Plant Gene Research, School of Advanced Agricultural Sciences and School of Life Sciences, Peking University, Beijing 100871, China
- Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing 100871, China
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2
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Soylu I, Lakshman DK, Tatineni S, Galvez LC, Mitra A. Differential regulation of miRNAs involved in the susceptible and resistance responses of wheat cultivars to wheat streak mosaic virus and Triticum mosaic virus. BMC Genomics 2024; 25:221. [PMID: 38418960 PMCID: PMC10900693 DOI: 10.1186/s12864-024-10128-1] [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: 09/15/2023] [Accepted: 02/15/2024] [Indexed: 03/02/2024] Open
Abstract
BACKGROUND Wheat streak mosaic virus (WSMV) and Triticum mosaic virus (TriMV) are components of the wheat streak mosaic virus disease complex in the Great Plains region of the U.S.A. and elsewhere. Co-infection of wheat with WSMV and TriMV causes synergistic interaction with more severe disease symptoms compared to single infections. Plants are equipped with multiple antiviral mechanisms, of which regulation of microRNAs (miRNAs) is a potentially effective constituent. In this investigation, we have analyzed the total and relative expression of miRNA transcriptome in two wheat cultivars, Arapahoe (susceptible) and Mace (temperature-sensitive-resistant), that were mock-inoculated or inoculated with WSMV, TriMV, or both at 18 °C and 27 °C. RESULTS Our results showed that the most abundant miRNA family among all the treatments was miRNA166, followed by 159a and 168a, although the order of the latter two changed depending on the infections. When comparing infected and control groups, twenty miRNAs showed significant upregulation, while eight miRNAs were significantly downregulated. Among them, miRNAs 9670-3p, 397-5p, and 5384-3p exhibited the most significant upregulation, whereas miRNAs 319, 9773, and 9774 were the most downregulated. The comparison of infection versus the control group for the cultivar Mace showed temperature-dependent regulation of these miRNAs. The principal component analysis confirmed that less abundant miRNAs among differentially expressed miRNAs were strongly correlated with the inoculated symptomatic wheat cultivars. Notably, miRNAs 397-5p, 398, and 9670-3p were upregulated in response to WSMV and TriMV infections, an observation not yet reported in this context. The significant upregulation of these three miRNAs was further confirmed with RT-qPCR analysis; in general, the RT-qPCR results were in agreement with our computational analysis. Target prediction analysis showed that the miRNAs standing out in our analysis targeted genes involved in defense response and regulation of transcription. CONCLUSION Investigation into the roles of these miRNAs and their corresponding targets holds promise for advancing our understanding of the mechanisms of virus infection and possible manipulation of these factors for developing durable virus resistance in crop plants.
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Affiliation(s)
- Inanc Soylu
- Department of Plant Pathology, University of Nebraska, Lincoln, NE, USA
| | - Dilip K Lakshman
- USDA-ARS Sustainable Agricultural Systems Laboratory, Beltsville, MD, USA
| | - Satyanarayana Tatineni
- Department of Plant Pathology, University of Nebraska, Lincoln, NE, USA
- USDA-ARS Wheat, Sorghum, and Forage Research Unit, University of Nebraska, Lincoln, NE, USA
| | - Leny C Galvez
- Department of Plant Pathology, University of Nebraska, Lincoln, NE, USA
| | - Amitava Mitra
- Department of Plant Pathology, University of Nebraska, Lincoln, NE, USA.
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3
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Sun L, Zhou J, Xu X, Liu Y, Ma N, Liu Y, Nie W, Zou L, Deng XW, He H. Mapping nucleosome-resolution chromatin organization and enhancer-promoter loops in plants using Micro-C-XL. Nat Commun 2024; 15:35. [PMID: 38167349 PMCID: PMC10762229 DOI: 10.1038/s41467-023-44347-z] [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: 02/17/2023] [Accepted: 12/10/2023] [Indexed: 01/05/2024] Open
Abstract
Although chromatin organizations in plants have been dissected at the scales of compartments and topologically associating domain (TAD)-like domains, there remains a gap in resolving fine-scale structures. Here, we use Micro-C-XL, a high-throughput chromosome conformation capture (Hi-C)-based technology that involves micrococcal nuclease (instead of restriction enzymes) and long cross-linkers, to dissect single nucleosome-resolution chromatin organization in Arabidopsis. Insulation analysis reveals more than 14,000 boundaries, which mostly include chromatin accessibility, epigenetic modifications, and transcription factors. Micro-C-XL reveals associations between RNA Pols and local chromatin organizations, suggesting that gene transcription substantially contributes to the establishment of local chromatin domains. By perturbing Pol II both genetically and chemically at the gene level, we confirm its function in regulating chromatin organization. Visible loops and stripes are assigned to super-enhancers and their targeted genes, thus providing direct insights for the identification and mechanistic analysis of distal CREs and their working modes in plants. We further investigate possible factors regulating these chromatin loops. Subsequently, we expand Micro-C-XL to soybean and rice. In summary, we use Micro-C-XL for analyses of plants, which reveal fine-scale chromatin organization and enhancer-promoter loops and provide insights regarding three-dimensional genomes in plants.
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Affiliation(s)
- Linhua Sun
- Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agricultural Sciences at Weifang, Shandong, 261000, China
- School of Advanced Agriculture Sciences and School of Life Sciences, State Key Laboratory of Protein and Plant Gene Research, Peking University, Beijing, 100871, China
| | - Jingru Zhou
- Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agricultural Sciences at Weifang, Shandong, 261000, China
| | - Xiao Xu
- Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agricultural Sciences at Weifang, Shandong, 261000, China
| | - Yi Liu
- School of Advanced Agriculture Sciences and School of Life Sciences, State Key Laboratory of Protein and Plant Gene Research, Peking University, Beijing, 100871, China
| | - Ni Ma
- Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agricultural Sciences at Weifang, Shandong, 261000, China
- PKU-Tsinghua-NIBS Graduate Program, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, 100871, China
| | - Yutong Liu
- Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agricultural Sciences at Weifang, Shandong, 261000, China
| | - Wenchao Nie
- Wuhan Frasergen Bioinformatics Co., Ltd., Wuhan, 430075, China
| | - Ling Zou
- Wuhan Frasergen Bioinformatics Co., Ltd., Wuhan, 430075, China
| | - Xing Wang Deng
- Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agricultural Sciences at Weifang, Shandong, 261000, China.
- School of Advanced Agriculture Sciences and School of Life Sciences, State Key Laboratory of Protein and Plant Gene Research, Peking University, Beijing, 100871, China.
| | - Hang He
- Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agricultural Sciences at Weifang, Shandong, 261000, China.
- School of Advanced Agriculture Sciences and School of Life Sciences, State Key Laboratory of Protein and Plant Gene Research, Peking University, Beijing, 100871, China.
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4
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Li C, Yue L, Ju Y, Wang J, Lu H, Li L, Chen M, Wang C, Li S, Liu T, Liu S, Lu T, Wang J, Hu X, Jiang C, Zhou D, Chen F. Transcriptomic analysis for the retested positive COVID-19 patients with long-term persistent SARS-CoV-2 but without symptoms in Wuhan. Clin Transl Med 2023; 13:e1172. [PMID: 36610051 PMCID: PMC9825106 DOI: 10.1002/ctm2.1172] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2022] [Revised: 11/27/2022] [Accepted: 12/29/2022] [Indexed: 01/09/2023] Open
Affiliation(s)
- Cuidan Li
- CAS Key Laboratory of Genome Sciences & Information, Beijing Institute of GenomicsChinese Academy of Sciences and China National Center for BioinformationBeijingChina
| | - Liya Yue
- CAS Key Laboratory of Genome Sciences & Information, Beijing Institute of GenomicsChinese Academy of Sciences and China National Center for BioinformationBeijingChina
| | - Yingjiao Ju
- CAS Key Laboratory of Genome Sciences & Information, Beijing Institute of GenomicsChinese Academy of Sciences and China National Center for BioinformationBeijingChina,University of Chinese Academy of SciencesBeijingChina
| | - Jie Wang
- CAS Key Laboratory of Genome Sciences & Information, Beijing Institute of GenomicsChinese Academy of Sciences and China National Center for BioinformationBeijingChina,University of Chinese Academy of SciencesBeijingChina
| | - Hao Lu
- CAS Key Laboratory of Genome Sciences & Information, Beijing Institute of GenomicsChinese Academy of Sciences and China National Center for BioinformationBeijingChina,University of Chinese Academy of SciencesBeijingChina
| | - Lin Li
- State Key Laboratory of Pathogen and BiosecurityBeijing Institute of Microbiology and EpidemiologyBeijingChina
| | - Mengfan Chen
- CAS Key Laboratory of Genome Sciences & Information, Beijing Institute of GenomicsChinese Academy of Sciences and China National Center for BioinformationBeijingChina,University of Chinese Academy of SciencesBeijingChina
| | - Chenyang Wang
- CAS Key Laboratory of Genome Sciences & Information, Beijing Institute of GenomicsChinese Academy of Sciences and China National Center for BioinformationBeijingChina,University of Chinese Academy of SciencesBeijingChina
| | - Shuangshuang Li
- CAS Key Laboratory of Genome Sciences & Information, Beijing Institute of GenomicsChinese Academy of Sciences and China National Center for BioinformationBeijingChina,University of Chinese Academy of SciencesBeijingChina
| | - Tao Liu
- CAS Key Laboratory of Genome Sciences & Information, Beijing Institute of GenomicsChinese Academy of Sciences and China National Center for BioinformationBeijingChina,University of Chinese Academy of SciencesBeijingChina
| | - Sitong Liu
- CAS Key Laboratory of Genome Sciences & Information, Beijing Institute of GenomicsChinese Academy of Sciences and China National Center for BioinformationBeijingChina,University of Chinese Academy of SciencesBeijingChina
| | - Tianyi Lu
- CAS Key Laboratory of Genome Sciences & Information, Beijing Institute of GenomicsChinese Academy of Sciences and China National Center for BioinformationBeijingChina,University of Chinese Academy of SciencesBeijingChina
| | - Jing Wang
- State Key Laboratory of Pathogenesis, PreventionTreatment of High Incidence Diseases in Central AsiaXinjiangChina
| | - Xin Hu
- State Key Laboratory of Pathogenesis, PreventionTreatment of High Incidence Diseases in Central AsiaXinjiangChina
| | - Chunlai Jiang
- National Engineering Laboratory for AIDS Vaccine, School of Life ScienceJilin UniversityChangchunChina
| | - Dongsheng Zhou
- State Key Laboratory of Pathogen and BiosecurityBeijing Institute of Microbiology and EpidemiologyBeijingChina
| | - Fei Chen
- CAS Key Laboratory of Genome Sciences & Information, Beijing Institute of GenomicsChinese Academy of Sciences and China National Center for BioinformationBeijingChina,University of Chinese Academy of SciencesBeijingChina,State Key Laboratory of Pathogenesis, PreventionTreatment of High Incidence Diseases in Central AsiaXinjiangChina,Beijing Key Laboratory of Genome and Precision Medicine TechnologiesChinese Academy of Sciences and China National Center for BioinformationBeijingChina
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5
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Zhang R, Zhang C, Yu C, Dong J, Hu J. Integration of multi-omics technologies for crop improvement: Status and prospects. FRONTIERS IN BIOINFORMATICS 2022; 2:1027457. [PMID: 36438626 PMCID: PMC9689701 DOI: 10.3389/fbinf.2022.1027457] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2022] [Accepted: 09/28/2022] [Indexed: 08/03/2023] Open
Abstract
With the rapid development of next-generation sequencing (NGS), multi-omics techniques have been emerging as effective approaches for crop improvement. Here, we focus mainly on addressing the current status and future perspectives toward omics-related technologies and bioinformatic resources with potential applications in crop breeding. Using a large amount of omics-level data from the functional genome, transcriptome, proteome, epigenome, metabolome, and microbiome, clarifying the interaction between gene and phenotype formation will become possible. The integration of multi-omics datasets with pan-omics platforms and systems biology could predict the complex traits of crops and elucidate the regulatory networks for genetic improvement. Different scales of trait predictions and decision-making models will facilitate crop breeding more intelligent. Potential challenges that integrate the multi-omics data with studies of gene function and their network to efficiently select desirable agronomic traits are discussed by proposing some cutting-edge breeding strategies for crop improvement. Multi-omics-integrated approaches together with other artificial intelligence techniques will contribute to broadening and deepening our knowledge of crop precision breeding, resulting in speeding up the breeding process.
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Deng Y, Zhang H, Wang H, Xing G, Lei B, Kuang Z, Zhao Y, Li C, Dai S, Yang X, Wei J, Zhang J. The Construction and Exploration of a Comprehensive MicroRNA Centered Regulatory Network in Foxtail Millet ( Setaria italica L.). FRONTIERS IN PLANT SCIENCE 2022; 13:848474. [PMID: 35599893 PMCID: PMC9121102 DOI: 10.3389/fpls.2022.848474] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/04/2022] [Accepted: 04/14/2022] [Indexed: 06/15/2023]
Abstract
MicroRNA (miRNA) is an essential endogenous post-transcriptional regulatory factor, and foxtail millet (Setaria italica L.) is an ideal C4 model cereal that is a highly valuable crop in semiarid and arid areas. The Research on comprehensive and high confidence identification and annotation of foxtail millet miRNAs needs to be strengthened, and to our knowledge, there is no information on the regulatory network of foxtail millet miRNA. In this study, 136 high confidence miRNAs were identified through high-throughput sequencing of the small RNAs in seven tissues at the shooting and grain filling stages of foxtail millet. A total of 2,417 target genes were obtained by combining computational biology software and degradome sequencing methods. Furthermore, an analysis using transcriptome sequencing revealed the relationships between miRNAs and their target genes and simultaneously explored key regulatory modules in panicles during the grain filling stage. An miRNA regulatory network was constructed to explore the functions of miRNA in more detail. This network, centered on miRNAs and combining upstream transcriptional factors and downstream target genes, is primarily composed of feed forward loop motifs, which greatly enhances our knowledge of the potential functions of miRNAs and uncovers numerous previously unknown regulatory links. This study provides a solid foundation for research on the function and regulatory network of miRNAs in foxtail millet.
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Affiliation(s)
- Yang Deng
- Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
- Beijing Key Laboratory of Agricultural Genetic Resources and Biotechnology, Institute of Biotechnology, Beijing, China
| | - Haolin Zhang
- Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
- College of Life Science, Shanghai Normal University, Shanghai, China
| | - Hailong Wang
- Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
- Beijing Key Laboratory of Agricultural Genetic Resources and Biotechnology, Institute of Biotechnology, Beijing, China
| | - Guofang Xing
- College of Agricultural, Shanxi Agricultural University, Jinzhong, China
- Shanxi Key Laboratory of Minor Crop Germplasm Innovation and Molecular Breeding, College of Agriculture, Shanxi Agricultural University, Jinzhong, China
| | - Biao Lei
- College of Agricultural, Shanxi Agricultural University, Jinzhong, China
- Shanxi Key Laboratory of Minor Crop Germplasm Innovation and Molecular Breeding, College of Agriculture, Shanxi Agricultural University, Jinzhong, China
| | - Zheng Kuang
- Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
- Beijing Key Laboratory of Agricultural Genetic Resources and Biotechnology, Institute of Biotechnology, Beijing, China
| | - Yongxin Zhao
- Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
- Beijing Key Laboratory of Agricultural Genetic Resources and Biotechnology, Institute of Biotechnology, Beijing, China
| | - Congcong Li
- Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
- Beijing Key Laboratory of Agricultural Genetic Resources and Biotechnology, Institute of Biotechnology, Beijing, China
| | - Shaojun Dai
- College of Life Science, Shanghai Normal University, Shanghai, China
| | - Xiaozeng Yang
- Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
- Beijing Key Laboratory of Agricultural Genetic Resources and Biotechnology, Institute of Biotechnology, Beijing, China
| | - Jianhua Wei
- Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
- Beijing Key Laboratory of Agricultural Genetic Resources and Biotechnology, Institute of Biotechnology, Beijing, China
| | - Jiewei Zhang
- Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
- Beijing Key Laboratory of Agricultural Genetic Resources and Biotechnology, Institute of Biotechnology, Beijing, China
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7
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Jia Y, Niu Y, Zhao H, Wang Z, Gao C, Wang C, Chen S, Wang Y. Hierarchical transcription factor and regulatory network for drought response in Betula platyphylla. HORTICULTURE RESEARCH 2022; 9:uhac040. [PMID: 35184174 PMCID: PMC9070641 DOI: 10.1093/hr/uhac040] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/16/2021] [Revised: 01/03/2022] [Accepted: 02/05/2022] [Indexed: 05/16/2023]
Abstract
Although many genes and biological processes involved in abiotic stress response have been identified, how they are regulated remains largely unclear. Here, to study the regulatory mechanism of birch (Betula platyphylla) responding to drought induced by polyethylene glycol (PEG) 6000 (20%, w/v), a partial correlation coefficient-based algorithm for constructing gene regulatory network (GRN) was proposed, and a three-layer hierarchical GRN was constructed, including 68 transcription factors (TFs), and 252 structural genes. Totally, 1448 predicted regulatory relationships are included, and most of them are novel. The reliability of GRN was verified by ChIP-PCR and qRT-PCR based on transient transformation. About 55% of genes in the bottom layer of GRN could confer drought tolerance. We selected the two TFs, BpMADS11 and BpNAC090, from the up layer and characterized their function in drought tolerance. Overexpression of BpMADS11 and BpNAC090 both reduces electrolyte leakage, ROS and MDA contents, displaying increased drought tolerance than wild-type birch. According to this GRN, the important biological processes involved in drought were identified, including "signaling hormone pathways", "water transport", "regulation of stomatal movement" and "response to oxidative stress". This work indicated that BpERF017, BpAGL61 and BpNAC090 are the key upstream regulators in birch drought tolerance. Our data clearly revealed the upstream regulators and TF-DNA interaction regulate different biological processes to adapt drought stress.
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Affiliation(s)
- Yaqi Jia
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, 26 Hexing Road, Harbin 150040, China
| | - Yani Niu
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, 26 Hexing Road, Harbin 150040, China
| | - Huimin Zhao
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, 26 Hexing Road, Harbin 150040, China
| | - Zhibo Wang
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, 26 Hexing Road, Harbin 150040, China
| | - Caiqiu Gao
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, 26 Hexing Road, Harbin 150040, China
| | - Chao Wang
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, 26 Hexing Road, Harbin 150040, China
| | - Su Chen
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, 26 Hexing Road, Harbin 150040, China
| | - Yucheng Wang
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, 26 Hexing Road, Harbin 150040, China
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8
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Deng Y, Qin Y, Yang P, Du J, Kuang Z, Zhao Y, Wang Y, Li D, Wei J, Guo X, Li L, Yang X. Comprehensive Annotation and Functional Exploration of MicroRNAs in Lettuce. FRONTIERS IN PLANT SCIENCE 2021; 12:781836. [PMID: 35003165 PMCID: PMC8739914 DOI: 10.3389/fpls.2021.781836] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/23/2021] [Accepted: 10/28/2021] [Indexed: 05/28/2023]
Abstract
MicroRNA (miRNA) is an important endogenous post-transcriptional regulator, while lettuce (Lactuca sativa) is a leafy vegetable of global economic significance. However, there are few studies on miRNAs in lettuce, and research on miRNA regulatory network in lettuce is absent. In this study, through deep sequencing of small RNAs in different tissues, together with a reference genome, 157 high-confidence miRNA loci in lettuce were comprehensively identified, and their expression patterns were determined. Using a combination of computational prediction and high-throughput experimental verification, a set of reliable lettuce miRNA targets were obtained. Furthermore, through RNA-Seq, the expression profiles of these targets and a comprehensive view of the negative regulatory relationship between miRNAs and their targets was acquired based on a correlation analysis. To further understand miRNA functions, a miRNA regulatory network was constructed, with miRNAs at the core and combining transcription factors and miRNA target genes. This regulatory network, mainly composed of feed forward loop motifs, greatly increases understanding of the potential functions of miRNAs, and many unknown potential regulatory links were discovered. Finally, considering its specific expression pattern, Lsa-MIR408 as a hub gene was employed to illustrate the function of the regulatory network, and genetic experiments revealed its ability to increase the fresh weight and achene size of lettuce. In short, this work lays a solid foundation for the study of miRNA functions and regulatory networks in lettuce.
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Affiliation(s)
- Yang Deng
- Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
- Beijing Key Laboratory of Agricultural Genetic Resources and Biotechnology, Beijing Agro-Biotechnology Research Center, Beijing, China
| | - Yajuan Qin
- Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
- Beijing Key Laboratory of Agricultural Genetic Resources and Biotechnology, Beijing Agro-Biotechnology Research Center, Beijing, China
| | - Pan Yang
- Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
- College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
- State Key Laboratory of Protein and Plant Gene Research, Peking-Tsinghua Center for Life Sciences, School of Advanced Agricultural Sciences and School of Life Sciences, Peking University, Beijing, China
| | - Jianjun Du
- Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
- Beijing Key Lab of Digital Plant, Beijing Research Center for Information Technology in Agriculture, Beijing, China
| | - Zheng Kuang
- Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
- State Key Laboratory of Protein and Plant Gene Research, Peking-Tsinghua Center for Life Sciences, School of Advanced Agricultural Sciences and School of Life Sciences, Peking University, Beijing, China
| | - Yongxin Zhao
- Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
- Beijing Key Laboratory of Agricultural Genetic Resources and Biotechnology, Beijing Agro-Biotechnology Research Center, Beijing, China
| | - Ying Wang
- State Key Laboratory of Protein and Plant Gene Research, Peking-Tsinghua Center for Life Sciences, School of Advanced Agricultural Sciences and School of Life Sciences, Peking University, Beijing, China
| | - Dayong Li
- Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
- Beijing Key Laboratory of Vegetable Germplasm Improvement, Beijing Vegetable Research Center, Beijing, China
| | - Jianhua Wei
- Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
- Beijing Key Laboratory of Agricultural Genetic Resources and Biotechnology, Beijing Agro-Biotechnology Research Center, Beijing, China
| | - Xinyu Guo
- Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
- Beijing Key Lab of Digital Plant, Beijing Research Center for Information Technology in Agriculture, Beijing, China
| | - Lei Li
- State Key Laboratory of Protein and Plant Gene Research, Peking-Tsinghua Center for Life Sciences, School of Advanced Agricultural Sciences and School of Life Sciences, Peking University, Beijing, China
| | - Xiaozeng Yang
- Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
- Beijing Key Laboratory of Agricultural Genetic Resources and Biotechnology, Beijing Agro-Biotechnology Research Center, Beijing, China
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9
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Guo Z, Kuang Z, Zhao Y, Deng Y, He H, Wan M, Tao Y, Wang D, Wei J, Li L, Yang X. PmiREN2.0: from data annotation to functional exploration of plant microRNAs. Nucleic Acids Res 2021; 50:D1475-D1482. [PMID: 34554254 PMCID: PMC8728213 DOI: 10.1093/nar/gkab811] [Citation(s) in RCA: 38] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2021] [Revised: 08/31/2021] [Accepted: 09/08/2021] [Indexed: 11/21/2022] Open
Abstract
Nearly 200 plant genomes have been sequenced over the last two years, and new functions of plant microRNAs (miRNAs) have been revealed. Therefore, timely update of the plant miRNA databases by incorporating miRNAs from the newly sequenced species and functional information is required to provide useful resources for advancing plant miRNA research. Here we report the update of PmiREN2.0 (https://pmiren.com/) with an addition of 19 363 miRNA entries from 91 plants, doubling the amount of data in the original version. Meanwhile, abundant regulatory information centred on miRNAs was added, including predicted upstream transcription factors through binding motifs scanning and elaborate annotation of miRNA targets. As an example, a genome-wide regulatory network centred on miRNAs was constructed for Arabidopsis. Furthermore, phylogenetic trees of conserved miRNA families were built to expand the understanding of miRNA evolution across the plant lineages. These data are helpful to deduce the regulatory relationships concerning miRNA functions in diverse plants. Beside the new data, a suite of design tools was incorporated to facilitate experimental practice. Finally, a forum named ‘PmiREN Community’ was added for discussion and resource and new discovery sharing. With these upgrades, PmiREN2.0 should serve the community better and accelerate miRNA research in plants.
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Affiliation(s)
- Zhonglong Guo
- Beijing Agro-biotechnology Research Center, Beijing Key Laboratory of Agricultural Genetic Resources and Biotechnology, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, P.R. China.,State Key Laboratory of Protein and Plant Gene Research, Peking-Tsinghua Center for Life Sciences, School of Life Sciences and School of Advanced Agricultural Sciences, Peking University, Beijing 100871, P.R. China
| | - Zheng Kuang
- Beijing Agro-biotechnology Research Center, Beijing Key Laboratory of Agricultural Genetic Resources and Biotechnology, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, P.R. China.,State Key Laboratory of Protein and Plant Gene Research, Peking-Tsinghua Center for Life Sciences, School of Life Sciences and School of Advanced Agricultural Sciences, Peking University, Beijing 100871, P.R. China
| | - Yongxin Zhao
- Beijing Agro-biotechnology Research Center, Beijing Key Laboratory of Agricultural Genetic Resources and Biotechnology, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, P.R. China
| | - Yang Deng
- Beijing Agro-biotechnology Research Center, Beijing Key Laboratory of Agricultural Genetic Resources and Biotechnology, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, P.R. China
| | - Hao He
- Beijing Agro-biotechnology Research Center, Beijing Key Laboratory of Agricultural Genetic Resources and Biotechnology, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, P.R. China
| | - Miaomiao Wan
- State Key Laboratory of Protein and Plant Gene Research, Peking-Tsinghua Center for Life Sciences, School of Life Sciences and School of Advanced Agricultural Sciences, Peking University, Beijing 100871, P.R. China
| | - Yihan Tao
- State Key Laboratory of Protein and Plant Gene Research, Peking-Tsinghua Center for Life Sciences, School of Life Sciences and School of Advanced Agricultural Sciences, Peking University, Beijing 100871, P.R. China
| | - Dong Wang
- WeiRan Biotech, Beijing 100085, P.R. China
| | - Jianhua Wei
- Beijing Agro-biotechnology Research Center, Beijing Key Laboratory of Agricultural Genetic Resources and Biotechnology, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, P.R. China
| | - Lei Li
- State Key Laboratory of Protein and Plant Gene Research, Peking-Tsinghua Center for Life Sciences, School of Life Sciences and School of Advanced Agricultural Sciences, Peking University, Beijing 100871, P.R. China
| | - Xiaozeng Yang
- Beijing Agro-biotechnology Research Center, Beijing Key Laboratory of Agricultural Genetic Resources and Biotechnology, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, P.R. China
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Zhang H, Guo Z, Zhuang Y, Suo Y, Du J, Gao Z, Pan J, Li L, Wang T, Xiao L, Qin G, Jiao Y, Cai H, Li L. MicroRNA775 regulates intrinsic leaf size and reduces cell wall pectin levels by targeting a galactosyltransferase gene in Arabidopsis. THE PLANT CELL 2021; 33:581-602. [PMID: 33955485 PMCID: PMC8136896 DOI: 10.1093/plcell/koaa049] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/17/2020] [Accepted: 12/16/2020] [Indexed: 05/10/2023]
Abstract
Plants possess unique primary cell walls made of complex polysaccharides that play critical roles in determining intrinsic cell and organ size. How genes responsible for synthesizing and modifying the polysaccharides in the cell wall are regulated by microRNAs (miRNAs) to control plant size remains largely unexplored. Here we identified 23 putative cell wall-related miRNAs, termed as CW-miRNAs, in Arabidopsis thaliana and characterized miR775 as an example. We showed that miR775 post-transcriptionally silences GALT9, which encodes an endomembrane-located galactosyltransferase belonging to the glycosyltransferase 31 family. Over-expression of miR775 and deletion of GALT9 led to significantly enlarged leaf-related organs, primarily due to increased cell size. Monosaccharide quantification, confocal Raman imaging, and immunolabeling combined with atomic force microscopy revealed that the MIR775A-GALT9 circuit modulates pectin levels and the elastic modulus of the cell wall. We also showed that MIR775A is directly repressed by the transcription factor ELONGATED HYPOCOTYL5 (HY5). Genetic analysis confirmed that HY5 is a negative regulator of leaf size that acts through the HY5-MIR775A-GALT9 repression cascade to control pectin levels. These findings demonstrate that miR775-regulated cell wall remodeling is an integral determinant of intrinsic leaf size in A. thaliana. Studying other CW-miRNAs would provide more insights into cell wall biology.
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Affiliation(s)
- He Zhang
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences and School of Advanced Agricultural Sciences, Peking University, Beijing 100871, China
| | - Zhonglong Guo
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences and School of Advanced Agricultural Sciences, Peking University, Beijing 100871, China
| | - Yan Zhuang
- Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing 100871, China
| | - Yuanzhen Suo
- Biomedical Pioneering Innovation Center, School of Life Sciences and Beijing Advanced Innovation Center for Genomics, Peking University, Beijing 100871, China
| | - Jianmei Du
- Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing 100871, China
| | - Zhaoxu Gao
- Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing 100871, China
| | - Jiawei Pan
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences and School of Advanced Agricultural Sciences, Peking University, Beijing 100871, China
| | - Li Li
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences and School of Advanced Agricultural Sciences, Peking University, Beijing 100871, China
| | - Tianxin Wang
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences and School of Advanced Agricultural Sciences, Peking University, Beijing 100871, China
| | - Liang Xiao
- College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, China
| | - Genji Qin
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences and School of Advanced Agricultural Sciences, Peking University, Beijing 100871, China
| | - Yuling Jiao
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, and National Center for Plant Gene Research, 100101 Beijing, China
| | - Huaqing Cai
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Lei Li
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences and School of Advanced Agricultural Sciences, Peking University, Beijing 100871, China
- Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing 100871, China
- Author for correspondence:
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