151
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Zhu H, Li X, Xi D, Zhai W, Zhang Z, Zhu Y. Integrating long noncoding RNAs and mRNAs expression profiles of response to Plasmodiophora brassicae infection in Pakchoi (Brassica campestris ssp. chinensis Makino). PLoS One 2019; 14:e0224927. [PMID: 31805057 PMCID: PMC6894877 DOI: 10.1371/journal.pone.0224927] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2019] [Accepted: 10/24/2019] [Indexed: 01/18/2023] Open
Abstract
The biotrophic protist Plasmodiophora brassicae causes serious damage to Brassicaceae crops grown worldwide. However, the molecular mechanism of the Brassica rapa response remains has not been determined. Long noncoding RNA and mRNA expression profiles in response to Plasmodiophora brassicae infection were investigated using RNA-seq on the Chinese cabbage inbred line C22 infected with P. brassicae. Approximately 5,193 mRNAs were significantly differentially expressed, among which 1,345 were upregulated and 3,848 were downregulated. The GO enrichment analysis shows that most of these mRNAs are related to the defense response. Meanwhile, 114 significantly differentially expressed lncRNAs were identified, including 31 upregulated and 83 downregulated. Furthermore, a total of 2,344 interaction relationships were detected between 1,725 mRNAs and 103 lncRNAs with a correlation coefficient greater than 0.8. We also found 15 P. brassicaerelated mRNAs and 16 lncRNA interactions within the correlation network. The functional annotation showed that 15 mRNAs belong to defense response proteins (66.67%), protein phosphorylation (13.33%), root hair cell differentiation (13.33%) and regulation of salicylic acid biosynthetic process (6.67%). KEGG annotation showed that the vast majority of these genes are involved in the biosynthesis of secondary metabolism pathways and plant-pathogen interactions. These results provide a new perspective on lncRNA-mRNA network function and help to elucidate the molecular mechanism of P. brassicae infection.
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Affiliation(s)
- Hongfang Zhu
- Horticulture Research Institute, Shanghai Academy of Agricultural Sciences, Shanghai, China
- Shanghai Key Lab of Protected Horticultural Technology, Shanghai, China
| | - Xiaofeng Li
- Horticulture Research Institute, Shanghai Academy of Agricultural Sciences, Shanghai, China
- Shanghai Key Lab of Protected Horticultural Technology, Shanghai, China
| | - Dandan Xi
- Horticulture Research Institute, Shanghai Academy of Agricultural Sciences, Shanghai, China
- Shanghai Key Lab of Protected Horticultural Technology, Shanghai, China
| | - Wen Zhai
- East China University of Technology, Nanchang, China
| | - Zhaohui Zhang
- Horticulture Research Institute, Shanghai Academy of Agricultural Sciences, Shanghai, China
- Shanghai Key Lab of Protected Horticultural Technology, Shanghai, China
| | - Yuying Zhu
- Horticulture Research Institute, Shanghai Academy of Agricultural Sciences, Shanghai, China
- Shanghai Key Lab of Protected Horticultural Technology, Shanghai, China
- * E-mail:
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152
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Tang J, Xu Z, Huang L, Luo H, Zhu X. Transcriptional regulation in model organisms: recent progress and clinical implications. Open Biol 2019; 9:190183. [PMID: 31744421 PMCID: PMC6893401 DOI: 10.1098/rsob.190183] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
In this review, we will summarize model organisms used by scientists in the laboratory, including Escherichia coli, yeast, Arabidopsis thaliana, nematodes, Drosophila, zebrafish, mice and other animals. We focus on the progress in research exploring different types of E. coli in the human body, and the specific molecular mechanisms by which they play a role in humans. First, we discuss the specific transcriptional regulation mechanism of E. coli in cell development, maturation, ageing and longevity, as well as tumorigenesis and development. Then, we discuss how the synthesis of some important substances in cells is regulated and how this affects biological behaviour. Understanding and applying these mechanisms, presumably, can greatly improve the quality of people's lives as well as increase their lifespan. For example, some E. coli can activate certain cells by secreting insulin-like growth factor-1, thus activating the inflammatory response of the body, while other E. coli can inactivate the immune response of the body by secreting toxic factors.
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Affiliation(s)
- Jiaqi Tang
- The Marine Biomedical Research Institute, Southern Marine Science and Engineering Guangdong Laboratory Zhanjiang, Guangdong Medical University, Zhanjiang 524023, People's Republic of China.,Guangdong Key Laboratory for Research and Development of Natural Drugs, Zhanjiang 524023, People's Republic of China
| | - Zhenhua Xu
- Center for Cancer and Immunology, Brain Tumor Institute, Children's National Health System, Washington, DC 20010, USA
| | - Lianfang Huang
- The Marine Biomedical Research Institute, Southern Marine Science and Engineering Guangdong Laboratory Zhanjiang, Guangdong Medical University, Zhanjiang 524023, People's Republic of China.,Guangdong Key Laboratory for Research and Development of Natural Drugs, Zhanjiang 524023, People's Republic of China
| | - Hui Luo
- The Marine Biomedical Research Institute, Southern Marine Science and Engineering Guangdong Laboratory Zhanjiang, Guangdong Medical University, Zhanjiang 524023, People's Republic of China
| | - Xiao Zhu
- The Marine Biomedical Research Institute, Southern Marine Science and Engineering Guangdong Laboratory Zhanjiang, Guangdong Medical University, Zhanjiang 524023, People's Republic of China.,Guangdong Key Laboratory for Research and Development of Natural Drugs, Zhanjiang 524023, People's Republic of China
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153
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Yang T, Ma H, Zhang J, Wu T, Song T, Tian J, Yao Y. Systematic identification of long noncoding RNAs expressed during light-induced anthocyanin accumulation in apple fruit. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2019; 100:572-590. [PMID: 31344284 DOI: 10.1111/tpj.14470] [Citation(s) in RCA: 65] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/02/2019] [Revised: 06/27/2019] [Accepted: 07/09/2019] [Indexed: 05/23/2023]
Abstract
Anthocyanin pigments contribute to the red color of apple (Malus × domestica) fruit and have a major influence on their ornamental, dietary and market value. In this study, we investigated the potential role of long noncoding RNAs (lncRNAs) in anthocyanin biosynthesis. RNA-seq analysis of apple peels from the 'Red Fuji' cultivar during light-induced rapid anthocyanin accumulation revealed 5297 putative lncRNAs. Differential expression analysis further showed that lncRNAs were induced during light treatment and were involved in photosynthesis. Using the miRNA-lncRNA-mRNA network and endogenous target mimic (eTM) analysis, we predicted that two differentially expressed lncRNAs, MLNC3.2 and MLNC4.6, were potential eTMs for miRNA156a and promoted the expression of the SPL2-like and SPL33 transcription factors. Transient expression in apple fruit and stable transformation of apple callus showed that overexpression of the eTMs and SPLs promoted anthocyanin accumulation, with the opposite results in eTM and SPL-silenced fruit. Silencing or overexpressing of miR156a also affected the expression of the identified eTMs and SPLs. These results indicated that MLNC3.2 and MLNC4.6 function as eTMs for miR156a and prevent cleavage of SPL2-like and SPL33 by miR156a during light-induced anthocyanin biosynthesis. Our study provides fundamental insights into lncRNA involvement in the anthocyanin biosynthetic pathway in apple fruit.
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Affiliation(s)
- Tuo Yang
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing University of Agriculture, Beijing, China
- Plant Science and Technology College, Beijing University of Agriculture, Beijing, China
- National Demonstration Center for Experimental Plant Production Education (Beijing University of Agriculture), Beijing, China
| | - Huaying Ma
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing University of Agriculture, Beijing, China
- Plant Science and Technology College, Beijing University of Agriculture, Beijing, China
- National Demonstration Center for Experimental Plant Production Education (Beijing University of Agriculture), Beijing, China
| | - Jie Zhang
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing University of Agriculture, Beijing, China
- Plant Science and Technology College, Beijing University of Agriculture, Beijing, China
- National Demonstration Center for Experimental Plant Production Education (Beijing University of Agriculture), Beijing, China
| | - Ting Wu
- College of Horticulture, China Agricultural University, Beijing, China
| | - Tingting Song
- Plant Science and Technology College, Beijing University of Agriculture, Beijing, China
| | - Ji Tian
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing University of Agriculture, Beijing, China
- Plant Science and Technology College, Beijing University of Agriculture, Beijing, China
- National Demonstration Center for Experimental Plant Production Education (Beijing University of Agriculture), Beijing, China
| | - Yuncong Yao
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing University of Agriculture, Beijing, China
- Plant Science and Technology College, Beijing University of Agriculture, Beijing, China
- National Demonstration Center for Experimental Plant Production Education (Beijing University of Agriculture), Beijing, China
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154
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Zhang X, Dong J, Deng F, Wang W, Cheng Y, Song L, Hu M, Shen J, Xu Q, Shen F. The long non-coding RNA lncRNA973 is involved in cotton response to salt stress. BMC PLANT BIOLOGY 2019; 19:459. [PMID: 31666019 PMCID: PMC6822370 DOI: 10.1186/s12870-019-2088-0] [Citation(s) in RCA: 52] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/12/2019] [Accepted: 10/20/2019] [Indexed: 05/22/2023]
Abstract
BACKGROUND Long non-coding (lnc) RNAs are a class of functional RNA molecules greater than 200 nucleotides in length, and lncRNAs play important roles in various biological regulatory processes and response to the biotic and abiotic stresses. LncRNAs associated with salt stress in cotton have been identified through RNA sequencing, but the function of lncRNAs has not been reported. We previously identified salt stress-related lncRNAs in cotton (Gossypium spp.), and discovered the salt-related lncRNA-lncRNA973. RESULTS In this study, we identified the expression level, localization, function, and preliminary mechanism of action of lncRNA973. LncRNA973, which was localized in the nucleus, was expressed at a low level under nonstress conditions but can be significantly increased by salt treatments. Here lncRNA973 was transformed into Arabidopsis and overexpressed. Along with the increased expression compared with wild type under salt stress conditions in transgenic plants, the seed germination rate, fresh weights and root lengths of the transgenic plants increased. We also knocked down the expression of lncRNA973 using virus-induced gene silencing technology. The lncRNA973 knockdown plants wilted, and the leaves became yellowed and dropped under salt-stress conditions, indicating that the tolerance to salt stress had decreased compared with wild type. LncRNA973 may be involved in the regulation of reactive oxygen species-scavenging genes, transcription factors and genes involved in salt stress-related processes in response to cotton salt stress. CONCLUSIONS LncRNA973 was localized in the nucleus and its expression was increased by salt treatment. The lncRNA973-overexpression lines had increased salt tolerance compared with the wild type, while the lncRNA973 knockdown plants had reduced salt tolerance. LncRNA973 regulated cotton responses to salt stress by modulating the expression of a series of salt stress-related genes. The data provides a basis for further studies on the mechanisms of lncRNA973-associated responses to salt stress in cotton.
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Affiliation(s)
- Xiaopei Zhang
- State Key Laboratory of Crop Biology, College of Agronomy, Shandong Agricultural University, NO. 61 Daizong Street, Tai'an, Shandong, 271018, People's Republic of China
| | - Jie Dong
- State Key Laboratory of Crop Biology, College of Agronomy, Shandong Agricultural University, NO. 61 Daizong Street, Tai'an, Shandong, 271018, People's Republic of China
| | - Fenni Deng
- State Key Laboratory of Crop Biology, College of Agronomy, Shandong Agricultural University, NO. 61 Daizong Street, Tai'an, Shandong, 271018, People's Republic of China
| | - Wei Wang
- State Key Laboratory of Crop Biology, College of Agronomy, Shandong Agricultural University, NO. 61 Daizong Street, Tai'an, Shandong, 271018, People's Republic of China
| | - Yingying Cheng
- State Key Laboratory of Crop Biology, College of Agronomy, Shandong Agricultural University, NO. 61 Daizong Street, Tai'an, Shandong, 271018, People's Republic of China
| | - Lirong Song
- State Key Laboratory of Crop Biology, College of Agronomy, Shandong Agricultural University, NO. 61 Daizong Street, Tai'an, Shandong, 271018, People's Republic of China
| | - Mengjiao Hu
- State Key Laboratory of Crop Biology, College of Agronomy, Shandong Agricultural University, NO. 61 Daizong Street, Tai'an, Shandong, 271018, People's Republic of China
| | - Jian Shen
- State Key Laboratory of Crop Biology, College of Agronomy, Shandong Agricultural University, NO. 61 Daizong Street, Tai'an, Shandong, 271018, People's Republic of China
| | - Qingjiang Xu
- State Key Laboratory of Crop Biology, College of Agronomy, Shandong Agricultural University, NO. 61 Daizong Street, Tai'an, Shandong, 271018, People's Republic of China
| | - Fafu Shen
- State Key Laboratory of Crop Biology, College of Agronomy, Shandong Agricultural University, NO. 61 Daizong Street, Tai'an, Shandong, 271018, People's Republic of China.
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155
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Baillo EH, Kimotho RN, Zhang Z, Xu P. Transcription Factors Associated with Abiotic and Biotic Stress Tolerance and Their Potential for Crops Improvement. Genes (Basel) 2019; 10:E771. [PMID: 31575043 PMCID: PMC6827364 DOI: 10.3390/genes10100771] [Citation(s) in RCA: 229] [Impact Index Per Article: 45.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2019] [Revised: 09/17/2019] [Accepted: 09/17/2019] [Indexed: 01/24/2023] Open
Abstract
In field conditions, crops are adversely affected by a wide range of abiotic stresses including drought, cold, salt, and heat, as well as biotic stresses including pests and pathogens. These stresses can have a marked effect on crop yield. The present and future effects of climate change necessitate the improvement of crop stress tolerance. Plants have evolved sophisticated stress response strategies, and genes that encode transcription factors (TFs) that are master regulators of stress-responsive genes are excellent candidates for crop improvement. Related examples in recent studies include TF gene modulation and overexpression approaches in crop species to enhance stress tolerance. However, much remains to be discovered about the diverse plant TFs. Of the >80 TF families, only a few, such as NAC, MYB, WRKY, bZIP, and ERF/DREB, with vital roles in abiotic and biotic stress responses have been intensively studied. Moreover, although significant progress has been made in deciphering the roles of TFs in important cereal crops, fewer TF genes have been elucidated in sorghum. As a model drought-tolerant crop, sorghum research warrants further focus. This review summarizes recent progress on major TF families associated with abiotic and biotic stress tolerance and their potential for crop improvement, particularly in sorghum. Other TF families and non-coding RNAs that regulate gene expression are discussed briefly. Despite the emphasis on sorghum, numerous examples from wheat, rice, maize, and barley are included. Collectively, the aim of this review is to illustrate the potential application of TF genes for stress tolerance improvement and the engineering of resistant crops, with an emphasis on sorghum.
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Affiliation(s)
- Elamin Hafiz Baillo
- Key Laboratory of Agricultural Water Resources, Hebei Laboratory of Agricultural Water Saving, Center for Agricultural Resources Research, Institute of Genetics and Developmental Biology, University of Chinese Academy of Sciences, Shijiazhuang, Hebei 050021, China.
- University of Chinese Academy of Sciences, Beijing 100049, China.
- Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing 100101, China.
- Agricultural Research Corporation (ARC), Ministry of Agriculture, Gezira 21111, Sudan.
| | - Roy Njoroge Kimotho
- Key Laboratory of Agricultural Water Resources, Hebei Laboratory of Agricultural Water Saving, Center for Agricultural Resources Research, Institute of Genetics and Developmental Biology, University of Chinese Academy of Sciences, Shijiazhuang, Hebei 050021, China.
- University of Chinese Academy of Sciences, Beijing 100049, China.
| | - Zhengbin Zhang
- Key Laboratory of Agricultural Water Resources, Hebei Laboratory of Agricultural Water Saving, Center for Agricultural Resources Research, Institute of Genetics and Developmental Biology, University of Chinese Academy of Sciences, Shijiazhuang, Hebei 050021, China.
- University of Chinese Academy of Sciences, Beijing 100049, China.
- Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing 100101, China.
| | - Ping Xu
- Key Laboratory of Agricultural Water Resources, Hebei Laboratory of Agricultural Water Saving, Center for Agricultural Resources Research, Institute of Genetics and Developmental Biology, University of Chinese Academy of Sciences, Shijiazhuang, Hebei 050021, China.
- University of Chinese Academy of Sciences, Beijing 100049, China.
- Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing 100101, China.
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156
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Ma J, Bai X, Luo W, Feng Y, Shao X, Bai Q, Sun S, Long Q, Wan D. Genome-Wide Identification of Long Noncoding RNAs and Their Responses to Salt Stress in Two Closely Related Poplars. Front Genet 2019; 10:777. [PMID: 31543901 PMCID: PMC6739720 DOI: 10.3389/fgene.2019.00777] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2018] [Accepted: 07/23/2019] [Indexed: 12/23/2022] Open
Abstract
Long noncoding RNAs (lncRNAs) are involved in various biological regulatory processes, but their roles in plants resistance to salt stress remain largely unknown. To systematically explore the characteristics of lncRNAs and their roles in plant salt responses, we conducted strand-specific RNA-sequencing of four tissue types with salt treatments in two closely related poplars (Populus euphratica and Populus alba var. pyramidalis), and a total of 10,646 and 10,531 lncRNAs were identified, respectively. These lncRNAs showed significantly lower values in terms of length, expression, and expression correction than with mRNA. We further found that about 40% and 60% of these identified lncRNAs responded to salt stress with tissue-specific expression patterns across the two poplars. Furthermore, lncRNAs showed weak evolutionary conservation in sequences and exhibited diverse regulatory styles; in particular, tissue- and species-specific responses to salt stress varied greatly in two poplars, for example, 322 lncRNAs were found highly expressed in P. euphratica but not in P. alba var. pyramidalis and 3,425 lncRNAs were identified to be species-specific in P. euphratica in response to salt stress. Moreover, tissue-specific expression of lncRNAs in two poplars were identified with predicted target genes included Aux/IAA, NAC, MYB, involved in regulating plant growth and the plant stress response. Taken together, the systematic analysis of lncRNAs between sister species enhances our understanding of the characteristics of lncRNAs and their roles in plant growth and salt response.
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Affiliation(s)
- Jianchao Ma
- State Key Laboratory of Grassland Agro-Ecosystem, School of Life Sciences, Lanzhou University, Lanzhou, China.,Key Laboratory of Plant Stress Biology, State Key Laboratory of Cotton Biology, School of Life Sciences, Henan University, Kaifeng, China
| | - Xiaotao Bai
- State Key Laboratory of Grassland Agro-Ecosystem, School of Life Sciences, Lanzhou University, Lanzhou, China
| | - Wenchun Luo
- State Key Laboratory of Grassland Agro-Ecosystem, School of Life Sciences, Lanzhou University, Lanzhou, China
| | - Yannan Feng
- State Key Laboratory of Grassland Agro-Ecosystem, School of Life Sciences, Lanzhou University, Lanzhou, China
| | - Xuemin Shao
- State Key Laboratory of Grassland Agro-Ecosystem, School of Life Sciences, Lanzhou University, Lanzhou, China
| | - Qiuxian Bai
- State Key Laboratory of Grassland Agro-Ecosystem, School of Life Sciences, Lanzhou University, Lanzhou, China
| | - Shujiao Sun
- State Key Laboratory of Grassland Agro-Ecosystem, School of Life Sciences, Lanzhou University, Lanzhou, China
| | - Qiming Long
- State Key Laboratory of Grassland Agro-Ecosystem, School of Life Sciences, Lanzhou University, Lanzhou, China
| | - Dongshi Wan
- State Key Laboratory of Grassland Agro-Ecosystem, School of Life Sciences, Lanzhou University, Lanzhou, China
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157
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Rai MI, Alam M, Lightfoot DA, Gurha P, Afzal AJ. Classification and experimental identification of plant long non-coding RNAs. Genomics 2019; 111:997-1005. [DOI: 10.1016/j.ygeno.2018.04.014] [Citation(s) in RCA: 56] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2018] [Revised: 04/13/2018] [Accepted: 04/17/2018] [Indexed: 02/07/2023]
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158
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Yu Y, Zhang Y, Chen X, Chen Y. Plant Noncoding RNAs: Hidden Players in Development and Stress Responses. Annu Rev Cell Dev Biol 2019; 35:407-431. [PMID: 31403819 DOI: 10.1146/annurev-cellbio-100818-125218] [Citation(s) in RCA: 194] [Impact Index Per Article: 38.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
A large and significant portion of eukaryotic transcriptomes consists of noncoding RNAs (ncRNAs) that have minimal or no protein-coding capacity but are functional. Diverse ncRNAs, including both small RNAs and long ncRNAs (lncRNAs), play essential regulatory roles in almost all biological processes by modulating gene expression at the transcriptional and posttranscriptional levels. In this review, we summarize the current knowledge of plant small RNAs and lncRNAs, with a focus on their biogenesis, modes of action, local and systemic movement, and functions at the nexus of plant development and environmental responses. The complex connections among small RNAs, lncRNAs, and small peptides in plants are also discussed, along with the challenges of identifying and investigating new classes of ncRNAs.
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Affiliation(s)
- Yu Yu
- Guangdong Provincial Key Laboratory for Plant Epigenetics, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen 518060, China
| | - Yuchan Zhang
- Guangdong Provincial Key Laboratory of Plant Resources, State Key Laboratory for Biocontrol, and School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China;
| | - Xuemei Chen
- Department of Botany and Plant Sciences and Institute of Integrative Genome Biology, University of California, Riverside, California 92521, USA;
| | - Yueqin Chen
- Guangdong Provincial Key Laboratory of Plant Resources, State Key Laboratory for Biocontrol, and School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China;
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159
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Qin T, Xiong L. Subcellular Localization and Functions of Plant lncRNAs in Drought and Salt Stress Tolerance. Methods Mol Biol 2019; 1933:173-186. [PMID: 30945184 DOI: 10.1007/978-1-4939-9045-0_9] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/01/2023]
Abstract
Plant lncRNAs are expected to play important roles in various plant processes including response to abiotic stress, although the functions of most plant lncRNAs are still unknown. To investigate these potential functions, integrated approaches that employ genetic, transgenic, and molecular biology methods are required. Here, we describe general methods to study the function of lncRNAs in plant response to drought and salt stresses. First, the expression pattern and subcellular localization of lncRNA are analyzed by GUS staining and RNA fluorescence in situ hybridization (FISH). Then the responses of lncRNA mutant and overexpressing transgenic plants to drought and salt stress treatments are characterized, and their sensitivities to ABA are also assayed. To understand the molecular mechanism of lncRNAs' function in stress response, transcriptome sequencing (RNA-seq) and real-time quantitative PCR are performed to analyze altered expression of stress-related genes. Finally, proline content and ROS content are measured to reveal the accumulation of osmolytes and second messengers in these plants in response to drought and salt stress treatments.
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Affiliation(s)
- Tao Qin
- Texas A&M AgriLife Research Center, Dallas, TX, USA
| | - Liming Xiong
- Texas A&M AgriLife Research Center, Dallas, TX, USA. .,Department of Biology, Hong Kong Baptist University, Kowloon Tong, Hong Kong.
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160
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Zhang P, Sun Y, Peng R, Chen W, Fu X, Zhang L, Peng H, Zhang Z. Long non-coding RNA Rpph1 promotes inflammation and proliferation of mesangial cells in diabetic nephropathy via an interaction with Gal-3. Cell Death Dis 2019; 10:526. [PMID: 31285427 PMCID: PMC6614467 DOI: 10.1038/s41419-019-1765-0] [Citation(s) in RCA: 61] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2018] [Revised: 06/02/2019] [Accepted: 06/25/2019] [Indexed: 12/28/2022]
Abstract
Diabetic nephropathy (DN) is one of the most significant complications of diabetes and is the primary cause of end-stage kidney disease. Cumulating evidence has shown that renal inflammation plays a role in the development and progression of DN, but the exact cellular mechanisms are unclear. Irregular expression of long non-coding RNAs (lncRNAs) is present in many diseases, including DN. However, the relationship between lncRNAs and inflammation in DN is unclear. In this study, we identified differentially expressed lncRNAs in DN using RNA-sequencing. Among these lncRNAs, we identified seven DN-related lncRNAs in vivo and in vitro using quantitative real-time PCR. One lncRNA in particular, Rpph1 (ribonuclease P RNA component H1), exhibited significantly increased expression. Further, over-expression or knockdown of Rpph1 was found to regulate cell proliferation and the expression of inflammatory cytokines in mesangial cells (MCs). The results revealed that Rpph1 directly interacts with the DN-related factor galectin-3 (Gal-3). Further, over-expression of Rpph1 promoted inflammation and cell proliferation through the Gal-3/Mek/Erk signaling pathway in MCs under low glucose conditions, while knockdown of Rpph1 inhibited inflammation and cell proliferation through the Gal-3/Mek/Erk pathway in MCs under high glucose conditions. These results provide new insight into the association between Rpph1 and the Gal-3/Mek/Erk signaling pathway during DN progression.
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Affiliation(s)
- Panyang Zhang
- Molecular Medicine and Cancer Research Center, Chongqing Medical University, 400016, Chongqing, China
| | - Yan Sun
- Molecular Medicine and Cancer Research Center, Chongqing Medical University, 400016, Chongqing, China
| | - Rui Peng
- Department of Bioinformatics, Chongqing Medical University, 400016, Chongqing, China
| | - Wenyun Chen
- Molecular Medicine and Cancer Research Center, Chongqing Medical University, 400016, Chongqing, China
| | - Xia Fu
- People's Hospital of Fuling District, 408000, Chongqing, China
| | - Luyu Zhang
- Molecular Medicine and Cancer Research Center, Chongqing Medical University, 400016, Chongqing, China
| | - Huimin Peng
- Molecular Medicine and Cancer Research Center, Chongqing Medical University, 400016, Chongqing, China
| | - Zheng Zhang
- Molecular Medicine and Cancer Research Center, Chongqing Medical University, 400016, Chongqing, China.
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161
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Hou J, Lu D, Mason AS, Li B, Xiao M, An S, Fu D. Non-coding RNAs and transposable elements in plant genomes: emergence, regulatory mechanisms and roles in plant development and stress responses. PLANTA 2019; 250:23-40. [PMID: 30993403 DOI: 10.1007/s00425-019-03166-7] [Citation(s) in RCA: 44] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/18/2018] [Accepted: 04/09/2019] [Indexed: 06/09/2023]
Abstract
This review will provide evidence for the indispensable function of these elements in regulating plant development and resistance to biotic and abiotic stresses, as well as their evolutionary role in facilitating plant adaptation. Over millions of years of evolution, plant genomes have acquired a complex constitution. Plant genomes consist not only of protein coding sequences, but also contain large proportions of non-coding sequences. These include introns of protein-coding genes, and intergenic sequences such as non-coding RNA, repeat sequences and transposable elements. These non-coding sequences help to regulate gene expression, and are increasingly being recognized as playing an important role in genome organization and function. In this review, we summarize the known molecular mechanisms by which gene expression is regulated by several species of non-coding RNAs (microRNAs, long non-coding RNAs, and circular RNAs) and by transposable elements. We further discuss how these non-coding RNAs and transposable elements evolve and emerge in the genome, and the potential influence and importance of these non-coding RNAs and transposable elements in plant development and in stress responses.
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Affiliation(s)
- Jinna Hou
- Crop Designing Centre, Henan Academy of Agricultural Sciences, Zhengzhou, 450002, China
| | - Dandan Lu
- Crop Designing Centre, Henan Academy of Agricultural Sciences, Zhengzhou, 450002, China
| | - Annaliese S Mason
- Plant Breeding Department, IFZ Research Centre for Biosystems, Land Use and Nutrition, Justus Liebig University, Heinrich-Buff-Ring 26-32, 35392, Giessen, Germany
| | - Baoquan Li
- Crop Designing Centre, Henan Academy of Agricultural Sciences, Zhengzhou, 450002, China
| | - Meili Xiao
- Key Laboratory of Crop Physiology, Ecology and Genetic Breeding, Ministry of Education, Agronomy College, Jiangxi Agricultural University, Nanchang, 330045, China
| | - Sufang An
- Crop Designing Centre, Henan Academy of Agricultural Sciences, Zhengzhou, 450002, China
| | - Donghui Fu
- Key Laboratory of Crop Physiology, Ecology and Genetic Breeding, Ministry of Education, Agronomy College, Jiangxi Agricultural University, Nanchang, 330045, China.
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162
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Ding Z, Wu C, Tie W, Yan Y, He G, Hu W. Strand-specific RNA-seq based identification and functional prediction of lncRNAs in response to melatonin and simulated drought stresses in cassava. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2019; 140:96-104. [PMID: 31085451 DOI: 10.1016/j.plaphy.2019.05.008] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/31/2019] [Revised: 05/05/2019] [Accepted: 05/06/2019] [Indexed: 05/20/2023]
Abstract
Melatonin (MT) plays important roles in mediating plant responses to abiotic stresses such as drought. lncRNAs also play crucial roles in regulating responses to drought stress, however, their roles in MT-mediated drought stress responses in plants remain largely unknown. In this study, a total of 1405 high-confidence lncRNAs were identified in leaves of cassava, an important food crop in tropical and sub-tropical regions, using strand-specific RNA-seq technology. Of which, 185 were differentially expressed between polyethylene glycol (PEG) or MT treatment and the control condition. Trans-regulatory co-expression network revealed that MT-uniquely-responsive lncRNAs were mainly involved in tetrapyrrole synthesis, cytochrome P450, and cell wall modification; PEG-uniquely-responsive lncRNAs mainly participated in RNA regulation of transcription, calcium signaling, mitochondrial electron transport/ATP synthesis, hormone metabolism, and transport; and MT and PEG both-responsive lncRNAs were mainly involved in light reaction, light signaling, FA synthesis and FA elongation, secondary metabolism, and tetrapyrrole synthesis. In addition, 28 lncRNA-mRNA pairs referred to cis-acting regulation were identified, and these lncRNAs regulated the expression of their neighboring genes mainly through calcium signaling, RNA regulation of transcription, ABA and ethylene metabolism, and redox homeostasis. Besides, 78 lncRNAs (especially TCONS_00003360, TCONS_00015102, and TCONS_00149293) responsive to MT and/or PEG treatment were identified as putative targets of cassava known miRNAs. These findings provide a comprehensive view of the lncRNAs and their roles in response to MT and drought stress in cassava, which will enable in-depth functional analyses in the near future.
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Affiliation(s)
- Zehong Ding
- Key Laboratory of Biology and Genetic Resources of Tropical Crops, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Xueyuan Road 4, Haikou, Hainan, China.
| | - Chunlai Wu
- Key Laboratory of Biology and Genetic Resources of Tropical Crops, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Xueyuan Road 4, Haikou, Hainan, China; Genetic Engineering International Cooperation Base of Chinese Ministry of Science and Technology, Chinese National Center of Plant Gene Research (Wuhan) HUST Part, Key Laboratory of Molecular Biophysics of Chinese Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology (HUST), Wuhan, China.
| | - Weiwei Tie
- Key Laboratory of Biology and Genetic Resources of Tropical Crops, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Xueyuan Road 4, Haikou, Hainan, China.
| | - Yan Yan
- Key Laboratory of Biology and Genetic Resources of Tropical Crops, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Xueyuan Road 4, Haikou, Hainan, China.
| | - Guangyuan He
- Genetic Engineering International Cooperation Base of Chinese Ministry of Science and Technology, Chinese National Center of Plant Gene Research (Wuhan) HUST Part, Key Laboratory of Molecular Biophysics of Chinese Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology (HUST), Wuhan, China.
| | - Wei Hu
- Key Laboratory of Biology and Genetic Resources of Tropical Crops, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Xueyuan Road 4, Haikou, Hainan, China.
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163
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Narnoliya LK, Kaushal G, Singh SP. Long noncoding RNAs and miRNAs regulating terpene and tartaric acid biosynthesis in rose-scented geranium. FEBS Lett 2019; 593:2235-2249. [PMID: 31210363 DOI: 10.1002/1873-3468.13493] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
This study aimed to explore the noncoding RNAs, which have emerged as key regulatory molecules in biological processes, in rose-scented geranium. We analyzed RNA-seq data revealing 26 784 long noncoding RNAs (lncRNAs) and 871 miRNAs in rose-scented geranium. A total of 466 lncRNAs were annotated using different plant lncRNA public databases. Furthermore, 372 lncRNAs and 99 miRNAs were detected that target terpene and tartarate biosynthetic pathways. An interactome, comprising of lncRNAs, miRNAs, and mRNAs, was constructed that represents a noncoding RNA regulatory network of the target mRNAs. Real-time quantitative PCR expression validation was done for selected lncRNAs involved in the regulation of terpene and tartaric acid pathways. This study provides the first insights into the regulatory functioning of noncoding RNAs in rose-scented geranium.
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Affiliation(s)
| | - Girija Kaushal
- Center of Innovative and Applied Bioprocessing, S.A.S. Nagar, Mohali, India
| | - Sudhir P Singh
- Center of Innovative and Applied Bioprocessing, S.A.S. Nagar, Mohali, India
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164
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Comparative physiology and transcriptome analysis allows for identification of lncRNAs imparting tolerance to drought stress in autotetraploid cassava. BMC Genomics 2019; 20:514. [PMID: 31226927 PMCID: PMC6588902 DOI: 10.1186/s12864-019-5895-7] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2019] [Accepted: 06/10/2019] [Indexed: 01/21/2023] Open
Abstract
Background Polyploidization, pervasive among higher plant species, enhances adaptation to water deficit, but the physiological and molecular advantages need to be investigated widely. Long non-coding RNAs (lncRNAs) are involved in drought tolerance in various crops. Results Herein, we demonstrate that tetraploidy potentiates tolerance to drought stress in cassava (Manihot esculenta Crantz). Autotetraploidy reduces transpiration by lesser extent increasing of stomatal density, smaller stomatal aperture size, or greater stomatal closure, and reducing accumulation of H2O2 under drought stress. Transcriptome analysis of autotetraploid samples revealed down-regulation of genes involved in photosynthesis under drought stress, and less down-regulation of subtilisin-like proteases involved in increasing stomatal density. UDP-glucosyltransferases were increased more or reduced less in dehydrated leaves of autotetraploids compared with controls. Strand-specific RNA-seq data (validated by quantitative real time PCR) identified 2372 lncRNAs, and 86 autotetraploid-specific lncRNAs were differentially expressed in stressed leaves. The co-expressed network analysis indicated that LNC_001148 and LNC_000160 in autotetraploid dehydrated leaves regulated six genes encoding subtilisin-like protease above mentioned, thereby result in increasing the stomatal density to a lesser extent in autotetraploid cassava. Trans-regulatory network analysis suggested that autotetraploid-specific differentially expressed lncRNAs were associated with galactose metabolism, pentose phosphate pathway and brassinosteroid biosynthesis, etc. Conclusion Tetraploidy potentiates tolerance to drought stress in cassava, and LNC_001148 and LNC_000160 mediate drought tolerance by regulating stomatal density in autotetraploid cassava. Electronic supplementary material The online version of this article (10.1186/s12864-019-5895-7) contains supplementary material, which is available to authorized users.
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165
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Genome-wide analysis of long non-coding RNAs unveils the regulatory roles in the heat tolerance of Chinese cabbage (Brassica rapa ssp.chinensis). Sci Rep 2019; 9:5002. [PMID: 30899041 PMCID: PMC6428831 DOI: 10.1038/s41598-019-41428-2] [Citation(s) in RCA: 52] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2018] [Accepted: 03/05/2019] [Indexed: 01/12/2023] Open
Abstract
Long non-coding RNAs (lncRNAs) mediate important epigenetic regulation in various biological processes related to the stress response in plants. However, the systematic analysis of the lncRNAs expressed in Brassica rapa under heat stress has been elusive. In this study, we performed a genome-wide analysis of the lncRNA expression profiles in non-heading Chinese cabbage leaves using strand-specific RNA-sequencing. A total of 4594 putative lncRNAs were identified with a comprehensive landscape of dynamic lncRNA expression networks under heat stress. Co-expression networks of the interactions among the differentially expressed lncRNAs, mRNAs and microRNAs revealed that several phytohormones were associated with heat tolerance, including salicylic acid (SA) and brassinosteroid (BR) pathways. Of particular importance is the discovery of 25 lncRNAs that were highly co-expressed with 10 heat responsive genes. Thirty-nine lncRNAs were predicted as endogenous target mimics (eTMs) for 35 miRNAs, and five of them were validated to be involved in the heat tolerance of Chinese cabbage. Heat responsive lncRNA (TCONS_00048391) is an eTM for bra-miR164a, that could be a sponge for miRNA binding and may be a competing endogenous RNA (ceRNA) for the target gene NAC1 (Bra030820), affecting the expression of bra-miR164a in Chinese cabbage. Thus, these findings provide new insights into the functions of lncRNAs in heat tolerance and highlight a set of candidate lncRNAs for further studies in non-heading Chinese cabbage.
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166
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Ding Z, Tie W, Fu L, Yan Y, Liu G, Yan W, Li Y, Wu C, Zhang J, Hu W. Strand-specific RNA-seq based identification and functional prediction of drought-responsive lncRNAs in cassava. BMC Genomics 2019; 20:214. [PMID: 30866814 PMCID: PMC6417064 DOI: 10.1186/s12864-019-5585-5] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2018] [Accepted: 03/05/2019] [Indexed: 12/21/2022] Open
Abstract
Background Long noncoding RNAs (lncRNAs) have emerged as playing crucial roles in abiotic stress responsive regulation, however, the mechanism of lncRNAs underlying drought-tolerance remains largely unknown in cassava, an important tropical and sub-tropical root crop of remarkable drought tolerance. Results In this study, a total of 833 high-confidence lncRNAs, including 652 intergenic and 181 anti-sense lncRNAs, were identified in cassava leaves and root using strand-specific RNA-seq technology, of which 124 were drought-responsive. Trans-regulatory co-expression network revealed that lncRNAs exhibited tissue-specific expression patterns and they preferred to function differently in distinct tissues: e.g., cell-related metabolism, cell wall, and RNA regulation of transcription in folded leaf (FL); degradation of major carbohydrate (CHO) metabolism, calvin cycle and light reaction, light signaling, and tetrapyrrole synthesis in full expanded leaf (FEL); synthesis of major CHO metabolism, nitrogen-metabolism, photosynthesis, and redox in bottom leaf (BL); and hormone metabolism, secondary metabolism, calcium signaling, and abiotic stress in root (RT). In addition, 27 lncRNA-mRNA pairs referred to cis-acting regulation were identified, and these lncRNAs regulated the expression of their neighboring genes mainly through hormone metabolism, RNA regulation of transcription, and signaling of receptor kinase. Besides, 11 lncRNAs were identified acting as putative target mimics of known miRNAs in cassava. Finally, five drought-responsive lncRNAs and 13 co-expressed genes involved in trans-acting, cis-acting, or target mimic regulation were selected and confirmed by qRT-PCR. Conclusions These findings provide a comprehensive view of cassava lncRNAs in response to drought stress, which will enable in-depth functional analysis in the future. Electronic supplementary material The online version of this article (10.1186/s12864-019-5585-5) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Zehong Ding
- Key Laboratory of Biology and Genetic Resources of Tropical Crops, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Xueyuan Road 4, Haikou, Hainan, China.
| | - Weiwei Tie
- Key Laboratory of Biology and Genetic Resources of Tropical Crops, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Xueyuan Road 4, Haikou, Hainan, China
| | - Lili Fu
- Key Laboratory of Biology and Genetic Resources of Tropical Crops, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Xueyuan Road 4, Haikou, Hainan, China
| | - Yan Yan
- Key Laboratory of Biology and Genetic Resources of Tropical Crops, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Xueyuan Road 4, Haikou, Hainan, China
| | - Guanghua Liu
- Institute of Tropical and Sub-tropical Cash Crops, Yunnan Academy of Agricultural Sciences, Baoshan, Yunnan, China
| | - Wei Yan
- Institute of Tropical and Sub-tropical Cash Crops, Yunnan Academy of Agricultural Sciences, Baoshan, Yunnan, China
| | - Yanan Li
- Institute of Tropical and Sub-tropical Cash Crops, Yunnan Academy of Agricultural Sciences, Baoshan, Yunnan, China
| | - Chunlai Wu
- Key Laboratory of Biology and Genetic Resources of Tropical Crops, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Xueyuan Road 4, Haikou, Hainan, China.,Genetic Engineering International Cooperation Base of Chinese Ministry of Science and Technology, Chinese National Center of Plant Gene Research (Wuhan) HUST Part, Key Laboratory of Molecular Biophysics of Chinese Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology (HUST), Wuhan, China
| | - Jiaming Zhang
- Key Laboratory of Biology and Genetic Resources of Tropical Crops, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Xueyuan Road 4, Haikou, Hainan, China
| | - Wei Hu
- Key Laboratory of Biology and Genetic Resources of Tropical Crops, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Xueyuan Road 4, Haikou, Hainan, China.
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167
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Cui J, Jiang N, Meng J, Yang G, Liu W, Zhou X, Ma N, Hou X, Luan Y. LncRNA33732-respiratory burst oxidase module associated with WRKY1 in tomato- Phytophthora infestans interactions. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2019; 97:933-946. [PMID: 30472748 DOI: 10.1111/tpj.14173] [Citation(s) in RCA: 90] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/28/2017] [Revised: 11/10/2018] [Accepted: 11/15/2018] [Indexed: 05/09/2023]
Abstract
Our previous studies indicated that tomato WRKY1 transcription factor acts as a positive regulator during tomato resistance to Phytophthora infestans. However, the molecular mechanism of WRKY1-mediated resistance regulation remains unclear. Here, we used a comparative transcriptome analysis between wild-type and WRKY1-overexpressing tomato plants to identify differentially expressed genes (DEGs) and long non-coding RNAs (DELs), and we examined long non-coding RNA (lncRNA)-gene networks. The promoter sequences of the upregulated DEGs and DELs were analyzed. Among 1073 DEGs and 199 DELs, 1 kb 5'-upstream regions of 59 DEGs and 22 DELs contain the W-box, the target sequence of the WRKY1. The results of promoter-β-glucuronidase (GUS) fusion and yeast one-hybrid assay showed that lncRNA33732 was activated by WRKY1 through sequence-specific interactions with the W-box element in its promoter. The overexpression and silencing analysis of lncRNA33732 in tomato showed that lncRNA33732 acts as a positive regulator and enhanced tomato resistance to P. infestans by induction of the expression of respiratory burst oxidase (RBOH) and increase in the accumulation of H2 O2 . When the expression of RBOH gene was inhibited in tomato plants, H2 O2 accumulation decreased and resistance were impaired. These findings suggest that lncRNA33732 activated by WRKY1 induces RBOH expression to increase H2 O2 accumulation in early defense reaction of tomato to P. infestans attack. Our results provide insights into the WRKY1-lncRNA33732-RBOH module involved in the regulation of H2 O2 accumulation and resistance to P. infestans, as well as provide candidates to enhance broad-spectrum resistance to pathogens in tomato.
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Affiliation(s)
- Jun Cui
- School of Life Science and Biotechnology, Dalian University of Technology, Dalian, 116024, China
| | - Ning Jiang
- School of Life Science and Biotechnology, Dalian University of Technology, Dalian, 116024, China
| | - Jun Meng
- School of Computer Science and Technology, Dalian University of Technology, Dalian, 116024, China
| | - Guanglei Yang
- School of Life Science and Biotechnology, Dalian University of Technology, Dalian, 116024, China
| | - Weiwei Liu
- School of Life Science and Biotechnology, Dalian University of Technology, Dalian, 116024, China
| | - Xiaoxu Zhou
- School of Life Science and Biotechnology, Dalian University of Technology, Dalian, 116024, China
| | - Ning Ma
- School of Life Science and Biotechnology, Dalian University of Technology, Dalian, 116024, China
| | - Xinxin Hou
- School of Life Science and Biotechnology, Dalian University of Technology, Dalian, 116024, China
| | - Yushi Luan
- School of Life Science and Biotechnology, Dalian University of Technology, Dalian, 116024, China
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168
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Spatio-Temporal Transcriptional Dynamics of Maize Long Non-Coding RNAs Responsive to Drought Stress. Genes (Basel) 2019; 10:genes10020138. [PMID: 30781862 PMCID: PMC6410058 DOI: 10.3390/genes10020138] [Citation(s) in RCA: 40] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2018] [Revised: 01/23/2019] [Accepted: 02/04/2019] [Indexed: 02/08/2023] Open
Abstract
Long non-coding RNAs (lncRNAs) have emerged as important regulators in plant stress response. Here, we report a genome-wide lncRNA transcriptional analysis in response to drought stress using an expanded series of maize samples collected from three distinct tissues spanning four developmental stages. In total, 3488 high-confidence lncRNAs were identified, among which 1535 were characterized as drought responsive. By characterizing the genomic structure and expression pattern, we found that lncRNA structures were less complex than protein-coding genes, showing shorter transcripts and fewer exons. Moreover, drought-responsive lncRNAs exhibited higher tissue- and development-specificity than protein-coding genes. By exploring the temporal expression patterns of drought-responsive lncRNAs at different developmental stages, we discovered that the reproductive stage R1 was the most sensitive growth stage with more lncRNAs showing altered expression upon drought stress. Furthermore, lncRNA target prediction revealed 653 potential lncRNA-messenger RNA (mRNA) pairs, among which 124 pairs function in cis-acting mode and 529 in trans. Functional enrichment analysis showed that the targets were significantly enriched in molecular functions related to oxidoreductase activity, water binding, and electron carrier activity. Multiple promising targets of drought-responsive lncRNAs were discovered, including the V-ATPase encoding gene, vpp4. These findings extend our knowledge of lncRNAs as important regulators in maize drought response.
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169
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Wu J, Liu C, Liu Z, Li S, Li D, Liu S, Huang X, Liu S, Yukawa Y. Pol III-Dependent Cabbage BoNR8 Long ncRNA Affects Seed Germination and Growth in Arabidopsis. PLANT & CELL PHYSIOLOGY 2019; 60:421-435. [PMID: 30462304 DOI: 10.1093/pcp/pcy220] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/16/2018] [Accepted: 11/02/2018] [Indexed: 05/07/2023]
Abstract
Long non-coding RNAs (lncRNAs) are non-protein-coding transcripts longer than 200 nt that are distributed widely in organisms and play many physiological roles. The BoNR8 lncRNA is a 272 nt long transcript yielded by RNA polymerase III in cabbage that was identified as the closest homolog of the AtR8 lncRNA in Arabidopsis. The BoNR8 lncRNA was expressed extensively in the epidermal tissue in the root elongation zone of germinated seeds, and its accumulation was induced by abiotic stresses, auxins and ABA. To investigate the correlation between the BoNR8 lncRNA and germination, BoNR8-overexpressing Arabidopsis plants (BoNR8-AtOX) were prepared. Three independent BoNR8-AtOX lines showed less primary root elongation, incomplete silique development and decreased germination rates. The germination efficiencies were affected strongly by ABA and slightly by salt stress, and ABA-related gene expression was changed in the BoNR8-AtOX lines.
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Affiliation(s)
- Juan Wu
- Key Laboratory of Saline-Alkali Vegetation Ecology Restoration in Oil Field (SAVER), Ministry of Education, Alkali Soil Natural Environmental Science Center (ASNESC), Northeast Forestry University, Harbin, China
- Key Laboratory of Combining Farming and Animal Husbandry, Institute of Animal Husbandry of Heilongjiang Academy of Agricultural Sciences, Ministry of Agriculture and Rural Affairs, PR, Harbin, China
| | - Chunxiao Liu
- Key Laboratory of Saline-Alkali Vegetation Ecology Restoration in Oil Field (SAVER), Ministry of Education, Alkali Soil Natural Environmental Science Center (ASNESC), Northeast Forestry University, Harbin, China
| | - Ziguang Liu
- Key Laboratory of Combining Farming and Animal Husbandry, Institute of Animal Husbandry of Heilongjiang Academy of Agricultural Sciences, Ministry of Agriculture and Rural Affairs, PR, Harbin, China
| | - Shuang Li
- Graduate School of Natural Sciences, Nagoya City University, Nagoya, Japan
| | - Dandan Li
- Key Laboratory of Saline-Alkali Vegetation Ecology Restoration in Oil Field (SAVER), Ministry of Education, Alkali Soil Natural Environmental Science Center (ASNESC), Northeast Forestry University, Harbin, China
| | - Shengyi Liu
- Mudanjiang Medical University, Mudanjiang, Heilongjiang, China
| | - Xiaoqing Huang
- Key Laboratory of Saline-Alkali Vegetation Ecology Restoration in Oil Field (SAVER), Ministry of Education, Alkali Soil Natural Environmental Science Center (ASNESC), Northeast Forestry University, Harbin, China
| | - ShenKui Liu
- State Key Laboratory of Subtropical Silviculture, Zhejiang A and F University, Lin'an, Hangzhou, China
| | - Yasushi Yukawa
- Graduate School of Natural Sciences, Nagoya City University, Nagoya, Japan
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170
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Jiang N, Cui J, Shi Y, Yang G, Zhou X, Hou X, Meng J, Luan Y. Tomato lncRNA23468 functions as a competing endogenous RNA to modulate NBS-LRR genes by decoying miR482b in the tomato -Phytophthora infestans interaction. HORTICULTURE RESEARCH 2019; 6:28. [PMID: 30729018 PMCID: PMC6355781 DOI: 10.1038/s41438-018-0096-0] [Citation(s) in RCA: 90] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/08/2018] [Revised: 09/07/2018] [Accepted: 09/19/2018] [Indexed: 05/05/2023]
Abstract
Our previous studies indicated that tomato miR482b could negatively regulate the resistance of tomato to Phytophthora infestans and the expression of miR482b was decreased after inoculation with P. infestans. However, the mechanism by which the accumulation of miR482b is suppressed remains unclear. In this study, we wrote a program to identify 89 long noncoding RNA (lncRNA)-originated endogenous target mimics (eTMs) for 46 miRNAs from our RNA-Seq data. Three tomato lncRNAs, lncRNA23468, lncRNA01308 and lncRNA13262, contained conserved eTM sites for miR482b. When lncRNA23468 was overexpressed in tomato, miR482b expression was significantly decreased, and the expression of the target genes, NBS-LRRs, was significantly increased, resulting in enhanced resistance to P. infestans. Silencing lncRNA23468 in tomato led to the increased accumulation of miR482b and decreased accumulation of NBS-LRRs, as well as reduced resistance to P. infestans. In addition, the accumulation of both miR482b and NBS-LRRs was not significantly changed in tomato plants that overexpressed lncRNA23468 with a mutated eTM site. Based on the VIGS system, a target gene of miR482b, Solyc02g036270.2, was silenced. The disease symptoms of the VIGS-Solyc02g036270.2 tomato plants were in accordance with those of tomato plants in which lncRNA23468 was silenced after inoculation with P. infestans. More severe disease symptoms were found in the modified plants than in the control plants. Our results demonstrate that lncRNAs functioning as eTMs may modulate the effects of miRNAs in tomato and provide insight into how the lncRNA23468-miR482b-NBS-LRR module regulates tomato resistance to P. infestans.
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Affiliation(s)
- Ning Jiang
- School of Life Science and Biotechnology, Dalian University of Technology, 116024 Dalian, China
| | - Jun Cui
- School of Life Science and Biotechnology, Dalian University of Technology, 116024 Dalian, China
| | - Yunsheng Shi
- School of Computer Science and Technology, Dalian University of Technology, 116024 Dalian, China
| | - Guanglei Yang
- School of Life Science and Biotechnology, Dalian University of Technology, 116024 Dalian, China
| | - Xiaoxu Zhou
- School of Life Science and Biotechnology, Dalian University of Technology, 116024 Dalian, China
| | - Xinxin Hou
- School of Life Science and Biotechnology, Dalian University of Technology, 116024 Dalian, China
| | - Jun Meng
- School of Computer Science and Technology, Dalian University of Technology, 116024 Dalian, China
| | - Yushi Luan
- School of Life Science and Biotechnology, Dalian University of Technology, 116024 Dalian, China
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171
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Zhou Y, Cho WK, Byun HS, Chavan V, Kil EJ, Lee S, Hong SW. Genome-wide identification of long non-coding RNAs in tomato plants irradiated by neutrons followed by infection with Tomato yellow leaf curl virus. PeerJ 2019; 7:e6286. [PMID: 30713817 PMCID: PMC6354667 DOI: 10.7717/peerj.6286] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2018] [Accepted: 12/14/2018] [Indexed: 01/23/2023] Open
Abstract
Long non-coding RNAs (lncRNAs) play an important role in regulating many biological processes. In this study, tomato seeds were first irradiated by neutrons. Eight tomato mutants were then selected and infected by Tomato yellow leaf curl virus (TYLCV). RNA sequencing followed by bioinformatics analyses identified 1,563 tomato lncRNAs. About half of the lncRNAs were derived from intergenic regions, whereas antisense lncRNAs accounted for 35%. There were fewer lncRNAs identified in our study than in other studies identifying tomato lncRNAs. Functional classification of 794 lncRNAs associated with tomato genes showed that many lncRNAs were associated with binding functions required for interactions with other molecules and localized in the cytosol and membrane. In addition, we identified 19 up-regulated and 11 down-regulated tomato lncRNAs by comparing TYLCV infected plants to non-infected plants using previously published data. Based on these results, the lncRNAs identified in this study provide important resources for characterization of tomato lncRNAs in response to TYLCV infection.
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Affiliation(s)
- Yujie Zhou
- Department of Energy Science, Sungkyunkwan University, Suwon, South Korea
| | - Won Kyong Cho
- Research Institute of Agriculture and Life Sciences, College of Agriculture and Life Sciences, Seoul National University, Seoul, South Korea
| | - Hee-Seong Byun
- Department of Integrative Biotechnology, Sungkyunkwan University, Suwon, South Korea
| | - Vivek Chavan
- Department of Energy Science, Sungkyunkwan University, Suwon, South Korea
| | - Eui-Joon Kil
- Department of Integrative Biotechnology, Sungkyunkwan University, Suwon, South Korea
| | - Sukchan Lee
- Department of Integrative Biotechnology, Sungkyunkwan University, Suwon, South Korea
| | - Seung-Woo Hong
- Department of Physics, Sungkyunkwan University, Suwon, South Korea
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172
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Zhang G, Chen D, Zhang T, Duan A, Zhang J, He C. Transcriptomic and functional analyses unveil the role of long non-coding RNAs in anthocyanin biosynthesis during sea buckthorn fruit ripening. DNA Res 2019; 25:465-476. [PMID: 29873696 PMCID: PMC6191307 DOI: 10.1093/dnares/dsy017] [Citation(s) in RCA: 60] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2018] [Accepted: 05/10/2018] [Indexed: 01/22/2023] Open
Abstract
Fruit ripening is a developmental process regulated by a complex network of endogenous and exogenous cues. Sea buckthorn is an excellent material for fruit ripening studies due to its dramatic ripening process and high contents of nutritional and anti-oxidant compounds in berries. Here, the whole transcriptome of sea buckthorn fruit at three development stages were analysed using multiple high-throughput sequencings. We assembled and annotated 9,008 long non-coding RNAs (lncRNAs) in sea buckthorn fruits, and identified 118 differentially expressed lncRNAs (DE-lncRNAs) and 32 differentially expressed microRNAs in fruit developmental process. In addition, we predicted 1,061 cis-regulated and 782 trans-regulated targets of DE-lncRNAs, and these DE-lncRNAs are specifically enriched in the biosynthesis of ascorbic acid, carotenoids and flavonoids. Moreover, the silencing of two lncRNAs (LNC1 and LNC2) in vivo and expression analysis revealed that LNC1 and LNC2 can act as endogenous target mimics of miR156a and miR828a to reduce SPL9 and induce MYB114 expression, respectively, which lead to increased and decreased anthocyanin content as revealed by high-performance liquid chromatography analysis. Our results present the first global functional analysis of lncRNA in sea buckthorn and provide two essential regulators of anthocyanin biosynthesis, which provides new insights into the regulation of fruit quality.
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Affiliation(s)
- Guoyun Zhang
- State Key Laboratory of Tree Genetics and Breeding & Key Laboratory of Tree Breeding and Cultivation, State Forestry Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, China
| | - Daoguo Chen
- State Key Laboratory of Tree Genetics and Breeding & Key Laboratory of Tree Breeding and Cultivation, State Forestry Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, China
| | - Tong Zhang
- State Key Laboratory of Tree Genetics and Breeding & Key Laboratory of Tree Breeding and Cultivation, State Forestry Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, China
| | - Aiguo Duan
- State Key Laboratory of Tree Genetics and Breeding & Key Laboratory of Tree Breeding and Cultivation, State Forestry Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, China
| | - Jianguo Zhang
- State Key Laboratory of Tree Genetics and Breeding & Key Laboratory of Tree Breeding and Cultivation, State Forestry Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, China.,Collaborative Innovation Center of Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, China
| | - Caiyun He
- State Key Laboratory of Tree Genetics and Breeding & Key Laboratory of Tree Breeding and Cultivation, State Forestry Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, China
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173
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Calixto CPG, Tzioutziou NA, James AB, Hornyik C, Guo W, Zhang R, Nimmo HG, Brown JWS. Cold-Dependent Expression and Alternative Splicing of Arabidopsis Long Non-coding RNAs. FRONTIERS IN PLANT SCIENCE 2019; 10:235. [PMID: 30891054 PMCID: PMC6413719 DOI: 10.3389/fpls.2019.00235] [Citation(s) in RCA: 48] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/23/2018] [Accepted: 02/12/2019] [Indexed: 05/07/2023]
Abstract
Plants re-program their gene expression when responding to changing environmental conditions. Besides differential gene expression, extensive alternative splicing (AS) of pre-mRNAs and changes in expression of long non-coding RNAs (lncRNAs) are associated with stress responses. RNA-sequencing of a diel time-series of the initial response of Arabidopsis thaliana rosettes to low temperature showed massive and rapid waves of both transcriptional and AS activity in protein-coding genes. We exploited the high diversity of transcript isoforms in AtRTD2 to examine regulation and post-transcriptional regulation of lncRNA gene expression in response to cold stress. We identified 135 lncRNA genes with cold-dependent differential expression (DE) and/or differential alternative splicing (DAS) of lncRNAs including natural antisense RNAs, sORF lncRNAs, and precursors of microRNAs (miRNAs) and trans-acting small-interfering RNAs (tasiRNAs). The high resolution (HR) of the time-series allowed the dynamics of changes in transcription and AS to be determined and identified early and adaptive transcriptional and AS changes in the cold response. Some lncRNA genes were regulated only at the level of AS and using plants grown at different temperatures and a HR time-course of the first 3 h of temperature reduction, we demonstrated that the AS of some lncRNAs is highly sensitive to small temperature changes suggesting tight regulation of expression. In particular, a splicing event in TAS1a which removed an intron that contained the miR173 processing and phased siRNAs generation sites was differentially alternatively spliced in response to cold. The cold-induced reduction of the spliced form of TAS1a and of the tasiRNAs suggests that splicing may enhance production of the siRNAs. Our results identify candidate lncRNAs that may contribute to the regulation of expression that determines the physiological processes essential for acclimation and freezing tolerance.
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Affiliation(s)
- Cristiane P. G. Calixto
- Plant Sciences Division, School of Life Sciences, University of Dundee, Dundee, United Kingdom
| | - Nikoleta A. Tzioutziou
- Plant Sciences Division, School of Life Sciences, University of Dundee, Dundee, United Kingdom
| | - Allan B. James
- Institute of Molecular, Cell and Systems Biology, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, United Kingdom
| | - Csaba Hornyik
- Cell and Molecular Sciences, The James Hutton Institute, Dundee, United Kingdom
| | - Wenbin Guo
- Plant Sciences Division, School of Life Sciences, University of Dundee, Dundee, United Kingdom
- Information and Computational Sciences, The James Hutton Institute, Dundee, United Kingdom
| | - Runxuan Zhang
- Information and Computational Sciences, The James Hutton Institute, Dundee, United Kingdom
| | - Hugh G. Nimmo
- Institute of Molecular, Cell and Systems Biology, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, United Kingdom
| | - John W. S. Brown
- Plant Sciences Division, School of Life Sciences, University of Dundee, Dundee, United Kingdom
- Cell and Molecular Sciences, The James Hutton Institute, Dundee, United Kingdom
- *Correspondence: John W. S. Brown,
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174
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Yuan F, Xu Y, Leng B, Wang B. Beneficial Effects of Salt on Halophyte Growth: Morphology, Cells, and Genes. Open Life Sci 2019; 14:191-200. [PMID: 33817151 PMCID: PMC7874760 DOI: 10.1515/biol-2019-0021] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2018] [Accepted: 11/26/2018] [Indexed: 11/17/2022] Open
Abstract
Halophytes can survive and complete their life cycle in the presence of ≥200 mM NaCl. These remarkable plants have developed various strategies to tolerate salinity and thrive in high-salt environments. At the appropriate levels, salt has a beneficial effect on the vegetative growth of halophytes but inhibits the growth of non-halophytes. In recent years, many studies have focused on elucidating the salt-tolerance mechanisms of halophytes at the molecular, physiological, and individual level. In this review, we focus on the mechanisms, from the macroscopic to the molecular, underlying the successful growth of halophytes in saline environments to explain why salt has beneficial effects on halophytes but harmful effects on non-halophytes. These mechanisms include the specialized organs of halophytes (for example, ion compartmentalization in succulent leaves), their unique structures (salt glands and hydrophobic barriers in roots), and their salt-tolerance genes. We hope to shed light on the use of halophytes for engineering salt-tolerant crops, soil conservation, and the protection of freshwater resources in the near future.
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Affiliation(s)
- Fang Yuan
- Shandong Provincial Key Laboratory of Plant Stress, College of Life Sciences, Shandong Normal University, Ji’nan, Shandong, 250014, P.R. China
| | - Yanyu Xu
- Shandong Provincial Key Laboratory of Plant Stress, College of Life Sciences, Shandong Normal University, Ji’nan, Shandong, 250014, P.R. China
| | - Bingying Leng
- Shandong Provincial Key Laboratory of Plant Stress, College of Life Sciences, Shandong Normal University, Ji’nan, Shandong, 250014, P.R. China
| | - Baoshan Wang
- Shandong Provincial Key Laboratory of Plant Stress, College of Life Sciences, Shandong Normal University, Ji’nan, Shandong, 250014, P.R. China
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175
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Li Y, Wu C, Liu C, Yu J, Duan X, Fan W, Wang J, Zhang X, Yan G, Li T, Zhang K. Functional identification of lncRNAs in sweet cherry ( Prunus avium) pollen tubes via transcriptome analysis using single-molecule long-read sequencing. HORTICULTURE RESEARCH 2019; 6:135. [PMID: 31814988 PMCID: PMC6885045 DOI: 10.1038/s41438-019-0218-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/02/2019] [Revised: 09/27/2019] [Accepted: 10/27/2019] [Indexed: 05/05/2023]
Abstract
Sweet cherry (Prunus avium) is a popular fruit with high nutritional value and excellent flavor. Although pollen plays an important role in the double fertilization and subsequent fruit production of this species, little is known about its pollen tube transcriptome. In this study, we identified 16,409 transcripts using single-molecule sequencing. After filtering 292 transposable elements, we conducted further analyses including mRNA classification, gene function prediction, alternative splicing (AS) analysis, and long noncoding RNA (lncRNA) identification to gain insight into the pollen transcriptome. The filtered transcripts could be matched with 3,438 coding region sequences from the sweet cherry genome. GO and KEGG analyses revealed complex biological processes during pollen tube elongation. A total of 2043 AS events were predicted, 7 of which were identified in different organs, such as the leaf, pistil and pollen tube. Using BLASTnt and the Coding-Potential Assessment Tool (CPAT), we distinguished a total of 284 lncRNAs, among which 154 qualified as natural antisense transcripts (NATs). As the NATs could be the reverse complements of coding mRNA sequences, they might bind to coding sequences. Antisense transfection assays showed that the NATs could regulate the expression levels of their complementary sequences and even affect the growth conditions of pollen tubes. In summary, this research characterizes the transcripts of P. avium pollen and lays the foundation for elucidating the physiological and biochemical mechanisms underlying sexual reproduction in the male gametes of this species.
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Affiliation(s)
- Yang Li
- Laboratory of Fruit Cell and Molecular Breeding, China Agricultural University, Beijing, China
| | - Chuanbao Wu
- Laboratory of Fruit Cell and Molecular Breeding, China Agricultural University, Beijing, China
| | - Chunsheng Liu
- Laboratory of Fruit Cell and Molecular Breeding, China Agricultural University, Beijing, China
| | - Jie Yu
- Laboratory of Fruit Cell and Molecular Breeding, China Agricultural University, Beijing, China
| | - Xuwei Duan
- Institute of Forestry and Pomology, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China), Ministry of Agriculture, Beijing, China
- Beijing Engineering Research Center for Deciduous Fruit Trees, Beijing, China
| | - Wenqi Fan
- Laboratory of Fruit Cell and Molecular Breeding, China Agricultural University, Beijing, China
| | - Jing Wang
- Institute of Forestry and Pomology, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China), Ministry of Agriculture, Beijing, China
- Beijing Engineering Research Center for Deciduous Fruit Trees, Beijing, China
| | - Xiaoming Zhang
- Institute of Forestry and Pomology, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China), Ministry of Agriculture, Beijing, China
- Beijing Engineering Research Center for Deciduous Fruit Trees, Beijing, China
| | - Guohua Yan
- Institute of Forestry and Pomology, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China), Ministry of Agriculture, Beijing, China
- Beijing Engineering Research Center for Deciduous Fruit Trees, Beijing, China
| | - Tianzhong Li
- Laboratory of Fruit Cell and Molecular Breeding, China Agricultural University, Beijing, China
| | - Kaichun Zhang
- Institute of Forestry and Pomology, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China), Ministry of Agriculture, Beijing, China
- Beijing Engineering Research Center for Deciduous Fruit Trees, Beijing, China
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176
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Wang Y, Wang Y, Zhao J, Huang J, Shi Y, Deng D. Unveiling gibberellin-responsive coding and long noncoding RNAs in maize. PLANT MOLECULAR BIOLOGY 2018; 98:427-438. [PMID: 30341662 DOI: 10.1007/s11103-018-0788-8] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/19/2018] [Accepted: 10/12/2018] [Indexed: 05/23/2023]
Abstract
We report coding and long noncoding RNAs in maize upon phytohormone gibberellin stimulation. Plant hormone gibberellin (GA) orchestrates various facets of biological processes. Dissection the transcriptomic dynamics upon GA stimulation has biological significance. Feature of maize transcriptome in response to GA application remains largely elusive. Herein, two types of plants, one was with normal height, the other was GA-sensitive dwarfism, were selected from advanced backcross population for GA3 treatment with different concentrations. In control and GA3-treated plants, we identified a large number of coding and long noncoding RNAs (lncRNAs) through sequencing eight ribosomal-depleted RNA libraries. Transcripts encoding GA biosynthetic and metabolic enzymes KS, GA20ox, GA3ox, and GA2ox were significantly differentially expressed in GA3-treated samples. A total of 78 protein-coding transcripts were shared between GA3-treated normal height and dwarf plants. Shared transcripts encoding terpene synthase, MYB transcription factor, and receptor-like protein kinase were co-regulated with their corresponding partners. Out of identified lncRNAs, 22 and 34 significantly differentially expressed lncRNAs were responsive to GA application in normal height and dwarf plants, respectively. Shared GA-responsive lncRNAs were found in GA3-treated normal height and dwarf plants. Some lncRNAs corresponded to precursors of known miRNA, such as zma-miR528a and zma-miR528b. Multiple promising targets of significantly differentially expressed lncRNAs were discovered, including Lazy plant1 for auxin- and GA-mediated shoot gravitropism, bZIP transcription factor member for GA-controlled cell elongation. This study will improve our knowledge of GA-triggered transcriptome change and facilitate a comprehensive understanding of regulatory cascade centering on GA.
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Affiliation(s)
- Yijun Wang
- Jiangsu Key Laboratory of Crop Genetics and Physiology/Key Laboratory of Plant Functional Genomics of the Ministry of Education/Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, Agricultural College of Yangzhou University, Yangzhou, 225009, China.
- Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou University, Yangzhou, 225009, China.
| | - Yali Wang
- Jiangsu Key Laboratory of Crop Genetics and Physiology/Key Laboratory of Plant Functional Genomics of the Ministry of Education/Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, Agricultural College of Yangzhou University, Yangzhou, 225009, China
- Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou University, Yangzhou, 225009, China
| | - Jia Zhao
- Jiangsu Key Laboratory of Crop Genetics and Physiology/Key Laboratory of Plant Functional Genomics of the Ministry of Education/Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, Agricultural College of Yangzhou University, Yangzhou, 225009, China
- Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou University, Yangzhou, 225009, China
| | - Jiayu Huang
- Jiangsu Key Laboratory of Crop Genetics and Physiology/Key Laboratory of Plant Functional Genomics of the Ministry of Education/Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, Agricultural College of Yangzhou University, Yangzhou, 225009, China
- Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou University, Yangzhou, 225009, China
| | - Yining Shi
- Jiangsu Key Laboratory of Crop Genetics and Physiology/Key Laboratory of Plant Functional Genomics of the Ministry of Education/Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, Agricultural College of Yangzhou University, Yangzhou, 225009, China
- Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou University, Yangzhou, 225009, China
| | - Dexiang Deng
- Jiangsu Key Laboratory of Crop Genetics and Physiology/Key Laboratory of Plant Functional Genomics of the Ministry of Education/Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, Agricultural College of Yangzhou University, Yangzhou, 225009, China
- Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou University, Yangzhou, 225009, China
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177
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178
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Borah P, Das A, Milner MJ, Ali A, Bentley AR, Pandey R. Long Non-Coding RNAs as Endogenous Target Mimics and Exploration of Their Role in Low Nutrient Stress Tolerance in Plants. Genes (Basel) 2018; 9:E459. [PMID: 30223541 PMCID: PMC6162444 DOI: 10.3390/genes9090459] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2018] [Revised: 09/05/2018] [Accepted: 09/07/2018] [Indexed: 12/14/2022] Open
Abstract
Long non-coding RNA (lncRNA) research in plants has recently gained momentum taking cues from studies in animals systems. The availability of next-generation sequencing has enabled genome-wide identification of lncRNA in several plant species. Some lncRNAs are inhibitors of microRNA expression and have a function known as target mimicry with the sequestered transcript known as an endogenous target mimic (eTM). The lncRNAs identified to date show diverse mechanisms of gene regulation, most of which remain poorly understood. In this review, we discuss the role of identified putative lncRNAs that may act as eTMs for nutrient-responsive microRNAs (miRNAs) in plants. If functionally validated, these putative lncRNAs would enhance current understanding of the role of lncRNAs in nutrient homeostasis in plants.
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Affiliation(s)
- Priyanka Borah
- Mineral Nutrition Laboratory, Division of Plant Physiology, ICAR-Indian Agricultural Research Institute, New Delhi 110 012, India.
- Department of Biosciences, Jamia Millia Islamia, New Delhi 110025, India.
| | - Antara Das
- ICAR-National Research Centre on Plant Biotechnology, New Delhi 110012, India.
| | - Matthew J Milner
- The John Bingham Laboratory, National Institute of Agricultural Botany (NIAB), Huntingdon Road, Cambridge CB30LE, UK.
| | - Arif Ali
- Department of Biosciences, Jamia Millia Islamia, New Delhi 110025, India.
| | - Alison R Bentley
- The John Bingham Laboratory, National Institute of Agricultural Botany (NIAB), Huntingdon Road, Cambridge CB30LE, UK.
| | - Renu Pandey
- Mineral Nutrition Laboratory, Division of Plant Physiology, ICAR-Indian Agricultural Research Institute, New Delhi 110 012, India.
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179
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Regulation mechanism of long non-coding RNA in plant response to stress. Biochem Biophys Res Commun 2018; 503:402-407. [PMID: 30055799 DOI: 10.1016/j.bbrc.2018.07.072] [Citation(s) in RCA: 42] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2018] [Accepted: 07/16/2018] [Indexed: 12/29/2022]
Abstract
Long non-coding RNA (lncRNA) is a non-coding RNA greater than 200 nucleotides in length. LncRNAs can regulate gene expression at transcription and post-transcription, epigenetic level, and plays an important role in a wide range of biological processes such as genomic imprinting, chromatin remodeling, transcriptional activation, transcriptional interference and cell cycle. It becomes the current hot topics in the study of molecular biology and genetics. Emerging evidence proposed that lncRNAs play important roles in response to both abiotic and biotic stress. In this review, we discuss the role of lncRNAs in drought resistance, salt resistance, disease resistance, and immunity of plants, providing strong evidence for exploring the important role of lncRNAs in plant resistance, in order to explore new ideas and new targets for prevention and control.
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180
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Genome-wide identification and characterization of mRNAs and lncRNAs involved in cold stress in the wild banana (Musa itinerans). PLoS One 2018; 13:e0200002. [PMID: 29985922 PMCID: PMC6037364 DOI: 10.1371/journal.pone.0200002] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2017] [Accepted: 06/18/2018] [Indexed: 12/19/2022] Open
Abstract
Cold stress seriously affects banana growth, yield and fruit quality. Long noncoding RNAs (lncRNAs) have been demonstrated as key regulators of biotic and abiotic stress in plants, but the identification and prediction of cold responsive mRNAs and lncRNAs in wild banana remains unexplored. In present study, a cold resistant wild banana line from China was used to profile the cold-responsive mRNAs and lncRNAs by RNA-seq under cold stress conditions, i.e. 13°C (critical growth temperature), 4°C (chilling temperature), 0°C (freezing temperature) and normal growing condition, i.e. 28°C (control group). A total of 12,462 lncRNAs were identified in cold-stressed wild banana. In mRNA, much more alternative splicing events occurred in wild banana under the cold stress conditions compared with that in the normal growing condition. The GO analysis of differential expression genes (DEGs) showed the biochemical processes and membrane related genes responded positively to the cold stress. The KEGG pathway enrichment analysis of the DEGs showed that the pathways of photosynthesis, photosynthesis–antenna proteins, circadian rhythm–plant, glutathione metabolism, starch and sucrose metabolism, cutin/suberine/biosynthesis were altered or affected by the cold stress conditions. Our analyses of the generated transcriptome and lncRNAs provide new insights into regulating expression of genes and lncRNAs that respond to cold stress in the wild banana.
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181
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Wang Y, Gao L, Li J, Zhu B, Zhu H, Luo Y, Wang Q, Zuo J. Analysis of long-non-coding RNAs associated with ethylene in tomato. Gene 2018; 674:151-160. [PMID: 29958947 DOI: 10.1016/j.gene.2018.06.089] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2018] [Revised: 06/06/2018] [Accepted: 06/25/2018] [Indexed: 11/18/2022]
Abstract
Long-Non-Coding RNAs (LncRNAs) are a class of non-coding endogenous RNAs contributing to numerous biological processes. LeERF1 is a tomato ethylene response factor (ERF) near the end of the ethylene signal transduction pathway. To identify lncRNAs in tomato and elucidate their roles in ethylene signaling, deep sequencing was deployed in over-expression and repression LeERF1 transgenic and control tomato fruits. A total of 397 lncRNAs were identified, including 169 tomato lncRNAs that had not previously been identified. Among these, 12 were differentially expressed between the transgenic and control tomato fruits. Numerous lncRNA target genes were identified including many associated with ethylene signaling including auxin response factors and auxin-induced proteins, F-box proteins, ERFs and MADS-box proteins. In addition, two lncRNAs were found to be the precursor of three miRNAs and four lncRNAs could be targeted by five miRNAs. We propose a regulatory model highlighting the relationships between lncRNAs and their targets involved in ethylene signal transduction which establishes a foundation for addressing the role of LncRNAs in ethylene response.
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Affiliation(s)
- Yunxiang Wang
- Key Laboratory of the Vegetable Postharvest Treatment of Ministry of Agriculture, Beijing Key Laboratory of Fruits and Vegetable Storage and Processing, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China) of Ministry of Agriculture, Key Laboratory of Urban Agriculture (North) of Ministry of Agriculture, Beijing Vegetable Research Center, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China; Beijing Academy of Forestry and Pomology Sciences, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, China
| | - Lipu Gao
- Key Laboratory of the Vegetable Postharvest Treatment of Ministry of Agriculture, Beijing Key Laboratory of Fruits and Vegetable Storage and Processing, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China) of Ministry of Agriculture, Key Laboratory of Urban Agriculture (North) of Ministry of Agriculture, Beijing Vegetable Research Center, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
| | - Jian Li
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, Beijing Technology and Business University, Beijing 100048,China
| | - Benzhong Zhu
- Laboratory of Postharvest Molecular Biology of Fruits and Vegetables, Department of Food Biotechnology, College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083, China
| | - Hongliang Zhu
- Laboratory of Postharvest Molecular Biology of Fruits and Vegetables, Department of Food Biotechnology, College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083, China
| | - Yunbo Luo
- Laboratory of Postharvest Molecular Biology of Fruits and Vegetables, Department of Food Biotechnology, College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083, China
| | - Qing Wang
- Key Laboratory of the Vegetable Postharvest Treatment of Ministry of Agriculture, Beijing Key Laboratory of Fruits and Vegetable Storage and Processing, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China) of Ministry of Agriculture, Key Laboratory of Urban Agriculture (North) of Ministry of Agriculture, Beijing Vegetable Research Center, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China.
| | - Jinhua Zuo
- Key Laboratory of the Vegetable Postharvest Treatment of Ministry of Agriculture, Beijing Key Laboratory of Fruits and Vegetable Storage and Processing, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China) of Ministry of Agriculture, Key Laboratory of Urban Agriculture (North) of Ministry of Agriculture, Beijing Vegetable Research Center, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China; Boyce Thompson Institute for Plant Research, Cornell University Campus, Ithaca, NY 14853, USA.
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182
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Yuan Y, Chen S. Widespread antisense transcription of Populus genome under drought. Mol Genet Genomics 2018; 293:1017-1033. [PMID: 29876646 DOI: 10.1007/s00438-018-1456-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2017] [Accepted: 05/31/2018] [Indexed: 12/18/2022]
Abstract
Antisense transcription is widespread in many genomes and plays important regulatory roles in gene expression. The objective of our study was to investigate the extent and functional relevance of antisense transcription in forest trees. We employed Populus, a model tree species, to probe the antisense transcriptional response of tree genome under drought, through stranded RNA-seq analysis. We detected nearly 48% of annotated Populus gene loci with antisense transcripts and 44% of them with co-transcription from both DNA strands. Global distribution of reads pattern across annotated gene regions uncovered that antisense transcription was enriched in untranslated regions while sense reads were predominantly mapped in coding exons. We further detected 1185 drought-responsive sense and antisense gene loci and identified a strong positive correlation between the expression of antisense and sense transcripts. Additionally, we assessed the antisense expression in introns and found a strong correlation between intronic expression and exonic expression, confirming antisense transcription of introns contributes to transcriptional activity of Populus genome under drought. Finally, we functionally characterized drought-responsive sense-antisense transcript pairs through gene ontology analysis and discovered that functional groups including transcription factors and histones were concordantly regulated at both sense and antisense transcriptional level. Overall, our study demonstrated the extensive occurrence of antisense transcripts of Populus genes under drought and provided insights into genome structure, regulation pattern and functional significance of drought-responsive antisense genes in forest trees. Datasets generated in this study serve as a foundation for future genetic analysis to improve our understanding of gene regulation by antisense transcription.
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Affiliation(s)
- Yinan Yuan
- School of Forest Resources and Environmental Science, Michigan Technological University, Houghton, MI, 49931, USA.
| | - Su Chen
- School of Forest Resources and Environmental Science, Michigan Technological University, Houghton, MI, 49931, USA
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183
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Liu X, Hou X. Antagonistic Regulation of ABA and GA in Metabolism and Signaling Pathways. FRONTIERS IN PLANT SCIENCE 2018; 9:251. [PMID: 29535756 PMCID: PMC5834473 DOI: 10.3389/fpls.2018.00251] [Citation(s) in RCA: 92] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/30/2017] [Accepted: 02/12/2018] [Indexed: 05/18/2023]
Abstract
The phytohormones gibberellic acid (GA) and abscisic acid (ABA) are widely recognized as essential endogenous regulators that mostly play antagonistic roles in plant developmental processes and environmental responses. A variety of both internal and external cues oppositely regulate GA and ABA biosynthesis and catabolism, which directly and indirectly affect their signaling pathways and subsequent responses. Recent discoveries have revealed direct molecular links between GA- and ABA-signaling components, which provide novel insights into their antagonistic regulation. In this review, we mainly focus on these recent reports and the growing understanding of GA and ABA antagonism in metabolic regulation and signaling interactions, and attempt to clarify the problems and challenges involved in exploring the complicated regulatory events associated with these two phytohormones.
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184
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Ma K, Shi W, Xu M, Liu J, Zhang F. Genome-Wide Identification and Characterization of Long Non-Coding RNA in Wheat Roots in Response to Ca 2+ Channel Blocker. FRONTIERS IN PLANT SCIENCE 2018; 9:244. [PMID: 29559983 PMCID: PMC5845709 DOI: 10.3389/fpls.2018.00244] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/12/2017] [Accepted: 02/12/2018] [Indexed: 05/12/2023]
Abstract
It remains unclear whether plant lncRNAs are responsive to Ca2+-channel blocking. When using the Ca2+-channel blocker, LaCl3, to treat germinated wheat seeds for 24 h, we found that both root length and mitosis were inhibited in the LaCl3-treated groups. The effect of the Ca2+-channel blocker was verified in three ways: a [Ca2+]cyt decrease detected using Fluo-3/AM staining, a decrease in the Ca content measured using inductively coupled plasma mass spectrometry, and an inhibition of Ca2+ influx detected using Non-invasive Micro-test Technology. Genome-wide high throughput RNA-seq and bioinformatical methods were used to identify lncRNAs, and found 177 differentially expressed lncRNAs that might be in responsive to Ca2+-channel blocking. Among these, 108 were up-regulated and 69 were down-regulated. The validity of identified lncRNAs data from RNA-seq was verified using qPCR. GO and KEGG analysis indicated that a number of lncRNAs might be involved in diverse biological processes upon Ca2+-channel blocking. Further GO analysis showed that 23 lncRNAs might play roles as transcription factor (TF); Moreover, eight lncRNAs might participate in cell cycle regulation, and their relative expressions were detected using qPCR. This study also provides diverse data on wheat lncRNAs that can deepen our understanding of the function and regulatory mechanism of Ca2+-channel blocking in plants.
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Affiliation(s)
- Keshi Ma
- College of Life Sciences, Capital Normal University, Beijing, China
- College of Life Science and Agronomy, Zhoukou Normal University, Zhoukou, China
| | - Wenshuo Shi
- College of Life Sciences, Capital Normal University, Beijing, China
| | - Mengyue Xu
- College of Life Sciences, Capital Normal University, Beijing, China
| | - Jiaxi Liu
- College of Life Sciences, Capital Normal University, Beijing, China
- *Correspondence: Jiaxi Liu
| | - Feixiong Zhang
- College of Life Sciences, Capital Normal University, Beijing, China
- Feixiong Zhang
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