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Wang R, Wu M, Zhang X, Jiang T, Wei Z. Methylation of microRNA genes and its effect on secondary xylem development of stem in poplar. THE PLANT GENOME 2024; 17:e20446. [PMID: 38528365 DOI: 10.1002/tpg2.20446] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/10/2023] [Revised: 02/21/2024] [Accepted: 02/27/2024] [Indexed: 03/27/2024]
Abstract
MicroRNAs (miRNAs) and DNA methylation are both vital regulators of gene expression. DNA methylation can affect the transcription of miRNAs, just like coding genes, through methylating the CpG islands in the gene regions of miRNAs. Although previous studies have shown that DNA methylation and miRNAs can each be involved in the process of wood formation, the relationship between the two has been relatively little studied in plant wood formation. Studies have shown that the second internode (IN2) (from top to bottom) of 3-month-old poplar trees can represent the primary stage of poplar stem development and IN8 can represent the secondary stage. There were also significant differences in DNA methylation patterns and miRNA expression patterns obtained from PS and SS. In this study, we first interactively analyzed methylation and miRNA sequencing data to identify 43 differentially expressed miRNAs regulated by differential methylation from the primary stage and secondary stage, which were found to be involved in multiple biological processes related to wood formation by enrichment analysis. In addition, six miRNA/target gene modules were finally identified as potentially involved in secondary xylem development of poplar stems through degradome sequencing and functional analysis. In conclusion, this study provides important reference information on the mechanism of interaction between different regulatory pathways of wood formation.
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Affiliation(s)
- Ruiqi Wang
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, China
| | - Meixuan Wu
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, China
| | - Xiao Zhang
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, China
| | - Tingbo Jiang
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, China
| | - Zhigang Wei
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, China
- Engineering Research Center of Agricultural Microbiology Technology, Ministry of Education, Heilongjiang University, Harbin, China
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Fan J, Zhang H, Shi Y, Li Y, He Y, Wang Q, Liu S, Yao Y, Zhou X, Liao J, Huang Y, Wang Z. Systematic identification and characterization of microRNAs with target genes involved in high night temperature stress at the filling stage of rice. PHYSIOLOGIA PLANTARUM 2024; 176:e14305. [PMID: 38659134 DOI: 10.1111/ppl.14305] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/08/2024] [Revised: 04/07/2024] [Accepted: 04/10/2024] [Indexed: 04/26/2024]
Abstract
High night temperature stress is one of the main environmental factors affecting rice yield and quality. More and more evidence shows that microRNA (miRNA) plays an important role in various abiotic stresses. However, the molecular network of miRNA regulation on rice tolerance to high night temperatures remains unclear. Here, small RNA, transcriptome and degradome sequencing were integrated to identify differentially expressed miRNAs, genes, and key miRNA-target gene pairs in rice heat-sensitive and heat-tolerant lines at the filling stage suffering from high night temperature stress. It was discovered that there were notable differences in the relative expression of 102 miRNAs between the two rice lines under stress. Meanwhile, 5263 and 5405 mRNAs were differentially expressed in the heat-sensitive line and heat-tolerant line, and functional enrichment analysis revealed that these genes were involved in heat-related processes and pathways. The miRNAs-mRNAs target relationship was further verified by degradome sequencing. Eventually, 49 miRNAs-222 mRNAs target pairs with reverse expression patterns showed significant relative expression changes between the heat-tolerant and the heat-sensitive line, being suggested to be responsible for the heat tolerance difference of these two rice lines. Functional analysis of these 222 mRNA transcripts showed that high night temperature-responsive miRNAs targeted these mRNAs involved in many heat-related biological processes, such as transcription regulation, chloroplast regulation, mitochondrion regulation, protein folding, hormone regulation and redox process. This study identified possible miRNA-mRNA regulation relationships in response to high night temperature stress in rice and potentially contributed to heat resistance breeding of rice in the future.
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Affiliation(s)
- Jiangmin Fan
- Key Laboratory of Crop Physiology, Ecology and Genetic Breeding (Jiangxi Agricultural University), Ministry of Education of the P.R. China, Nanchang, Jiangxi Province, China
- Key Laboratory of Agriculture Responding to Climate Change (Jiangxi Agricultural University), Nanchang, Jiangxi Province, China
| | - Hongyu Zhang
- Key Laboratory of Crop Physiology, Ecology and Genetic Breeding (Jiangxi Agricultural University), Ministry of Education of the P.R. China, Nanchang, Jiangxi Province, China
- Key Laboratory of Agriculture Responding to Climate Change (Jiangxi Agricultural University), Nanchang, Jiangxi Province, China
| | - Yan Shi
- Key Laboratory of Crop Physiology, Ecology and Genetic Breeding (Jiangxi Agricultural University), Ministry of Education of the P.R. China, Nanchang, Jiangxi Province, China
- Key Laboratory of Agriculture Responding to Climate Change (Jiangxi Agricultural University), Nanchang, Jiangxi Province, China
| | - Yuewu Li
- Key Laboratory of Crop Physiology, Ecology and Genetic Breeding (Jiangxi Agricultural University), Ministry of Education of the P.R. China, Nanchang, Jiangxi Province, China
- Key Laboratory of Agriculture Responding to Climate Change (Jiangxi Agricultural University), Nanchang, Jiangxi Province, China
| | - Yuxiang He
- Key Laboratory of Crop Physiology, Ecology and Genetic Breeding (Jiangxi Agricultural University), Ministry of Education of the P.R. China, Nanchang, Jiangxi Province, China
- Key Laboratory of Agriculture Responding to Climate Change (Jiangxi Agricultural University), Nanchang, Jiangxi Province, China
| | - Qiang Wang
- Key Laboratory of Crop Physiology, Ecology and Genetic Breeding (Jiangxi Agricultural University), Ministry of Education of the P.R. China, Nanchang, Jiangxi Province, China
- Key Laboratory of Agriculture Responding to Climate Change (Jiangxi Agricultural University), Nanchang, Jiangxi Province, China
| | - Siyi Liu
- Key Laboratory of Crop Physiology, Ecology and Genetic Breeding (Jiangxi Agricultural University), Ministry of Education of the P.R. China, Nanchang, Jiangxi Province, China
- Key Laboratory of Agriculture Responding to Climate Change (Jiangxi Agricultural University), Nanchang, Jiangxi Province, China
| | - Youmin Yao
- Key Laboratory of Crop Physiology, Ecology and Genetic Breeding (Jiangxi Agricultural University), Ministry of Education of the P.R. China, Nanchang, Jiangxi Province, China
- Key Laboratory of Agriculture Responding to Climate Change (Jiangxi Agricultural University), Nanchang, Jiangxi Province, China
| | - Xiaoya Zhou
- Key Laboratory of Crop Physiology, Ecology and Genetic Breeding (Jiangxi Agricultural University), Ministry of Education of the P.R. China, Nanchang, Jiangxi Province, China
- Key Laboratory of Agriculture Responding to Climate Change (Jiangxi Agricultural University), Nanchang, Jiangxi Province, China
| | - Jianglin Liao
- Key Laboratory of Crop Physiology, Ecology and Genetic Breeding (Jiangxi Agricultural University), Ministry of Education of the P.R. China, Nanchang, Jiangxi Province, China
- Key Laboratory of Agriculture Responding to Climate Change (Jiangxi Agricultural University), Nanchang, Jiangxi Province, China
| | - Yingjin Huang
- Key Laboratory of Crop Physiology, Ecology and Genetic Breeding (Jiangxi Agricultural University), Ministry of Education of the P.R. China, Nanchang, Jiangxi Province, China
- Key Laboratory of Agriculture Responding to Climate Change (Jiangxi Agricultural University), Nanchang, Jiangxi Province, China
| | - Zhaohai Wang
- Key Laboratory of Crop Physiology, Ecology and Genetic Breeding (Jiangxi Agricultural University), Ministry of Education of the P.R. China, Nanchang, Jiangxi Province, China
- Key Laboratory of Agriculture Responding to Climate Change (Jiangxi Agricultural University), Nanchang, Jiangxi Province, China
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Seem K, Kaur S, Kumar S, Mohapatra T. Epigenome editing for targeted DNA (de)methylation: a new perspective in modulating gene expression. Crit Rev Biochem Mol Biol 2024; 59:69-98. [PMID: 38440883 DOI: 10.1080/10409238.2024.2320659] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2023] [Accepted: 02/15/2024] [Indexed: 03/06/2024]
Abstract
Traditionally, it has been believed that inheritance is driven as phenotypic variations resulting from changes in DNA sequence. However, this paradigm has been challenged and redefined in the contemporary era of epigenetics. The changes in DNA methylation, histone modification, non-coding RNA biogenesis, and chromatin remodeling play crucial roles in genomic functions and regulation of gene expression. More importantly, some of these changes are inherited to the next generations as a part of epigenetic memory and play significant roles in gene expression. The sum total of all changes in DNA bases, histone proteins, and ncRNA biogenesis constitutes the epigenome. Continuous progress in deciphering epigenetic regulations and the existence of heritable epigenetic/epiallelic variations associated with trait of interest enables to deploy epigenome editing tools to modulate gene expression. DNA methylation marks can be utilized in epigenome editing for the manipulation of gene expression. Initially, genome/epigenome editing technologies relied on zinc-finger protein or transcriptional activator-like effector protein. However, the discovery of clustered regulatory interspaced short palindromic repeats CRISPR)/deadCRISPR-associated protein 9 (dCas9) enabled epigenome editing to be more specific/efficient for targeted DNA (de)methylation. One of the major concerns has been the off-target effects, wherein epigenome editing may unintentionally modify gene/regulatory element which may cause unintended change/harmful effects. Moreover, epigenome editing of germline cell raises several ethical/safety issues. This review focuses on the recent developments in epigenome editing tools/techniques, technological limitations, and future perspectives of this emerging technology in therapeutics for human diseases as well as plant improvement to achieve sustainable developmental goals.
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Affiliation(s)
- Karishma Seem
- Division of Biochemistry, ICAR-Indian Agricultural Research Institute, New Delhi, India
| | - Simardeep Kaur
- Division of Biochemistry, ICAR-Indian Agricultural Research Institute, New Delhi, India
| | - Suresh Kumar
- Division of Biochemistry, ICAR-Indian Agricultural Research Institute, New Delhi, India
| | - Trilochan Mohapatra
- Protection of Plant Varieties and Farmers' Rights Authority, New Delhi, India
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Zhou C, Wu S, Li C, Quan W, Wang A. Response Mechanisms of Woody Plants to High-Temperature Stress. PLANTS (BASEL, SWITZERLAND) 2023; 12:3643. [PMID: 37896106 PMCID: PMC10610489 DOI: 10.3390/plants12203643] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/14/2023] [Revised: 10/12/2023] [Accepted: 10/17/2023] [Indexed: 10/29/2023]
Abstract
High-temperature stress is the main environmental stress that restricts the growth and development of woody plants, and the growth and development of woody plants are affected by high-temperature stress. The influence of high temperature on woody plants varies with the degree and duration of the high temperature and the species of woody plants. Woody plants have the mechanism of adapting to high temperature, and the mechanism for activating tolerance in woody plants mainly counteracts the biochemical and physiological changes induced by stress by regulating osmotic adjustment substances, antioxidant enzyme activities and transcription control factors. Under high-temperature stress, woody plants ability to perceive high-temperature stimuli and initiate the appropriate physiological, biochemical and genomic changes is the key to determining the survival of woody plants. The gene expression induced by high-temperature stress also greatly improves tolerance. Changes in the morphological structure, physiology, biochemistry and genomics of woody plants are usually used as indicators of high-temperature tolerance. In this paper, the effects of high-temperature stress on seed germination, plant morphology and anatomical structure characteristics, physiological and biochemical indicators, genomics and other aspects of woody plants are reviewed, which provides a reference for the study of the heat-tolerance mechanism of woody plants.
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Affiliation(s)
- Chao Zhou
- Key Laboratory for Information System of Mountainous Area and Protection of Ecological Environment of Guizhou Province, Guizhou Normal University, Guiyang 550001, China; (C.Z.); (C.L.)
| | - Shengjiang Wu
- Guizhou Academy of Tobacco Science, Guiyang 550081, China;
| | - Chaochan Li
- Key Laboratory for Information System of Mountainous Area and Protection of Ecological Environment of Guizhou Province, Guizhou Normal University, Guiyang 550001, China; (C.Z.); (C.L.)
| | - Wenxuan Quan
- Key Laboratory for Information System of Mountainous Area and Protection of Ecological Environment of Guizhou Province, Guizhou Normal University, Guiyang 550001, China; (C.Z.); (C.L.)
| | - Anping Wang
- Key Laboratory for Information System of Mountainous Area and Protection of Ecological Environment of Guizhou Province, Guizhou Normal University, Guiyang 550001, China; (C.Z.); (C.L.)
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Balyan S, Kansal S, Jajo R, Behere PR, Chatterjee R, Raghuvanshi S. Delineating the tissue-mediated drought stress governed tuning of conserved miR408 and its targets in rice. Funct Integr Genomics 2023; 23:187. [PMID: 37243818 DOI: 10.1007/s10142-023-01111-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2022] [Revised: 05/13/2023] [Accepted: 05/16/2023] [Indexed: 05/29/2023]
Abstract
Engineering drought tolerance in rice needs to focus on regulators that enhance tolerance while boosting plant growth and vigor. The present study delineated the concealed function and tissue-mediated interplay of the miR408/target module in imparting drought stress tolerance in rice. The plant miR408 family comprises three dominant mature forms (21 nt), including a distinct monocot variant (F-7 with 5' C) and is divided into six groups. miR408 majorly cleaves genes belonging to the blue copper protein in addition to several other species-specific targets in plants. Comparative sequence analysis in 4726 rice accessions identified 22 sequence variants (SNP and InDELs) in its promoter (15) and pre-miR408 region. Haplotype analysis of the sequence variants indicated eight haplotypes (three: Japonica-specific and five: Indica-specific) of the miR408 promoter. In drought-tolerant Nagina 22, miR408 follows flag leaf preferential expression. Under drought conditions, its levels are upregulated in flag leaf and roots which seems to be regulated by a differential fraction of methylated cytosines (mCs) in the precursor region. The active pool of miR408 regulated targets under control and drought conditions is impacted by the tissue type. Comparative expression analysis of the miR408/target module under different sets of conditions features 83 targets exhibiting antagonistic expression in rice, out of which 12 genes, including four PLANTACYANINS (OsUCL6, 7, 9 and 30), PIRIN, OsLPR1, OsCHUP1, OsDOF12, OsBGLU1, glycine-rich cell wall gene, OsDUT, and OsERF7, are among the high confidence targets. Further, overexpression of MIR408 in drought-sensitive rice cultivar (PB1) leads to the massive enhancement of vegetative growth in rice with improved ETR and Y(II) and enhanced dehydration stress tolerance. The above results suggest that miR408 is likely to act as a positive regulator of growth and vigor, as well as dehydration stress, making it a potential candidate for engineering drought tolerance in rice.
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Affiliation(s)
- Sonia Balyan
- Department of Plant Molecular Biology, University of Delhi South Campus, New Delhi, 110021, India
| | - Shivani Kansal
- Department of Plant Molecular Biology, University of Delhi South Campus, New Delhi, 110021, India
| | - Ringyao Jajo
- Department of Plant Molecular Biology, University of Delhi South Campus, New Delhi, 110021, India
| | - Pratyush Rajiv Behere
- Department of Plant Molecular Biology, University of Delhi South Campus, New Delhi, 110021, India
| | - Rishika Chatterjee
- Department of Plant Molecular Biology, University of Delhi South Campus, New Delhi, 110021, India
| | - Saurabh Raghuvanshi
- Department of Plant Molecular Biology, University of Delhi South Campus, New Delhi, 110021, India.
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Genome-wide identification of drought-responsive microRNAs and their target genes in Chinese jujube by deep sequencing. Genes Genomics 2023; 45:231-245. [PMID: 35819623 DOI: 10.1007/s13258-022-01274-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2022] [Accepted: 05/22/2022] [Indexed: 01/25/2023]
Abstract
BACKGROUND MicroRNAs (miRNAs) are about 21 snucleotide (nt) long, non-coding RNAs that play an important role in plant abiotic stress responses. Chinese jujube is a native fruit tree in China, which is also an admittedly drought-resistant plant. But the drought-related miRNAs have little been reported in jujube. OBJECTIVE To identify possibly drought-responsive microRNAs and their target genes in Chinese Jujube. METHODS Twelve small RNA libraries were constructed from two jujube genotypes both drought treated and control samples with three replicates to identify known and novel miRNAs in Chinese Jujube, DESeq2 was used to identify expression pattern of miRNAs between drought treatment and control samples, TargetFinder program was used to predict potential target genes of conserved and novel miRNAs, RT-qPCR were used to analysis the expression levels of drought-related miRNAs and their potential targets. The RNA ligase-mediated RLM-5' RACE experiments were performed to validate predicted target genes of drought-related miRNAs. RESULTS 43 known miRNAs and 431 novel miRNAs were identified in Chinese jujube. Expression analysis showed that 28 miRNAs were differential expressed under drought stress in jujube variety "Dongzao", including 21 up-regulated miRNAs and 7 down-regulated miRNAs, 61 miRNAs were differential expressed under drought stress in Chinese jujube variety "Zanhuangdazao", including 23 up-regulated miRNAs and 37 down-regulated miRNAs. Depend on miRNAs target prediction, functional annotation and expression analysis, we identified 9 drought-related miRNAs, and 7 target genes of 6 miRNAs were confirmed using the modified 5'-RACE method. Also, RT-qPCR analyses revealed that relative expression of those miRNAs and their targets have negative tendency. CONCLUSION We identified 6 drought-related miRNAs by high-throughout sequencing and target gene annotation from Chinese jujube, and targets of those miRNAs were confirmed by the modified 5'-RACE method. These findings provide molecular evidence for enhancing drought tolerance in Chinese jujube and other plants.
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Shi M, Wang C, Wang P, Zhang M, Liao W. Methylation in DNA, histone, and RNA during flowering under stress condition: A review. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2022; 324:111431. [PMID: 36028071 DOI: 10.1016/j.plantsci.2022.111431] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/14/2022] [Revised: 08/07/2022] [Accepted: 08/19/2022] [Indexed: 06/15/2023]
Abstract
Flowering is the most critical transition period in the whole lifecycle of plants, and it is a highly sensitive period to stress. New combinations of temperature, drought stress, carbon dioxide and other abiotic/biotic conditions resulting from contemporary climate change affect the flowering process. Plants have evolved several strategies to deal with environmental stresses, including epigenetic modifications. Numerous studies show that environmental stresses trigger methylation/demethylation during flowering to preserve/accelerate plant lifecycle. What's more, histone and DNA methylation can be induced to respond to stresses, resulting in changes of flowering gene expression and enhancing stress tolerance in plants. Furthermore, RNA methylation may influence stress-regulated flowering by regulating mRNA stability and antioxidant mechanism. Our review presents the involvement of methylation in stress-repressed and stress-induced flowering. The crosstalk between methylation and small RNAs, phytohormones and exogenous substances (such as salicylic acid, nitric oxide) during flowering under different stresses were discussed. The latest regulatory evidence of RNA methylation in stress-regulated flowering was collected for the first time. Meanwhile, the limited evidences of methylation in biotic stress-induced flowering were summarized. Thus, the review provides insights into understanding of methylation mechanism in stress-regulated flowering and makes use for the development of regulating plant flowering at epigenetic level in the future.
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Affiliation(s)
- Meimei Shi
- College of Horticulture, Gansu Agricultural University, Lanzhou 730070, China
| | - Chunlei Wang
- College of Horticulture, Gansu Agricultural University, Lanzhou 730070, China
| | - Peng Wang
- College of Horticulture, Gansu Agricultural University, Lanzhou 730070, China
| | - Meiling Zhang
- College of Science, Gansu Agricultural University, Lanzhou 730070, China
| | - Weibiao Liao
- College of Horticulture, Gansu Agricultural University, Lanzhou 730070, China.
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Xing C, Li J, Yuan H, Yang J. Physiological and transcription level responses of microalgae Auxenochlorella protothecoides to cold and heat induced oxidative stress. ENVIRONMENTAL RESEARCH 2022; 211:113023. [PMID: 35276186 DOI: 10.1016/j.envres.2022.113023] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/05/2021] [Revised: 02/16/2022] [Accepted: 02/23/2022] [Indexed: 06/14/2023]
Abstract
Temperature is a crucial factor affecting microalgae CO2 capture and utilization. However, an in-depth understanding of how microalgae respond to temperature stress is still unclear. In particular, the regulation mechanism under opposite temperature (heat and cold) stress had not yet been reported. In this study, the physicochemical properties and transcription level of related genes of microalgae Auxenochlorella protothecoides UTEX 2341 under heat and cold stress were investigated. Heat stress (Hs) caused a drastic increase of reactive oxygen species (ROS) in UTEX 2341. As key elements responded to Hs, superoxide dismutase (SOD) enzyme increased by 150%, 70%, and 30% in activity, and nitric oxide (NO) grew by 409.6%, 212.5%, and 990.4% in content compared with the control at 48 h, 96 h, 168 h. Under cold stress (Cs), ROS increased in the early stage and decreased in the later stage. As key factors responded to Cs, proline (Pro) increased respectively by 285%, 383%, and 81% in content, and heat shock transcriptional factor HSFA1d increased respectively by 161%, 71%, and 204% in transcript level compared with the control at 48 h, 96 h, 168 h. Furthermore, the transcript level of antioxidant enzymes or antioxidant coding genes was consistent with the changing trend of enzymes activity or antioxidant content. Notably, both glutathione (GSH) and heat shock protein 97 (hsp 97) were up-regulated in response to Hs and Cs. In conclusion, GSH and hsp 97 were the core elements of UTEX 2341 in response to both Hs and Cs. SOD and NO were the key elements that responded to Hs, while proline and HSFA1d were the key elements that responded to Cs. This study provided a basis for the understanding of the response mechanism of microalgae under temperature stress and the improvement of the microalgae tolerance to temperature stress.
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Affiliation(s)
- Chao Xing
- State Key Laboratory of Agrobiotechnology and Key Laboratory of Soil Microbiology, Ministry of Agriculture, College of Biological Sciences, China Agricultural University, Beijing, 100193, China.
| | - Jinyu Li
- State Key Laboratory of Agrobiotechnology and Key Laboratory of Soil Microbiology, Ministry of Agriculture, College of Biological Sciences, China Agricultural University, Beijing, 100193, China.
| | - Hongli Yuan
- State Key Laboratory of Agrobiotechnology and Key Laboratory of Soil Microbiology, Ministry of Agriculture, College of Biological Sciences, China Agricultural University, Beijing, 100193, China.
| | - Jinshui Yang
- State Key Laboratory of Agrobiotechnology and Key Laboratory of Soil Microbiology, Ministry of Agriculture, College of Biological Sciences, China Agricultural University, Beijing, 100193, China.
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Sun M, Yang Z, Liu L, Duan L. DNA Methylation in Plant Responses and Adaption to Abiotic Stresses. Int J Mol Sci 2022; 23:ijms23136910. [PMID: 35805917 PMCID: PMC9266845 DOI: 10.3390/ijms23136910] [Citation(s) in RCA: 32] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2022] [Revised: 06/11/2022] [Accepted: 06/15/2022] [Indexed: 02/07/2023] Open
Abstract
Due to their sessile state, plants are inevitably affected by and respond to the external environment. So far, plants have developed multiple adaptation and regulation strategies to abiotic stresses. One such system is epigenetic regulation, among which DNA methylation is one of the earliest and most studied regulatory mechanisms, which can regulate genome functioning and induce plant resistance and adaption to abiotic stresses. In this review, we outline the most recent findings on plant DNA methylation responses to drought, high temperature, cold, salt, and heavy metal stresses. In addition, we discuss stress memory regulated by DNA methylation, both in a transient way and the long-term memory that could pass to next generations. To sum up, the present review furnishes an updated account of DNA methylation in plant responses and adaptations to abiotic stresses.
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Affiliation(s)
| | | | - Li Liu
- Correspondence: (L.L.); (L.D.)
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The Intersection of Non-Coding RNAs Contributes to Forest Trees' Response to Abiotic Stress. Int J Mol Sci 2022; 23:ijms23126365. [PMID: 35742808 PMCID: PMC9223653 DOI: 10.3390/ijms23126365] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2022] [Revised: 05/15/2022] [Accepted: 06/01/2022] [Indexed: 12/10/2022] Open
Abstract
Non-coding RNAs (ncRNAs) play essential roles in plants by modulating the expression of genes at the transcriptional or post-transcriptional level. In recent years, ncRNAs have been recognized as crucial regulators for growth and development in forest trees, and ncRNAs that respond to various abiotic stresses are now under intense study. In this review, we summarized recent advances in the understanding of abiotic stress-responsive microRNAs (miRNAs), long non-coding RNAs (lncRNAs), and circular RNAs (circRNAs) in forest trees. Furthermore, we analyzed the intersection of miRNAs, and epigenetic modified ncRNAs of forest trees in response to abiotic stress. In particular, the abiotic stress-related lncRNA/circRNA-miRNA-mRNA regulatory network of forest trees was explored.
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Sammarco I, Münzbergová Z, Latzel V. DNA Methylation Can Mediate Local Adaptation and Response to Climate Change in the Clonal Plant Fragaria vesca: Evidence From a European-Scale Reciprocal Transplant Experiment. FRONTIERS IN PLANT SCIENCE 2022; 13:827166. [PMID: 35295625 PMCID: PMC8919072 DOI: 10.3389/fpls.2022.827166] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/01/2021] [Accepted: 02/07/2022] [Indexed: 06/01/2023]
Abstract
The ongoing climate crisis represents a growing threat for plants and other organisms. However, how and if plants will be able to adapt to future environmental conditions is still debated. One of the most powerful mechanisms allowing plants to tackle the changing climate is phenotypic plasticity, which can be regulated by epigenetic mechanisms. Environmentally induced epigenetic variation mediating phenotypic plasticity might be heritable across (a)sexual generations, thus potentially enabling rapid adaptation to climate change. Here, we assessed whether epigenetic mechanisms, DNA methylation in particular, enable for local adaptation and response to increased and/or decreased temperature of natural populations of a clonal plant, Fragaria vesca (wild strawberry). We collected ramets from three populations along a temperature gradient in each of three countries covering the southern (Italy), central (Czechia), and northern (Norway) edges of the native European range of F. vesca. After clonal propagation and alteration of DNA methylation status of half of the plants via 5-azacytidine, we reciprocally transplanted clones to their home locality and to the other two climatically distinct localities within the country of their origin. At the end of the growing season, we recorded survival and aboveground biomass as fitness estimates. We found evidence for local adaptation in intermediate and cold populations in Italy and maladaptation of plants of the warmest populations in all countries. Plants treated with 5-azacytidine showed either better or worse performance in their local conditions than untreated plants. Application of 5-azacytidine also affected plant response to changed climatic conditions when transplanted to the colder or warmer locality than was their origin, and the response was, however, country-specific. We conclude that the increasing temperature will probably be the limiting factor determining F. vesca survival and distribution. DNA methylation may contribute to local adaptation and response to climatic change in natural ecosystems; however, its role may depend on the specific environmental conditions. Since adaptation mediated by epigenetic variation may occur faster than via natural selection on genetic variants, epigenetic adaptation might to some degree help plants in keeping up with the ongoing environmental crisis.
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Affiliation(s)
- Iris Sammarco
- Institute of Botany, Czech Academy of Sciences, Průhonice, Czechia
- Department of Botany, Faculty of Science, Charles University, Prague, Czechia
| | - Zuzana Münzbergová
- Institute of Botany, Czech Academy of Sciences, Průhonice, Czechia
- Department of Botany, Faculty of Science, Charles University, Prague, Czechia
| | - Vít Latzel
- Institute of Botany, Czech Academy of Sciences, Průhonice, Czechia
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12
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Genomics Associated Interventions for Heat Stress Tolerance in Cool Season Adapted Grain Legumes. Int J Mol Sci 2021; 23:ijms23010399. [PMID: 35008831 PMCID: PMC8745526 DOI: 10.3390/ijms23010399] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2021] [Revised: 12/22/2021] [Accepted: 12/27/2021] [Indexed: 11/16/2022] Open
Abstract
Cool season grain legumes occupy an important place among the agricultural crops and essentially provide multiple benefits including food supply, nutrition security, soil fertility improvement and revenue for farmers all over the world. However, owing to climate change, the average temperature is steadily rising, which negatively affects crop performance and limits their yield. Terminal heat stress that mainly occurred during grain development phases severely harms grain quality and weight in legumes adapted to the cool season, such as lentils, faba beans, chickpeas, field peas, etc. Although, traditional breeding approaches with advanced screening procedures have been employed to identify heat tolerant legume cultivars. Unfortunately, traditional breeding pipelines alone are no longer enough to meet global demands. Genomics-assisted interventions including new-generation sequencing technologies and genotyping platforms have facilitated the development of high-resolution molecular maps, QTL/gene discovery and marker-assisted introgression, thereby improving the efficiency in legumes breeding to develop stress-resilient varieties. Based on the current scenario, we attempted to review the intervention of genomics to decipher different components of tolerance to heat stress and future possibilities of using newly developed genomics-based interventions in cool season adapted grain legumes.
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Zhu Y, Liu Q, Xu W, Yao L, Wang X, Wang H, Xu Y, Li L, Duan C, Yi Z, Lin C. Identification of novel drought-responsive miRNA regulatory network of drought stress response in common vetch ( Vicia sativa). Open Life Sci 2021; 16:1111-1121. [PMID: 34712821 PMCID: PMC8511966 DOI: 10.1515/biol-2021-0109] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2021] [Revised: 08/06/2021] [Accepted: 08/19/2021] [Indexed: 11/15/2022] Open
Abstract
Drought is among the most important natural disasters with severe effects on animals and plants. MicroRNAs are a class of noncoding RNAs that play a crucial role in plant growth, development, and response to stress factors, including drought. However, the microRNAs in drought responses in common vetch (Vicia sativa), an annual herbaceous leguminous plant commonly used for forage by including it in mixed seeding during winter and spring, have not been characterized. To explore the microRNAs’ response to drought in common vetch, we sequenced 10 small RNA (sRNA) libraries by the next-generation sequencing technology. We obtained 379 known miRNAs belonging to 38 families and 47 novel miRNAs. The two groups had varying numbers of differentially expressed miRNAs: 85 in the comparison group D5 vs C5 and 38 in the comparison group D3 vs C3. Combined analysis of mRNA and miRNA in the same samples under drought treatment identified 318 different target genes of 123 miRNAs. Functional annotation of the target genes revealed that the miRNAs regulate drought-responsive genes, such as leucine-rich repeat receptor-like kinase-encoding genes (LRR-RLKs), ABC transporter G family member 1 (ABCG1), and MAG2-interacting protein 2 (MIP2). The genes were involved in various pathways, including cell wall biosynthesis, reactive oxygen removal, and protein transport. The findings in this study provide new insights into the miRNA-mediated regulatory networks of drought stress response in common vetch.
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Affiliation(s)
- Yongqun Zhu
- Soil and Fertilizer Research Institute, Sichuan Academy of Agricultural Sciences, Chengdu, Sichuan 610066, People's Republic of China
| | - Qiuxu Liu
- Soil and Fertilizer Research Institute, Sichuan Academy of Agricultural Sciences, Chengdu, Sichuan 610066, People's Republic of China
| | - Wenzhi Xu
- Soil and Fertilizer Research Institute, Sichuan Academy of Agricultural Sciences, Chengdu, Sichuan 610066, People's Republic of China
| | - Li Yao
- Soil and Fertilizer Research Institute, Sichuan Academy of Agricultural Sciences, Chengdu, Sichuan 610066, People's Republic of China
| | - Xie Wang
- Soil and Fertilizer Research Institute, Sichuan Academy of Agricultural Sciences, Chengdu, Sichuan 610066, People's Republic of China
| | - Hong Wang
- Soil and Fertilizer Research Institute, Sichuan Academy of Agricultural Sciences, Chengdu, Sichuan 610066, People's Republic of China
| | - Yalin Xu
- Soil and Fertilizer Research Institute, Sichuan Academy of Agricultural Sciences, Chengdu, Sichuan 610066, People's Republic of China
| | - Linxiang Li
- Bazhong Green Agriculture Innovation and Development Research Institute, Sichuan Academy of Agricultural Sciences, Bazhong, Sichuan 636000, People's Republic of China
| | - Chunhua Duan
- Soil and Fertilizer Research Institute, Sichuan Academy of Agricultural Sciences, Chengdu, Sichuan 610066, People's Republic of China
| | - Zhixin Yi
- Bazhong Green Agriculture Innovation and Development Research Institute, Sichuan Academy of Agricultural Sciences, Bazhong, Sichuan 636000, People's Republic of China
| | - Chaowen Lin
- Soil and Fertilizer Research Institute, Sichuan Academy of Agricultural Sciences, Chengdu, Sichuan 610066, People's Republic of China
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Luo L, Zhu Y, Gui J, Yin T, Luo W, Liu J, Li L. A Comparative Analysis of Transcription Networks Active in Juvenile and Mature Wood in Populus. FRONTIERS IN PLANT SCIENCE 2021; 12:675075. [PMID: 34122491 PMCID: PMC8193101 DOI: 10.3389/fpls.2021.675075] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/02/2021] [Accepted: 04/07/2021] [Indexed: 06/12/2023]
Abstract
Juvenile wood (JW) and mature wood (MW) have distinct physical and chemical characters, resulting from wood formation at different development phases over tree lifespan. However, the regulatory mechanisms that distinguish or modulate the characteristics of JW and MW in relation to each other have not been mapped. In this study, by employing the Populus trees with an identical genetic background, we carried out RNA sequencing (RNA-seq) and whole genome bisulfite sequencing (WGBS) in JW and MW forming tissue and analyzed the transcriptional programs in association with the wood formation in different phrases. JW and MW of Populus displayed different wood properties, including higher content of cellulose and hemicelluloses, less lignin, and longer and larger fiber cells and vessel elements in MW as compared with JW. Significant differences in transcriptional programs and patterns of DNA methylation were detected between JW and MW. The differences were concentrated in gene networks involved in regulating hormonal signaling pathways responsible for auxin distribution and brassinosteroids biosynthesis as well as genes active in regulating cell expansion and secondary cell wall biosynthesis. An observed correlation between gene expression profiling and DNA methylation indicated that DNA methylation affected expression of the genes related to auxin distribution and brassinosteroids signal transduction, cell expansion in JW, and MW formation. The results suggest that auxin distribution, brassinosteroids biosynthesis, and signaling be the critical molecular modules in formation of JW and MW. DNA methylation plays a role in formatting the molecular modules which contribute to the transcriptional programs of wood formation in different development phases. The study sheds light into better understanding of the molecular networks underlying regulation of wood properties which would be informative for genetic manipulation for improvement of wood formation.
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Affiliation(s)
- Laifu Luo
- State Key Laboratory of Grassland Agro-Ecosystem, School of Life Sciences, Lanzhou University, Lanzhou, China
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China
| | - Yingying Zhu
- State Key Laboratory of Grassland Agro-Ecosystem, School of Life Sciences, Lanzhou University, Lanzhou, China
| | - Jinshan Gui
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China
| | - Tongmin Yin
- College of Forestry, Nanjing Forestry University, Nanjing, China
| | - Wenchun Luo
- State Key Laboratory of Grassland Agro-Ecosystem, School of Life Sciences, Lanzhou University, Lanzhou, China
| | - Jianquan Liu
- State Key Laboratory of Grassland Agro-Ecosystem, School of Life Sciences, Lanzhou University, Lanzhou, China
| | - Laigeng Li
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China
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Catalase (CAT) Gene Family in Rapeseed ( Brassica napus L.): Genome-Wide Analysis, Identification, and Expression Pattern in Response to Multiple Hormones and Abiotic Stress Conditions. Int J Mol Sci 2021; 22:ijms22084281. [PMID: 33924156 PMCID: PMC8074368 DOI: 10.3390/ijms22084281] [Citation(s) in RCA: 57] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2021] [Revised: 04/15/2021] [Accepted: 04/19/2021] [Indexed: 12/28/2022] Open
Abstract
Catalase (CAT) is an antioxidant enzyme expressed by the CAT gene family and exists in almost all aerobic organisms. Environmental stresses induce the generation of reactive oxygen species (ROS) that eventually hinder plant growth and development. The CAT enzyme translates the hydrogen peroxide (H2O2) to water (H2O) and reduce the ROS levels to shelter the cells’ death. So far, the CAT gene family has not been reported in rapeseed (Brassica napus L.). Therefore, a genome-wide comprehensive analysis was conducted to classify the CAT genes in the rapeseed genome. The current study identified 14 BnCAT genes in the rapeseed genome. Based on phylogenetic and synteny analysis, the BnCATs belong to four groups (Groups I–IV). A gene structure and conserved motif analysis showed that Group I, Group II, and Group IV possess almost the same intron/exon pattern, and an equal number of motifs, while Group III contains diverse structures and contain 15 motifs. By analyzing the cis-elements in the promoters, we identified five hormone-correlated responsive elements and four stress-related responsive elements. Further, six putative bna-miRNAs were also identified, targeting three genes (BnCAT4, BnCAT6, and BnCAT8). Gene ontology (GO) enrichment analysis showed that the BnCAT genes were largely related to cellular organelles, ROS response, stimulus response, stress response, and antioxidant enzymes. Almost 10 BnCAT genes showed higher expression levels in different tissues, i.e., root, leaf, stem, and silique. The expression analysis showed that BnCAT1–BnCAT3 and BnCAT11–BnCAT13 were significantly upregulated by cold, salinity, abscisic acid (ABA), and gibberellic acid (GA) treatment, but not by drought and methyl jasmonate (MeJA). Notably, most of the genes were upregulated by waterlogging stress, except BnCAT6, BnCAT9, and BnCAT10. Our results opened new windows for future investigations and provided insights into the CAT family genes in rapeseed.
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Ding X, Guo J, Zhang Q, Yu L, Zhao T, Yang S. Heat-Responsive miRNAs Participate in the Regulation of Male Fertility Stability in Soybean CMS-Based F 1 under High Temperature Stress. Int J Mol Sci 2021; 22:2446. [PMID: 33671046 PMCID: PMC7957588 DOI: 10.3390/ijms22052446] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2020] [Revised: 02/10/2021] [Accepted: 02/24/2021] [Indexed: 11/18/2022] Open
Abstract
MicroRNAs (miRNAs), a class of noncoding small RNAs (sRNAs), are widely involved in the response to high temperature (HT) stress at both the seedling and flowering stages. To dissect the roles of miRNAs in regulating male fertility in soybean cytoplasmic male sterility (CMS)-based F1 under HT, sRNA sequencing was performed using flower buds from HT-tolerant and HT-sensitive CMS-based F1 combinations (NF1 and YF1, respectively). A total of 554 known miRNAs, 59 new members of known miRNAs, 712 novel miRNAs, and 1145 target genes of 580 differentially expressed miRNAs (DEMs) were identified under normal temperature and HT conditions. Further integrated analysis of sRNA and transcriptome sequencing found that 21 DEMs and 15 differentially expressed target genes, such as gma-miR397a/Laccase 2, gma-miR399a/Inorganic phosphate transporter 1-4, and gma-miR4413a/PPR proteins, mitochondrial-like, were negatively regulated under HT stress. Furthermore, all members of the gma-miR156 family were suppressed by HT stress in both NF1 and YF1, but were highly expressed in YF1 under HT condition. The negative correlation between gma-miR156b and its target gene squamosa promoter-binding protein-like 2b was confirmed by expression analysis, and overexpression of gma-miR156b in Arabidopsis led to male sterility under HT stress. With these results, we proposed that miRNAs play an important role in the regulation of male fertility stability in soybean CMS-based F1 under HT stress.
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Affiliation(s)
| | | | | | | | - Tuanjie Zhao
- Soybean Research Institute, National Center for Soybean Improvement, Key Laboratory of Biology and Genetic Improvement of Soybean (General, Ministry of Agriculture), State Key Laboratory of Crop Genetics and Germplasm Enhancement, Jiangsu Collaborative Innovation Center for Modern Crop Production, College of Agriculture, Nanjing Agricultural University, Nanjing 210095, China; (X.D.); (J.G.); (Q.Z.); (L.Y.)
| | - Shouping Yang
- Soybean Research Institute, National Center for Soybean Improvement, Key Laboratory of Biology and Genetic Improvement of Soybean (General, Ministry of Agriculture), State Key Laboratory of Crop Genetics and Germplasm Enhancement, Jiangsu Collaborative Innovation Center for Modern Crop Production, College of Agriculture, Nanjing Agricultural University, Nanjing 210095, China; (X.D.); (J.G.); (Q.Z.); (L.Y.)
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Korotko U, Chwiałkowska K, Sańko-Sawczenko I, Kwasniewski M. DNA Demethylation in Response to Heat Stress in Arabidopsis thaliana. Int J Mol Sci 2021; 22:ijms22041555. [PMID: 33557095 PMCID: PMC7913789 DOI: 10.3390/ijms22041555] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Revised: 01/28/2021] [Accepted: 02/02/2021] [Indexed: 02/07/2023] Open
Abstract
Environmental stress is one of the most important factors affecting plant growth and development. Recent studies have shown that epigenetic mechanisms, such as DNA methylation, play a key role in adapting plants to stress conditions. Here, we analyzed the dynamics of changes in the level of DNA methylation in Arabidopsis thaliana (L.) Heynh. (Brassicaceae) under the influence of heat stress. For this purpose, whole-genome sequencing of sodium bisulfite-treated DNA was performed. The analysis was performed at seven time points, taking into account the control conditions, heat stress, and recovery to control conditions after the stress treatment was discontinued. In our study we observed decrease in the level of DNA methylation under the influence of heat stress, especially after returning to control conditions. Analysis of the gene ontology enrichment and regulatory pathways showed that genes characterized by differential DNA methylation are mainly associated with stress response, including heat stress. These are the genes encoding heat shock proteins and genes associated with translation regulation. A decrease in the level of DNA methylation in such specific sites suggests that under the influence of heat stress we observe active demethylation phenomenon rather than passive demethylation, which is not locus specific.
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Affiliation(s)
- Urszula Korotko
- Centre for Bioinformatics and Data Analysis, Medical University of Bialystok, 15-089 Bialystok, Poland; (U.K.); (K.C.)
- Department of Genetics, University of Silesia in Katowice, 40-007 Katowice, Poland
| | - Karolina Chwiałkowska
- Centre for Bioinformatics and Data Analysis, Medical University of Bialystok, 15-089 Bialystok, Poland; (U.K.); (K.C.)
| | - Izabela Sańko-Sawczenko
- Department of Botany, Institute of Biology, Warsaw University of Life Sciences, 02-787 Warszawa, Poland;
| | - Miroslaw Kwasniewski
- Centre for Bioinformatics and Data Analysis, Medical University of Bialystok, 15-089 Bialystok, Poland; (U.K.); (K.C.)
- Correspondence:
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Zhan J, Diao Y, Yin G, Sajjad M, Wei X, Lu Z, Wang Y. Integration of mRNA and miRNA Analysis Reveals the Molecular Mechanism of Cotton Response to Salt Stress. FRONTIERS IN PLANT SCIENCE 2021; 12:767984. [PMID: 34956267 PMCID: PMC8695560 DOI: 10.3389/fpls.2021.767984] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Accepted: 11/09/2021] [Indexed: 05/13/2023]
Abstract
To identify the regulatory network of known and novel microRNAs (miRNAs) and their targets responding to salt stress, a combined analysis of mRNA libraries, small RNA libraries, and degradome libraries were performed. In this study, we used unique molecular identifiers (UMIs), which are more sensitive, accurate, and reproducible than traditional methods of sequencing, to quantify the number of molecules and correct for amplification bias. We identified a total of 312 cotton miRNAs using seedlings at 0, 1, 3, and 6 h after NaCl treatment, including 80 known ghr-miRNAs and 232 novel miRNAs and found 155 miRNAs that displayed significant differential expression under salt stress. Among them, fifty-nine differentially expressed miRNAs were simultaneously induced in two or three tissues, while 66, 11, and 19 were specifically expressed in the roots, leaves, and stems, respectively. It is indicated there were different populations of miRNAs against salt stress in roots, leaves and stems. 399 candidate targets of salt-induced miRNAs showed significant differential expression before and after salt treatment, and 72 targets of 25 miRNAs were verified by degradome sequencing data. Furthermore, the regulatory relationship of miRNA-target gene was validated experimentally via 5'RLM-RACE, proving our data reliability. Gene ontology and KEGG pathway analysis found that salt-responsive miRNA targets among the differentially expressed genes were significantly enriched, and mainly involved in response to the stimulus process and the plant hormone signal transduction pathway. Furthermore, the expression levels of newly identified miRNA mir1 and known miRNAs miR390 and miR393 gradually decreased when subjected to continuous salt stress, while overexpression of these miRNAs both increased sensitivity to salt stress. Those newly identified miRNAs and mRNA pairs were conducive to genetic engineering and better understanding the mechanisms responding to salt stress in cotton.
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Affiliation(s)
- Jingjing Zhan
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Anyang, China
| | - Yangyang Diao
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Anyang, China
| | - Guo Yin
- Handan Academy of Agricultural Sciences, Handan, China
| | - Muhammad Sajjad
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Anyang, China
| | - Xi Wei
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Anyang, China
| | - Zhengying Lu
- Handan Academy of Agricultural Sciences, Handan, China
- *Correspondence: Zhengying Lu,
| | - Ye Wang
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Anyang, China
- Ye Wang,
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Rambani A, Hu Y, Piya S, Long M, Rice JH, Pantalone V, Hewezi T. Identification of Differentially Methylated miRNA Genes During Compatible and Incompatible Interactions Between Soybean and Soybean Cyst Nematode. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2020; 33:1340-1352. [PMID: 32757880 DOI: 10.1094/mpmi-07-20-0196-r] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/09/2023]
Abstract
DNA methylation is a widespread epigenetic mark that affects gene expression and transposon mobility during plant development and stress responses. However, the role of DNA methylation in regulating the expression of microRNA (miRNA) genes remains largely unexplored. Here, we analyzed DNA methylation changes of miRNA genes using a pair of soybean (Glycine max) near-isogenic lines (NILs) differing in their response to soybean cyst nematode (SCN; Heterodera glycines). Differences in global DNA methylation levels over miRNA genes in response to SCN infection were observed between the isogenic lines. miRNA genes with significant changes in DNA methylation levels in the promoter and primary transcript-coding regions were detected in both lines. In the susceptible isogenic line (NIL-S), 82 differentially methylated miRNAs were identified in response to SCN infection whereas, in the resistant isogenic line (NIL-R), only 16 differentially methylated miRNAs were identified. Interestingly, gma-miR5032, gma-miR5043, gma-miR1520b, and gma-2107-ch16 showed opposite methylation patterns in the isogenic lines. In addition, the miRNA paralogs gma-miR5770a and gma-miR5770b showed hypermethylation and hypomethylation in NIL-S and NIL-R, respectively. Gene expression quantification of gma-miR5032, gma-miR5043, gma-miR1520b, and gma-miR5770a/b and their confirmed targets indicated a role of DNA methylation in regulating miRNA expression and, thus, their targets upon SCN infection. Furthermore, overexpression of these four miRNAs in NIL-S using transgenic hairy root system enhanced plant resistance to SCN to various degrees with a key role observed for miR5032. Together, our results provide new insights into the role of epigenetic mechanisms in controlling miRNA regulatory function during SCN-soybean interactions.[Formula: see text] Copyright © 2020 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license.
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Affiliation(s)
- Aditi Rambani
- Department of Plant Sciences, University of Tennessee, Knoxville, TN 37996, U.S.A
| | - Yanfeng Hu
- Department of Plant Sciences, University of Tennessee, Knoxville, TN 37996, U.S.A
- Key Laboratory of Mollisols Agroecology, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Harbin, China
| | - Sarbottam Piya
- Department of Plant Sciences, University of Tennessee, Knoxville, TN 37996, U.S.A
| | - Miao Long
- Department of Plant Sciences, University of Tennessee, Knoxville, TN 37996, U.S.A
| | - J Hollis Rice
- Department of Plant Sciences, University of Tennessee, Knoxville, TN 37996, U.S.A
| | - Vince Pantalone
- Department of Plant Sciences, University of Tennessee, Knoxville, TN 37996, U.S.A
| | - Tarek Hewezi
- Department of Plant Sciences, University of Tennessee, Knoxville, TN 37996, U.S.A
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Abstract
The importance of tree genetic variability in the ability of forests to respond and adapt to environmental changes is crucial in forest management and conservation. Along with genetics, recent advances have highlighted “epigenetics” as an emerging and promising field of research for the understanding of tree phenotypic plasticity and adaptive responses. In this paper, we review recent advances in this emerging field and their potential applications for tree researchers and breeders, as well as for forest managers. First, we present the basics of epigenetics in plants before discussing its potential for trees. We then propose a bibliometric and overview of the literature on epigenetics in trees, including recent advances on tree priming. Lastly, we outline the promises of epigenetics for forest research and management, along with current gaps and future challenges. Research in epigenetics could use highly diverse paths to help forests adapt to global change by eliciting different innovative silvicultural approaches for natural- and artificial-based forest management.
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Rehman M, Tanti B. Understanding epigenetic modifications in response to abiotic stresses in plants. BIOCATALYSIS AND AGRICULTURAL BIOTECHNOLOGY 2020. [DOI: 10.1016/j.bcab.2020.101673] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
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Bulut B, Aydinli Z, Türktaş-Erken M. MSAP analysis reveals diverse epigenetic statuses in opium poppy varieties with different benzyisoquinoline alkaloid content. ACTA ACUST UNITED AC 2020; 44:103-109. [PMID: 32256146 PMCID: PMC7129067 DOI: 10.3906/biy-1911-69] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
DNA methylation is one of the major epigenetic modifications influencing the regulation of gene expression. The opium poppy is an important medicinal plant. Its latex contains opium, which is a rich source of pharmaceutical benzyisoquinoline alkaloids (BIA). Here, the methylation-sensitive amplification polymorphism (MSAP) profiling technique using 21 MSAP molecular markers was applied in order to compare levels of DNA methylation between 6 opium poppy varieties. MSAP profiling reflected the different methylation statuses among opium poppy varieties having divergent BIA content. Moreover, different organ-specific epigenetic profiles were observed between the samples. Differential epigenetic profiles of capsules and shoots from the leaves pointed to the impact of methylation on BIA biosynthesis. The data implied that the different DNA methylation status may have important biological significance, in the case of alkaloid content in opium poppy in particular.
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Affiliation(s)
- Betül Bulut
- Department of Biology, Faculty of Science, Çankırı Karatekin University, Çankırı Turkey
| | - Zehra Aydinli
- Department of Biology, Faculty of Science, Çankırı Karatekin University, Çankırı Turkey
| | - Mine Türktaş-Erken
- Department of Biology, Faculty of Science, Çankırı Karatekin University, Çankırı Turkey
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Different MicroRNA Families Involved in Regulating High Temperature Stress Response during Cotton ( Gossypium hirsutum L.) Anther Development. Int J Mol Sci 2020; 21:ijms21041280. [PMID: 32074966 PMCID: PMC7072957 DOI: 10.3390/ijms21041280] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2019] [Revised: 01/26/2020] [Accepted: 02/12/2020] [Indexed: 11/16/2022] Open
Abstract
MicroRNAs (miRNAs) are small molecule RNAs widely involved in responses to plant abiotic stresses. We performed small RNA sequencing of cotton anthers at four developmental stages under normal and high temperature (NT and HT, respectively) conditions to investigate the stress response characteristics of miRNA to HT. A total of 77 miRNAs, including 33 known miRNAs and 44 novel miRNAs, were identified, and 41 and 28 miRNAs were differentially expressed under NT and HT stress conditions, respectively. The sporogenous cell proliferation (SCP), meiotic phase (MP), microspore release period (MRP), and pollen maturity (PM) stages had 10 (including 12 miRNAs), four (including six miRNAs), four (including five miRNAs), and seven (including 11 miRNAs) HT stress-responsive miRNA families, respectively, which were identified after removing the changes in genotype-specific miRNAs under NT condition. Seven miRNA families (miR2949, miR167, and miR160 at the SCP stage; miR156 and miR172 at the MP stage; miR156 at the MRP stage; and miR393 and miR3476 at the PM stage), which had expression abundance of more than 10% of the total expression abundance, served as the main regulators responding to HT stress with positive or negative regulation patterns. These miRNAs orchestrated the expression of the corresponding target genes and led to different responses in the HT-tolerant and the HT-sensitive lines. The results revealed that the HT stress response of miRNAs in cotton anthers were stage-specific and differed with the development of anthers. Our study may enhance the understanding of the response of miRNAs to HT stress in cotton anthers and may clarify the mechanism of plant tolerance to HT stress.
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Rippin M, Borchhardt N, Karsten U, Becker B. Cold Acclimation Improves the Desiccation Stress Resilience of Polar Strains of Klebsormidium (Streptophyta). Front Microbiol 2019; 10:1730. [PMID: 31447802 PMCID: PMC6691101 DOI: 10.3389/fmicb.2019.01730] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2019] [Accepted: 07/12/2019] [Indexed: 11/13/2022] Open
Abstract
Biological soil crusts (BSCs) are complex communities of autotrophic, heterotrophic, and saprotrophic (micro)organisms. In the polar regions, these biocrust communities have essential ecological functions such as primary production, nitrogen fixation, and ecosystem engineering while coping with extreme environmental conditions (temperature, desiccation, and irradiation). The microalga Klebsormidium is commonly found in BSCs all across the globe. The ecophysiological resilience of various Klebsormidium species to desiccation and other stresses has been studied intensively. Here we present the results of transcriptomic analyses of two different Klebsormidium species, K. dissectum and K. flaccidum, isolated from Antarctic and Arctic BSCs. We performed desiccation stress experiments at two different temperatures mimicking fluctuations associated with global change. Cultures grown on agar plates were desiccated on membrane filters at 10% relative air humidity until the photosynthetic activity as reflected in the effective quantum yield of photosystem II [Y(II)] ceased. For both species, the response to dehydration was much faster at the higher temperature. At the transcriptome level both species responded more strongly to the desiccation stress at the higher temperature suggesting that adaptation to cold conditions enhanced the resilience of both algae to desiccation stress. Interestingly, the two different species responded differently to the applied desiccation stress with respect to the number as well as function of genes showing differential gene expression. The portion of differentially expressed genes shared between both taxa was surprisingly low indicating that both Klebsormidium species adapted independently to the harsh conditions of Antarctica and the Arctic, respectively. Overall, our results indicate that environmental acclimation has a great impact on gene expression and the response to desiccation stress in Klebsormidium.
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Affiliation(s)
- Martin Rippin
- Department of Biology, Botanical Institute, University of Cologne, Cologne, Germany
| | | | - Ulf Karsten
- Department of Biology, University of Rostock, Rostock, Germany
| | - Burkhard Becker
- Department of Biology, Botanical Institute, University of Cologne, Cologne, Germany
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Zhang Y, Xu W, Nan S, Chang M, Fan J. MicroRNA-326 Inhibits Apoptosis and Promotes Proliferation of Dopaminergic Neurons in Parkinson's Disease Through Suppression of KLK7-Mediated MAPK Signaling Pathway. J Mol Neurosci 2019; 69:197-214. [PMID: 31270675 DOI: 10.1007/s12031-019-01349-1] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2019] [Accepted: 05/22/2019] [Indexed: 10/26/2022]
Abstract
Parkinson's disease (PD), one of the motor system disorders, is characterized by the loss of dopamine-producing brain cells. Accumulating evidence has highlighted the involvement of microRNAs (miRs) in the development and progression of PD. Hence, we aimed at exploring possible effects of miR-326 on the progression of PD in mice in an attempt to elucidate the underlying mechanism associated with the kallikrein-related peptidase 7 (KLK7)-mediated mitogen-activated protein kinase (MAPK) signaling pathway. In order to identify the regulatory relationship between miR-326 and KLK7 and its biological significance in PD, PD mouse models were established and subsequently treated with mimics or inhibitors of miR-326 or siRNA-KLK7. The content of striatal dopamine (DA), 3,4-dihydroxyphenylacetic acid (DOPAC), homovanillic acid (HVA), 3-methoxytyrosine (3-MT), superoxide dismutase (SOD), glutathione peroxidase (GSH-Px), and malondialdehyde (MDA); positive expression of tyrosine hydroxylase (TH) and inducible nitric oxide synthase (iNOS); and the levels of IL-1, IL-6, TNF-α, INF-γ, and MAPK signaling pathway-related genes were determined accordingly. The results obtained indicated that KLK7 was negatively targeted by miR-326, with lower miR-326 and higher KLK7 detected among PD mice. The overexpression of miR-326 or silencing of KLK7 was demonstrated to increase the content of DA, DOPAC, HVA, 3-MT, SOD, GSH-Px, and TH positive expression, while reducing iNOS positive expression, MDA content and cell apoptosis, as well as inhibited levels of IL-1, IL-6, TNF-α, INF-γ, and mRNA and protein levels of p38, ERK, JNK, and caspase-3. Taken together, these results provided evidence suggesting that miR-326 could inhibit iNOS activation and apoptosis of dopaminergic neurons through inhibiting the MAPK signaling pathway and negatively regulating KLK7 in mice with PD. These findings highlight the potential of miR-326 as a novel target for future PD treatment.
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Affiliation(s)
- Yizhi Zhang
- Department of Neurology, The Second Hospital of Jilin University, No. 218, Ziqiang Street, Nanguan District, Changchun, 130041, Jilin Province, People's Republic of China
| | - Weiwei Xu
- Department of Neurology, The Second Hospital of Jilin University, No. 218, Ziqiang Street, Nanguan District, Changchun, 130041, Jilin Province, People's Republic of China
| | - Shanji Nan
- Department of Neurology, The Second Hospital of Jilin University, No. 218, Ziqiang Street, Nanguan District, Changchun, 130041, Jilin Province, People's Republic of China
| | - Meiji Chang
- Department of Neurology, Changchun Central Hospital, Changchun, 130000, People's Republic of China
| | - Jia Fan
- Department of Neurology, The Second Hospital of Jilin University, No. 218, Ziqiang Street, Nanguan District, Changchun, 130041, Jilin Province, People's Republic of China.
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Goel S, Goswami K, Pandey VK, Pandey M, Sanan-Mishra N. Identification of microRNA-target modules from rice variety Pusa Basmati-1 under high temperature and salt stress. Funct Integr Genomics 2019; 19:867-888. [PMID: 31127449 DOI: 10.1007/s10142-019-00673-4] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2018] [Revised: 03/18/2019] [Accepted: 03/21/2019] [Indexed: 12/11/2022]
Abstract
High temperature and salinity stress are major factors limiting the growth and productivity of rice crop on a global scale. It is therefore an essential prerequisite to understand the molecular genetic regulation of plant responses to dual stresses. MicroRNAs (miRs) are recognized as key controllers of gene expression which act mainly at the post-transcriptional level to regulate various aspects of plant development. The present study attempts to investigate the miR circuits that are modulated in response to high temperature and salinity stress in rice. To gain insights into the pathway, preliminary miR profiles were generated using the next-generation sequencing (NGS) datasets. The identified molecules were filtered on the basis of fold differential regulation under high temperature, and time kinetics of their expression under the two individual stresses was followed to capture the regulatory windows. The analysis revealed the involvement of common miR regulatory nodes in response to two different abiotic stresses, thereby broadening our perspective about the stress-mediated regulatory mechanisms operative in rice.
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Affiliation(s)
- Shikha Goel
- Discipline of Biochemistry, SOS, Indira Gandhi National Open University, New Delhi, 110068, India.,Plant RNAi Biology Group, International Centre for Genetic Engineering and Biotechnology, New Delhi, 110067, India
| | - Kavita Goswami
- Plant RNAi Biology Group, International Centre for Genetic Engineering and Biotechnology, New Delhi, 110067, India
| | - Vimal K Pandey
- Plant RNAi Biology Group, International Centre for Genetic Engineering and Biotechnology, New Delhi, 110067, India
| | - Maneesha Pandey
- Discipline of Biochemistry, SOS, Indira Gandhi National Open University, New Delhi, 110068, India
| | - Neeti Sanan-Mishra
- Plant RNAi Biology Group, International Centre for Genetic Engineering and Biotechnology, New Delhi, 110067, India.
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Xu J, Hou QM, Khare T, Verma SK, Kumar V. Exploring miRNAs for developing climate-resilient crops: A perspective review. THE SCIENCE OF THE TOTAL ENVIRONMENT 2019; 653:91-104. [PMID: 30408672 DOI: 10.1016/j.scitotenv.2018.10.340] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/04/2018] [Revised: 10/24/2018] [Accepted: 10/25/2018] [Indexed: 05/21/2023]
Abstract
Climate changes and environmental stresses have significant implications on global crop production and necessitate developing crops that can withstand an array of climate changes and environmental perturbations such as irregular water-supplies leading to drought or water-logging, hyper soil-salinity, extreme and variable temperatures, ultraviolet radiations and metal stress. Plants have intricate molecular mechanisms to cope with these dynamic environmental changes, one of the most common and effective being the reprogramming of expression of stress-responsive genes. Plant microRNAs (miRNAs) have emerged as key post-transcriptional and translational regulators of gene-expression for modulation of stress implications. Recent reports are establishing their key roles in epigenetic regulations of stress/adaptive responses as well as in providing plants genome-stability. Several stress responsive miRNAs are being identified from different crop plants and miRNA-driven RNA-interference (RNAi) is turning into a technology of choice for improving crop traits and providing phenotypic plasticity in challenging environments. Here we presents a perspective review on exploration of miRNAs as potent targets for engineering crops that can withstand multi-stress environments via loss-/gain-of-function approaches. This review also shed a light on potential roles plant miRNAs play in genome-stability and their emergence as potent target for genome-editing. Current knowledge on plant miRNAs, their biogenesis, function, their targets, and latest developments in bioinformatics approaches for plant miRNAs are discussed. Though there are recent reviews discussing primarily the individual miRNAs responsive to single stress factors, however, considering practical limitation of this approach, special emphasis is given in this review on miRNAs involved in responses and adaptation of plants to multi-stress environments including at epigenetic and/or epigenomic levels.
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Affiliation(s)
- Jin Xu
- School of Environmental Science and Safety Engineering, Tianjin University of Technology, Tianjin 300384, China
| | - Qin-Min Hou
- School of Environmental Science and Safety Engineering, Tianjin University of Technology, Tianjin 300384, China.
| | - Tushar Khare
- Department of Biotechnology, Modern College of Arts, Science and Commerce (Savitribai Phule Pune University), Ganeshkhind, Pune 411016, India
| | - Sandeep Kumar Verma
- Biotechnology Laboratory (TUBITAK Fellow), Department of Biology, Bolu Abant Izeet Baysal University, 14030 Bolu, Turkey
| | - Vinay Kumar
- Department of Biotechnology, Modern College of Arts, Science and Commerce (Savitribai Phule Pune University), Ganeshkhind, Pune 411016, India; Department of Environmental Science, Savitribai Phule Pune University, Pune 411007, India.
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Sun X, Lin L, Sui N. Regulation mechanism of microRNA in plant response to abiotic stress and breeding. Mol Biol Rep 2018; 46:1447-1457. [PMID: 30465132 DOI: 10.1007/s11033-018-4511-2] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2018] [Accepted: 11/19/2018] [Indexed: 01/08/2023]
Abstract
microRNAs (miRNAs) in plants are a class of small RNAs consisting of approximately 21-24 nucleotides. The mature miRNA binds to the target mRNA through the formation of a miRNA-induced silencing complex (MIRISC), and cleaves or inhibits translation, thereby achieving negative regulation of the target gene. Based on miRNA plays an important role in regulating plant gene expression, studies on the prediction, identification, function and evolution of plant miRNAs have been carried out. In addition, many researches prove that miRNAs are also involved in many kinds of abiotic and biotic stress, under abiotic stress, plants can express some miRNA, and act on stress-related target genes, which can make plants adapt to stress in physiological response. In this review, the synthetic pathway and mechanism of plant miRNA are briefly described, and we discuss the biological functions and regulatory mechanisms of miRNAs responding to abiotic stresses including low temperature, salt, drought stress and breeding to lay the foundation for further exploring the mechanism of action of miRNAs in stress resistance of plant. And analyze its utilization prospects in plant stress resistance research.
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Affiliation(s)
- Xi Sun
- Shandong Provincial Key Laboratory of Plant Stress, College of Life Sciences, Shandong Normal University, Jinan, 250014, Shandong, People's Republic of China
| | - Lin Lin
- Water Research Institute of Shandong Province, Jinan, People's Republic of China
| | - Na Sui
- Shandong Provincial Key Laboratory of Plant Stress, College of Life Sciences, Shandong Normal University, Jinan, 250014, Shandong, People's Republic of China.
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Abdelrahman M, Jogaiah S, Burritt DJ, Tran LSP. Legume genetic resources and transcriptome dynamics under abiotic stress conditions. PLANT, CELL & ENVIRONMENT 2018; 41:1972-1983. [PMID: 29314055 DOI: 10.1111/pce.13123] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/19/2017] [Revised: 12/08/2017] [Accepted: 12/08/2017] [Indexed: 05/04/2023]
Abstract
Grain legumes are an important source of nutrition and income for billions of consumers and farmers around the world. However, the low productivity of new legume varieties, due to the limited genetic diversity available for legume breeding programmes and poor policymaker support, combined with an increasingly unpredictable global climate is resulting in a large gap between current yields and the increasing demand for legumes as food. Hence, there is a need for novel approaches to develop new high-yielding legume cultivars that are able to cope with a range of environmental stressors. Next-generation technologies are providing the tools that could enable the more rapid and cost-effective genomic and transcriptomic studies for most major crops, allowing the identification of key functional and regulatory genes involved in abiotic stress resistance. In this review, we provide an overview of the recent achievements regarding abiotic stress resistance in a wide range of legume crops and highlight the transcriptomic and miRNA approaches that have been used. In addition, we critically evaluate the availability and importance of legume genetic resources with desirable abiotic stress resistance traits.
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Affiliation(s)
- Mostafa Abdelrahman
- Laboratory of Genomic Reproductive Biology, Graduate School of Life Sciences, Tohoku University, 2-1-1 Katahira, Aoba-ku, Sendai, 980-8577, Japan
- Botany Department, Faculty of Science, Aswan University, Aswan, 81528, Egypt
| | - Sudisha Jogaiah
- Plant Healthcare and Diagnostic Center, Department of Studies in Biotechnology and Microbiology, Karnatak University, Dharwad, 580 003, India
| | - David J Burritt
- Department of Botany, University of Otago, P.O. Box 56, Dunedin, New Zealand
| | - Lam-Son Phan Tran
- Plant Stress Research Group & Faculty of Applied Sciences, Ton Duc Thang University, Ho Chi Minh City, Vietnam
- Signaling Pathway Research Unit, RIKEN Center for Sustainable Resource Science, Yokohama, Japan
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Kumar V, Khare T, Shriram V, Wani SH. Plant small RNAs: the essential epigenetic regulators of gene expression for salt-stress responses and tolerance. PLANT CELL REPORTS 2018; 37:61-75. [PMID: 28951953 DOI: 10.1007/s00299-017-2210-4] [Citation(s) in RCA: 55] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/17/2017] [Accepted: 09/12/2017] [Indexed: 05/07/2023]
Abstract
Saline environment cues distort the plant growth, development and crop yield. Epigenetics has emerged as one of the prime themes in plant functional genomics for molecular-stress-physiology research, as copious studies have provided new visions into the epigenetic control of stress adaptations. The epigenetic control is associated with the regulation of the expression of stress-related genes which also comprises many steady alterations inherited in next cellular generation as stress memory. These epigenetic amendments also implicate induction of small RNA (sRNA)-mediated fine-tuning of transcriptional and post-transcriptional regulations of gene expression. These tiny (19-24 nt) RNA species, particularly microRNAs (miRNAs) besides endogenous small interfering RNA (siRNA) have emerged as important responsive entities for epigenetic modulation of salt-stress effects on plants. There is a recent upsurge in development of tools and databases useful for prediction, identification and validation of small RNAs (sRNAs) and their target messenger RNAs (mRNAs). Therefore, these small but key regulatory molecules have received a wide attention in post-genomic era as potential targets for engineering stress tolerance in major glycophytic crops, though it is yet to be explored optimally. This review aims to provide critical updates on plant sRNAs as key epigenetic regulators of plant salt-stress responses, their target prediction and validation, computational tools and databases available for plant small RNAs, besides discussing their roles in salt-stress regulatory networks and adaptive mechanisms in plants, with special emphasis on their exploration for engineering salinity tolerance in plants.
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Affiliation(s)
- Vinay Kumar
- Department of Biotechnology, Modern College of Arts, Science and Commerce (Savitribai Phule Pune University), Ganeshkhind, Pune, 411016, India.
- Department of Environmental Science, Savitribai Phule Pune University, Ganeshkhind, Pune, 411007, India.
| | - Tushar Khare
- Department of Biotechnology, Modern College of Arts, Science and Commerce (Savitribai Phule Pune University), Ganeshkhind, Pune, 411016, India
| | - Varsha Shriram
- Department of Botany, Prof. Ramkrishna More College (Savitribai Phule Pune University), Akurdi, Pune, 411044, India
| | - Shabir H Wani
- Mountain Research Centre for Field Crops, Sher-e-Kashmir University of Agricultural Sciences and Technology of Kashmir, Khudwani, Anantnag, Jammu and Kashmir, 192101, India.
- Department of Plant Soil and Microbial Sciences, Michigan State University, East Lansing, MI, USA.
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Bai Q, Wang X, Chen X, Shi G, Liu Z, Guo C, Xiao K. Wheat miRNA TaemiR408 Acts as an Essential Mediator in Plant Tolerance to Pi Deprivation and Salt Stress via Modulating Stress-Associated Physiological Processes. FRONTIERS IN PLANT SCIENCE 2018; 9:499. [PMID: 29720988 PMCID: PMC5916090 DOI: 10.3389/fpls.2018.00499] [Citation(s) in RCA: 41] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/06/2017] [Accepted: 04/03/2018] [Indexed: 05/18/2023]
Abstract
MicroRNAs (miRNA) families act as critical regulators for plant growth, development, and responses to abiotic stresses. In this study, we characterized TaemiR408, a miRNA family member of wheat (Triticum aestivum), for the role in mediating plant responses to Pi starvation and salt stress. TaemiR408 targets six genes that encode proteins involving biochemical metabolism, microtubule organization, and signaling transduction. 5'- and 3'-RACE analyses confirmed the mRNA cleavage of target genes mediated by this wheat miRNA. TaemiR408 showed induced expression patterns upon Pi starvation and salt stress and whose upregulated expression was gradually repressed by the normal recovery treatments. The target genes of TaemiR408 exhibited reverse expression patterns to this miRNA, whose transcripts were downregulated under Pi starvation and salt stress and the reduced expression was recovered by the followed normal condition. These results suggest the regulation of the target genes under TaemiR408 through a cleavage mechanism. Tobacco lines with TaemiR408 overexpression exhibited enhanced stress tolerance, showing improved phenotype, biomass, and photosynthesis behavior compared with wild type under both Pi starvation and salt treatments, which closely associate increased P accumulation upon Pi deprivation and elevated osmolytes under salt stress, respectively. Phosphate transporter (PT) gene NtPT2 displays upregulated transcripts in the Pi-deprived TaemiR408 overexpressors; knockdown of this PT gene reduces Pi acquisition under low-Pi stress, confirming its role in improving plant Pi taken up. Likewise, NtPYL2 and NtSAPK3, genes encoding abscisic acid (ABA) receptor and SnRK2 protein, respectively, exhibited upregulated transcripts in salt-challenged TaemiR408 overexpressors; knockdown of them caused deteriorated growth and lowered osmolytes amounts of plants upon salt treatment. Thus, TaemiR408 is crucial for plant adaptations to Pi starvation and salt stress through regulating Pi acquisition under low-Pi stress and remodel ABA signaling pathway and osmoprotects biosynthesis under salt stress.
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Affiliation(s)
| | | | | | | | | | | | - Kai Xiao
- *Correspondence: Chengjin Guo, Kai Xiao,
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Dzialo M, Szopa J, Czuj T, Zuk M. Oligodeoxynucleotides Can Transiently Up- and Downregulate CHS Gene Expression in Flax by Changing DNA Methylation in a Sequence-Specific Manner. FRONTIERS IN PLANT SCIENCE 2017; 8:755. [PMID: 28555142 PMCID: PMC5430052 DOI: 10.3389/fpls.2017.00755] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/09/2017] [Accepted: 04/24/2017] [Indexed: 06/07/2023]
Abstract
Chalcone synthase (CHS) has been recognized as an essential enzyme in the phenylpropanoid biosynthesis pathway. Apart from the leading role in the production of phenolic compounds with many valuable biological activities beneficial to biomedicine, CHS is well appreciated in science. Genetic engineering greatly facilitates expanding knowledge on the function and genetics of CHS in plants. The CHS gene is one of the most intensively studied genes in flax. In our study, we investigated engineering of the CHS gene through genetic and epigenetic approaches. Considering the numerous restrictions concerning the application of genetically modified (GM) crops, the main purpose of this research was optimization of the plant's modulation via epigenetics. In our study, plants modified through two methods were compared: a widely popular agrotransformation and a relatively recent oligodeoxynucleotide (ODN) strategy. It was recently highlighted that the ODN technique can be a rapid and time-serving antecedent in quick analysis of gene function before taking vector-mediated transformation. In order to understand the molecular background of epigenetic variation in more detail and evaluate the use of ODNs as a tool for predictable and stable gene engineering, we concentrated on the integration of gene expression and gene-body methylation. The treatment of flax with a series of short oligonucleotides homologous to a different part of CHS gene isoforms revealed that those directed to regulatory gene regions (5'- and 3'-UTR) activated gene expression, directed to non-coding region (introns) caused gen activity reduction, while those homologous to a coding region may have a variable influence on its activity. Gene expression changes were accompanied by changes in its methylation status. However, only certain (CCGG) motifs along the gene sequence were affected. The analyzed DNA motifs of the CHS flax gene are more accessible for methylation when located within a CpG island. The methylation motifs also led to rearrangement of the nucleosome location. The obtained results suggest high specificity of ODN action and establish a potential valuable alternative for improvement of crops.
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Affiliation(s)
- Magdalena Dzialo
- Department of Genetic Biochemistry, Faculty of Biotechnology, University of WrocławWroclaw, Poland
| | - Jan Szopa
- Department of Genetic Biochemistry, Faculty of Biotechnology, University of WrocławWroclaw, Poland
- Linum FoundationWroclaw, Poland
- Department of Genetics, Plant Breeding and Seed Production, Wroclaw University of Environmental and Life SciencesWroclaw, Poland
| | - Tadeusz Czuj
- Department of Genetics, Plant Breeding and Seed Production, Wroclaw University of Environmental and Life SciencesWroclaw, Poland
| | - Magdalena Zuk
- Department of Genetic Biochemistry, Faculty of Biotechnology, University of WrocławWroclaw, Poland
- Linum FoundationWroclaw, Poland
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Li Y, Wan L, Bi S, Wan X, Li Z, Cao J, Tong Z, Xu H, He F, Li X. Identification of Drought-Responsive MicroRNAs from Roots and Leaves of Alfalfa by High-Throughput Sequencing. Genes (Basel) 2017; 8:genes8040119. [PMID: 28406444 PMCID: PMC5406866 DOI: 10.3390/genes8040119] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2017] [Revised: 04/05/2017] [Accepted: 04/06/2017] [Indexed: 12/13/2022] Open
Abstract
Alfalfa, an important forage legume, is an ideal crop for sustainable agriculture and a potential crop for bioenergy resources. Drought, one of the most common environmental stresses, substantially affects plant growth, development, and productivity. MicroRNAs (miRNAs) are newly discovered gene expression regulators that have been linked to several plant stress responses. To elucidate the role of miRNAs in drought stress regulation of alfalfa, a high-throughput sequencing approach was used to analyze 12 small RNA libraries comprising of four samples, each with three biological replicates. From the 12 libraries, we identified 348 known miRNAs belonging to 80 miRNA families, and 281 novel miRNAs, using Mireap software. Eighteen known miRNAs in roots and 12 known miRNAs in leaves were screened as drought-responsive miRNAs. With the exception of miR319d and miR157a which were upregulated under drought stress, the expression pattern of drought-responsive miRNAs was different between roots and leaves in alfalfa. This is the first study that has identified miR3512, miR3630, miR5213, miR5294, miR5368 and miR6173 as drought-responsive miRNAs. Target transcripts of drought-responsive miRNAs were computationally predicted. All 447 target genes for the known miRNAs were predicted using an online tool. This study provides a significant insight on understanding drought-responsive mechanisms of alfalfa.
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Affiliation(s)
- Yue Li
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, China.
| | - Liqiang Wan
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, China.
| | - Shuyi Bi
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, China.
| | - Xiufu Wan
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, China.
| | - Zhenyi Li
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, China.
| | - Jing Cao
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, China.
| | - Zongyong Tong
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, China.
| | - Hongyu Xu
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, China.
| | - Feng He
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, China.
| | - Xianglin Li
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, China.
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Schönberger B, Chen X, Mager S, Ludewig U. Site-Dependent Differences in DNA Methylation and Their Impact on Plant Establishment and Phosphorus Nutrition in Populus trichocarpa. PLoS One 2016; 11:e0168623. [PMID: 27992519 PMCID: PMC5167412 DOI: 10.1371/journal.pone.0168623] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2016] [Accepted: 12/02/2016] [Indexed: 12/20/2022] Open
Abstract
The propagation via clonal stem cuttings is a frequent practice in tree plantations. Despite their clonal origin, the trees establish differently according to weather, temperature and nutrient availability, as well as the presence of various stresses. Here, clonal Populus trichocarpa (cv. Muhle Larson) cuttings from different sites were transferred into a common, fully nutrient supplied environment. Despite identical underlying genetics, stem cuttings derived from sites with lower phosphorus availability established worse, independent of phosphorus (P) level after transplantation. Differential growth of material from the sites was reflected in differences in the whole genome DNA methylome. Methylation differences were sequence context-dependent, but differentially methylated regions (DMRs) were apparently unrelated to P nutrition genes. Despite the undisputed negative general correlation of DNA promoter methylation with gene repression, only few of the top-ranked DMRs resulted in differential gene expression in roots or shoots. However, differential methylation was associated with site-dependent, different total amounts of microRNAs (miRNAs), with few miRNAs sequences directly targeted by differential methylation. Interestingly, in roots and shoots, the miRNA amount was dependent on the previous habitat and changed in roots in a habitat-dependent way under phosphate starvation conditions. Differentially methylated miRNAs, together with their target genes, showed P-dependent expression profiles, indicating miRNA expression differences as a P-related epigenetic modification in poplar. Together with differences in DNA methylation, such epigenetic mechanisms may explain habitat or seasonal memory in perennials and site-dependent growth performances.
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Affiliation(s)
- Brigitte Schönberger
- Crop Science Institute, Department of Nutritional Crop Physiology, University of Hohenheim, Stuttgart, Germany
| | - Xiaochao Chen
- Crop Science Institute, Department of Nutritional Crop Physiology, University of Hohenheim, Stuttgart, Germany
| | - Svenja Mager
- Crop Science Institute, Department of Nutritional Crop Physiology, University of Hohenheim, Stuttgart, Germany
| | - Uwe Ludewig
- Crop Science Institute, Department of Nutritional Crop Physiology, University of Hohenheim, Stuttgart, Germany
- * E-mail:
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35
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Hung IC, Hsiao YC, Sun HS, Chen TM, Lee SJ. MicroRNAs regulate gene plasticity during cold shock in zebrafish larvae. BMC Genomics 2016; 17:922. [PMID: 27846817 PMCID: PMC5111229 DOI: 10.1186/s12864-016-3239-4] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2016] [Accepted: 11/01/2016] [Indexed: 12/19/2022] Open
Abstract
Background MicroRNAs (miRNAs) are critical regulators responding to acute environmental stresses in both plants and animals. By modulating gene expression, miRNAs either restore or reconstitute a new expression program to enhance cell tolerance to stresses. Cold shock is one of the stresses that can induce acute physiological responses and transcriptional changes in aquatic creatures. Previous genomic studies have revealed many cold-affected genes in fish larvae and adults, however, the role of miRNAs in acute cold response is still ambiguous. To elucidate the regulatory roles of miRNAs in the cold-inducible responses, we performed small RNA-seq and RNA-seq analyses and found potential cold regulatory miRNAs and genes. We further investigated their interactions and involvements in cold tolerance. Results Small RNA-seq and RNA-seq identified 29 up-/26 down-regulated miRNAs and 908 up-/468 down-regulated genes, respectively, in responding to cold shock for 4 h at 18 °C. miRNA and transcriptomic analyses showed these miRNAs and mRNAs are involved in similar biological processes and pathways. Gene ontology enrichment analyses revealed the cold-induced genes were enriched in pathways, including melanogenesis, GnRH pathway, circadian rhythm, etc. We were particularly interested in the changes in circadian clock genes that affect daily metabolism. The enrichment of circadian clock genes was also observed in previous fish cold acclimation studies, but have not been characterized. To characterize the functional roles of circadian clock genes in cold tolerance, we individually overexpressed selected clock genes in zebrafish larvae and found one of the core clock genes per2 resulted in better recovery from cold shock. In addition, we validated the interaction of per2 with its associate miRNA, dre-mir-29b, which is also cold-inducible. It suggests the transcription of per2 can be modulated by miRNA upon cold shock. Conclusions Collectively, our observations suggest that miRNAs are fine turners for regulating genomic plasticity against cold shock. We further showed that the fine tuning of core clock gene per2 via its associated miRNA, dre-mir-29b, can enhance the cold tolerance of zebrafish larvae. Electronic supplementary material The online version of this article (doi:10.1186/s12864-016-3239-4) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- I-Chen Hung
- Department of Life Science, National Taiwan University, Taipei, 10617, Taiwan
| | - Yu-Chuan Hsiao
- Department of Life Science, National Taiwan University, Taipei, 10617, Taiwan
| | - H Sunny Sun
- Institute of Molecular Medicine, College of Medicine, National Cheng Kung University, Tainan, 70456, Taiwan.,Institute of Basic Medical Sciences, College of Medicine, National Cheng Kung University, Tainan, 70456, Taiwan
| | - Tsung-Ming Chen
- Department and Graduate Institute of Aquaculture, National Kaohsiung Marine University, Kaohsiung 81157, Taiwan.
| | - Shyh-Jye Lee
- Department of Life Science, National Taiwan University, Taipei, 10617, Taiwan. .,Research Center for Developmental Biology and Regenerative Medicine, National Taiwan University, Taipei, 10617, Taiwan. .,Center for Biotechnology, National Taiwan University, Taipei, 10617, Taiwan. .,Center for Systems Biology, Taipei, 10617, Taiwan.
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Wang Q, Liu N, Yang X, Tu L, Zhang X. Small RNA-mediated responses to low- and high-temperature stresses in cotton. Sci Rep 2016; 6:35558. [PMID: 27752116 PMCID: PMC5067717 DOI: 10.1038/srep35558] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2016] [Accepted: 09/30/2016] [Indexed: 01/06/2023] Open
Abstract
MicroRNAs (miRNAs) are one class of endogenous non-coding RNAs modulating the expression of target genes involved in plant development and stress tolerance, by degrading mRNA or repressing translation. In this study, small RNA and mRNA degradome sequencing were used to identify low- and high-temperature stress-responsive miRNAs and their targets in cotton (Gossypium hirsutum). Cotton seedlings were treated under different temperature conditions (4, 12, 25, 35, and 42 °C) and then the effects were investigated. In total, 319 known miRNAs and 800 novel miRNAs were identified, and 168 miRNAs were differentially expressed between different treatments. The targets of these miRNAs were further analysed by degradome sequencing. Based on studies from Gene Ontology and Kyoto Encyclopedia of Genes and Genomes, the majority of the miRNAs are from genes that are likely involved in response to hormone stimulus, oxidation-reduction reaction, photosynthesis, plant-pathogen interaction and plant hormone signal transduction pathways. This study provides new insight into the molecular mechanisms of plant response to extreme temperature stresses, and especially the roles of miRNAs under extreme temperatures.
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Affiliation(s)
- Qiongshan Wang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, Hubei, 430070, China
| | - Nian Liu
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, Hubei, 430070, China
| | - Xiyan Yang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, Hubei, 430070, China
| | - Lili Tu
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, Hubei, 430070, China
| | - Xianlong Zhang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, Hubei, 430070, China
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Zhao J, He Q, Chen G, Wang L, Jin B. Regulation of Non-coding RNAs in Heat Stress Responses of Plants. FRONTIERS IN PLANT SCIENCE 2016; 7:1213. [PMID: 27588021 PMCID: PMC4988968 DOI: 10.3389/fpls.2016.01213] [Citation(s) in RCA: 66] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/03/2016] [Accepted: 07/29/2016] [Indexed: 05/18/2023]
Abstract
Heat stress is an important factor limiting plant growth, development, and productivity; thus, plants have evolved special adaptive mechanisms to cope with high-temperature stress. Non-coding RNAs (ncRNAs) are a class of regulatory RNAs that play an important role in many biological processes. Recently developed advanced technologies, such as genome-wide transcriptomic analysis, have revealed that abundant ncRNAs are expressed under heat stress. Although this area of research is still in its infancy, an increasing number of several classes of regulatory ncRNA (i.e., miRNA, siRNA, and lncRNA) related to heat stress responses have been reported. In this mini-review, we discuss our current understanding of the role of ncRNAs in heat stress responses in plants, especially miRNAs, siRNAs, and their targets. For example, the miR398-CSD/CCS-HSF, miR396-WRKY6, miR159-GAMYB, and TAS1-HTT-HSF pathways regulate plant heat tolerance. We highlight the hormone/development-related miRNAs involved in heat stress, and discuss the regulatory networks of miRNA-targets. We also note that DNA methylation and alternative splicing could affect miRNA expression under heat stress, and some lncRNAs could respond to heat stress. Finally, we briefly discuss future prospects concerning the ncRNA-related mechanisms of heat stress responses in plants.
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Affiliation(s)
- Jianguo Zhao
- College of Horticulture and Plant Protection, Yangzhou UniversityYangzhou, China
| | - Qingsong He
- College of Horticulture and Plant Protection, Yangzhou UniversityYangzhou, China
| | - Gang Chen
- College of Bio-Science and Bio-Technology, Yangzhou UniversityYangzhou, China
| | - Li Wang
- College of Horticulture and Plant Protection, Yangzhou UniversityYangzhou, China
| | - Biao Jin
- College of Horticulture and Plant Protection, Yangzhou UniversityYangzhou, China
- Key Laboratory of Crop Genetics and Physiology of Jiangsu ProvinceYangzhou, China
- *Correspondence: Biao Jin
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