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Piya S, Lopes-Caitar VS, Kim W, Pantalone V, Krishnan HB, Hewezi T. Title: Hypermethylation of miRNA Genes During Nodule Development. Front Mol Biosci 2021; 8:616623. [PMID: 33928115 PMCID: PMC8076613 DOI: 10.3389/fmolb.2021.616623] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2020] [Accepted: 02/05/2021] [Indexed: 12/30/2022] Open
Abstract
DNA methylation has recently emerged as a powerful regulatory mechanism controlling the expression of key regulators of various developmental processes, including nodulation. However, the functional role of DNA methylation in regulating the expression of microRNA (miRNA) genes during the formation and development of nitrogen-fixing nodules remains largely unknown. In this study, we profiled DNA methylation patterns of miRNA genes during nodule formation, development, and early senescence stages in soybean (Glycine max) through the analysis of methylC-seq data. Absolute DNA methylation levels in the CG, CHH, and CHH sequence contexts over the promoter and primary transcript regions of miRNA genes were significantly higher in the nodules compared with the corresponding root tissues at these three distinct nodule developmental stages. We identified a total of 82 differentially methylated miRNAs in the nodules compared with roots. Differential DNA methylation of these 82 miRNAs was detected only in the promoter (69), primary transcript region (3), and both in the promoter and primary transcript regions (10). The large majority of these differentially methylated miRNAs were hypermethylated in nodules compared with the corresponding root tissues and were found mainly in the CHH context and showed stage-specific methylation patterns. Differentially methylated regions in the promoters of 25 miRNAs overlapped with transposable elements, a finding that may explain the vulnerability of miRNAs to DNA methylation changes during nodule development. Gene expression analysis of a set of promoter-differentially methylated miRNAs pointed to a negative association between DNA methylation and miRNA expression. Gene Ontology and pathways analyses indicate that changes in DNA methylation of miRNA genes are reprogrammed and contribute to nodule development through indirect regulation of genes involved in cellular processes and pathways with well-established roles in nodulation.
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Affiliation(s)
- Sarbottam Piya
- Department of Plant Sciences, University of Tennessee, Knoxville, TN, United States
| | | | - Won‐Seok Kim
- Plant Science Division, University of Missouri, Columbia, MO, United States
| | - Vince Pantalone
- Department of Plant Sciences, University of Tennessee, Knoxville, TN, United States
| | - Hari B. Krishnan
- Plant Science Division, University of Missouri, Columbia, MO, United States
- Plant Genetics Research, USDA-Agricultural Research Service, Columbia, MO, United States
| | - Tarek Hewezi
- Department of Plant Sciences, University of Tennessee, Knoxville, TN, United States
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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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Wang Q, Yang Y, Lu G, Sun X, Feng Y, Yan S, Zhang H, Jiang Q, Zhang H, Hu Z, Chen R. Genome-wide identification of microRNAs and phased siRNAs in soybean roots under long-term salt stress. Genes Genomics 2020; 42:1239-1249. [PMID: 32939614 DOI: 10.1007/s13258-020-00990-0] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2020] [Accepted: 08/19/2020] [Indexed: 02/06/2023]
Abstract
BACKGROUND Salinity stress, as the key limiting factor for agricultural productivity, can activate a series of molecular responses and alter gene expression in plants. Endogenous regulatory small RNAs, such as microRNAs (miRNAs) and phased siRNAs (phasiRNAs), play crucial roles during stress adaptation and prevent the injury from environmental circumstances. OBJECTIVE To identify long-term salt stress responsive miRNAs and phasiRNAs as well as their associated genes and pathways in soybean roots. METHODS Small RNA and degradome sequencing strategies were applied to genome widely investigate miRNAs and phasiRNAs in soybean roots under control and long-term salt stress conditions. RESULTS In this study, stringent bioinformatic analysis led to the identification of 253 conserved and 38 novel miRNA candidates. Results of expression profiling, target and endogenous target mimics predictions provided valuable clues to their functional roles. Furthermore, 156 genes were identified to be capable of generating 21 nt and 24 nt phasiRNAs, in which 37 candidates were confirmed by degradome data for miRNA-directed cleavage. Approximately 90% of these phasiRNA loci were protein coding genes. And GO enrichment analysis pointed to "signal transduction" and "ADP binding" entries and reflected the functional roles of identified phasiRNA genes. CONCLUSION Taken together, our findings extended the knowledge of salt responsive miRNAs and phasiRNAs in soybean roots, and provided valuable information for a better understanding of the regulatory events caused by small RNAs underlying plant adaptations to long-term salt stress.
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Affiliation(s)
- Qian Wang
- Biotechnology Research Institute, Tianjin Academy of Agricultural Sciences, Tianjin, 300381, China
| | - Yingxia Yang
- Biotechnology Research Institute, Tianjin Academy of Agricultural Sciences, Tianjin, 300381, China
| | - Guoqing Lu
- Biotechnology Research Institute, Tianjin Academy of Agricultural Sciences, Tianjin, 300381, China
| | - Xianjun Sun
- The National Key Facilities for Crop Genetic Resources and Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Youren Feng
- Tianjin Academy of Agricultural Sciences, Tianjin, 300192, China
| | - Shuangyong Yan
- Tianjin Key Laboratory of Crop Genetics and Breeding, Tianjin Crop Research Institute, Tianjin Academy of Agricultural Sciences, Tianjin, 300384, China
| | - Huiyuan Zhang
- The National Key Facilities for Crop Genetic Resources and Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Qiyan Jiang
- The National Key Facilities for Crop Genetic Resources and Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Hui Zhang
- The National Key Facilities for Crop Genetic Resources and Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Zheng Hu
- The National Key Facilities for Crop Genetic Resources and Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China.
| | - Rui Chen
- Biotechnology Research Institute, Tianjin Academy of Agricultural Sciences, Tianjin, 300381, China.
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Ye W, Jiang J, Lin Y, Yeh KW, Lai Z, Xu X, Oelmüller R. Colonisation of Oncidium orchid roots by the endophyte Piriformospora indica restricts Erwinia chrysanthemi infection, stimulates accumulation of NBS-LRR resistance gene transcripts and represses their targeting micro-RNAs in leaves. BMC PLANT BIOLOGY 2019; 19:601. [PMID: 31888486 PMCID: PMC6937650 DOI: 10.1186/s12870-019-2105-3] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/28/2019] [Accepted: 10/28/2019] [Indexed: 05/30/2023]
Abstract
BACKGROUND Erwinia chrysanthemi (Ec) is a destructive pathogen which causes soft-rot diseases in diverse plant species including orchids. We investigated whether colonization of Oncidium roots by the endophytic fungus Piriformospora indica (Pi) restricts Ec-induced disease development in leaves, and whether this might be related to the regulation of nucleotide binding site-leucine rich repeat (NBS-LRR) Resistance (R) genes. RESULTS Root colonization of Oncidium stackings by Pi restricts progression of Ec-induced disease development in the leaves. Since Pi does not inhibit Ec growth on agar plates, we tested whether NBS-LRR R gene transcripts and the levels of their potential target miRNAs in Oncidium leaves might be regulated by Pi. Using bioinformatic tools, we first identified NBS-LRR R gene sequences from Oncidium, which are predicted to be targets of miRNAs. Among them, the expression of two R genes was repressed and the accumulation of several regulatory miRNA stimulated by Ec in the leaves of Oncidium plants. This correlated with the progression of disease development, jasmonic and salicylic acid accumulation, ethylene synthesis and H2O2 production after Ec infection of Oncidium leaves. Interestingly, root colonization by Pi restricted disease development in the leaves, and this was accompanied by higher expression levels of several defense-related R genes and lower expression level of their target miRNA. CONCLUSION Based on these data we propose that Pi controls the levels of NBS-LRR R mRNAs and their target miRNAs in leaves. This regulatory circuit correlates with the protection of Oncidium plants against Ec infection, and molecular and biochemical investigations will demonstrate in the future whether, and if so, to what extent these two observations are related to each other.
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Affiliation(s)
- Wei Ye
- Sanming Academy of Agricultural Sciences, Sanming, Fujian China
| | - Jinlan Jiang
- Sanming Academy of Agricultural Sciences, Sanming, Fujian China
| | - Yuling Lin
- Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, Fujian China
| | - Kai-Wun Yeh
- Matthias-Schleiden-Institute, Plant Physiology, Friedrich Schiller University Jena, Jena, Germany
| | - Zhongxiong Lai
- Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, Fujian China
| | - Xuming Xu
- Sanming Academy of Agricultural Sciences, Sanming, Fujian China
| | - Ralf Oelmüller
- Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, Fujian China
- Matthias-Schleiden-Institute, Plant Physiology, Friedrich Schiller University Jena, Jena, Germany
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5
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Molecular basis of transitivity in plant RNA silencing. Mol Biol Rep 2019; 46:4645-4660. [DOI: 10.1007/s11033-019-04866-9] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2018] [Accepted: 05/09/2019] [Indexed: 12/11/2022]
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Bao D, Ganbaatar O, Cui X, Yu R, Bao W, Falk BW, Wuriyanghan H. Down-regulation of genes coding for core RNAi components and disease resistance proteins via corresponding microRNAs might be correlated with successful Soybean mosaic virus infection in soybean. MOLECULAR PLANT PATHOLOGY 2018; 19:948-960. [PMID: 28695996 PMCID: PMC6638018 DOI: 10.1111/mpp.12581] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/19/2017] [Revised: 06/30/2017] [Accepted: 07/06/2017] [Indexed: 05/20/2023]
Abstract
Plants protect themselves from virus infections by several different defence mechanisms. RNA interference (RNAi) is one prominent antiviral mechanism, which requires the participation of AGO (Argonaute) and Dicer/DCL (Dicer-like) proteins. Effector-triggered immunity (ETI) is an antiviral mechanism mediated by resistance (R) genes, most of which encode nucleotide-binding site-leucine-rich repeat (NBS-LRR) family proteins. MicroRNAs (miRNAs) play important regulatory roles in plants, including the regulation of host defences. Soybean mosaic virus (SMV) is the most common virus in soybean and, in this work, we identified dozens of SMV-responsive miRNAs by microarray analysis in an SMV-susceptible soybean line. Amongst the up-regulated miRNAs, miR168a, miR403a, miR162b and miR1515a predictively regulate the expression of AGO1, AGO2, DCL1 and DCL2, respectively, and miR1507a, miR1507c and miR482a putatively regulate the expression of several NBS-LRR family disease resistance genes. The regulation of target gene expression by these seven miRNAs was validated by both transient expression assays and RNA ligase-mediated rapid amplification of cDNA ends (RLM-RACE) experiments. Transcript levels for AGO1, DCL1, DCL2 and five NBS-LRR family genes were repressed at different time points after SMV infection, whereas the corresponding miRNA levels were up-regulated at these same time points. Furthermore, inhibition of miR1507a, miR1507c, miR482a, miR168a and miR1515a by short tandem target mimic (STTM) technology compromised SMV infection efficiency in soybean. Our results imply that SMV can counteract soybean defence responses by the down-regulation of several RNAi pathway genes and NBS-LRR family resistance genes via the induction of the accumulation of their corresponding miRNA levels.
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Affiliation(s)
- Duran Bao
- School of Life Sciences, University of Inner MongoliaHohhotInner Mongolia 010021, China
| | - Oyunchuluun Ganbaatar
- School of Life Sciences, University of Inner MongoliaHohhotInner Mongolia 010021, China
| | - Xiuqi Cui
- School of Life Sciences, University of Inner MongoliaHohhotInner Mongolia 010021, China
| | - Ruonan Yu
- School of Life Sciences, University of Inner MongoliaHohhotInner Mongolia 010021, China
| | - Wenhua Bao
- School of Life Sciences, University of Inner MongoliaHohhotInner Mongolia 010021, China
| | - Bryce W. Falk
- Department of Plant PathologyUniversity of California DavisDavisCA 95616USA
| | - Hada Wuriyanghan
- School of Life Sciences, University of Inner MongoliaHohhotInner Mongolia 010021, China
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7
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Xu J, Li Y, Wang Y, Liu X, Zhu XG. Altered expression profiles of microRNA families during de-etiolation of maize and rice leaves. BMC Res Notes 2017; 10:108. [PMID: 28235420 PMCID: PMC5324284 DOI: 10.1186/s13104-016-2367-x] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2016] [Accepted: 12/28/2016] [Indexed: 01/08/2023] Open
Abstract
BACKGROUND MicroRNAs (miRNAs) are highly conserved small non-coding RNAs that play important regulatory roles in plants. Although many miRNA families are sequentially and functionally conserved across plant kingdoms (Dezulian et al. in Genome Biol 13, 2005), they still differ in many aspects such as family size, average length, genomic loci etc. (Unver et al. in Int J Plant Genomics, 2009). RESULTS In this study, we investigated changes of miRNA expression profiles during greening process of etiolated seedlings of Oryza sativa (C3) and Zea mays (C4) to explore conserved and species-specific characteristics of miRNAs between these two species. Futhermore, we predicted 47 and 42 candidate novel miRNAs using parameterized monocot specific miRDeep2 pipeline in maize and rice respectively. Potential targets of miRNAs comprising both mRNA and long non-coding RNA (lncRNA) were examined to clarify potential regulation of photosynthesis. Based on our result, two putative positive Kranz regulators reported by Wang et al. (2010) were predicted as potential targets of miR156. A few photosynthesis related genes such as sulfate adenylytransferase (APS3), chlorophyll a/b binding family protein etc. were suggested to be regulated by miRNAs. However, no C4 shuttle genes were predicted to be direct targets of either known or candidate novel miRNAs. CONCLUSIONS This study provided the comprehensive list of miRNA that showed altered expression during the de-etiolation process and a number of candidate miRNAs that might play regulatory roles in C3 and C4 photosynthesis.
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Affiliation(s)
- Jiajia Xu
- Key Laboratory of Computational Biology and Partner Institute for Computational Biology, Chinese Academy of Sciences, Shanghai, China
| | - Yuanyuan Li
- Key Laboratory of Computational Biology and Partner Institute for Computational Biology, Chinese Academy of Sciences, Shanghai, China
| | - Yaling Wang
- Key Laboratory of Computational Biology and Partner Institute for Computational Biology, Chinese Academy of Sciences, Shanghai, China
| | - Xinyu Liu
- Key Laboratory of Computational Biology and Partner Institute for Computational Biology, Chinese Academy of Sciences, Shanghai, China
| | - Xin-Guang Zhu
- Key Laboratory of Computational Biology and Partner Institute for Computational Biology, Chinese Academy of Sciences, Shanghai, China
- State Key Laboratory of Hybrid Rice Research, Shanghai Institute of Biological Sciences, Chinese Academy of Sciences, Shanghai, China
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8
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Liu T, Fang C, Ma Y, Shen Y, Li C, Li Q, Wang M, Liu S, Zhang J, Zhou Z, Yang R, Wang Z, Tian Z. Global investigation of the co-evolution of MIRNA genes and microRNA targets during soybean domestication. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2016; 85:396-409. [PMID: 26714457 DOI: 10.1111/tpj.13113] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/26/2015] [Revised: 11/26/2015] [Accepted: 12/21/2015] [Indexed: 05/24/2023]
Abstract
Although the selection of coding genes during plant domestication has been well studied, the evolution of MIRNA genes (MIRs) and the interaction between microRNAs (miRNAs) and their targets in this process are poorly understood. Here, we present a genome-wide survey of the selection of MIRs and miRNA targets during soybean domestication and improvement. Our results suggest that, overall, MIRs have higher evolutionary rates than miRNA targets. Nonetheless, they do demonstrate certain similar evolutionary patterns during soybean domestication: MIRs and miRNA targets with high expression and duplication status, and with greater numbers of partners, exhibit lower nucleotide divergence than their counterparts without these characteristics, suggesting that expression level, duplication status, and miRNA-target interaction are essential for evolution of MIRs and miRNA targets. Further investigation revealed that miRNA-target pairs that are subjected to strong purifying selection have greater similarities than those that exhibited genetic diversity. Moreover, mediated by domestication and improvement, the similarities of a large number of miRNA-target pairs in cultivated soybean populations were increased compared to those in wild soybeans, whereas a small number of miRNA-target pairs exhibited decreased similarity, which may be associated with the adoption of particular domestication traits. Taken together, our results shed light on the co-evolution of MIRs and miRNA targets during soybean domestication.
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Affiliation(s)
- Tengfei Liu
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Chao Fang
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Yanming Ma
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
- Beijing University of Agriculture, Beijing, China
| | - Yanting Shen
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Congcong Li
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Qing Li
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Min Wang
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Shulin Liu
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Jixiang Zhang
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Zhengkui Zhou
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
| | - Rui Yang
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
| | - Zheng Wang
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
| | - Zhixi Tian
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
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Ding X, Li J, Zhang H, He T, Han S, Li Y, Yang S, Gai J. Identification of miRNAs and their targets by high-throughput sequencing and degradome analysis in cytoplasmic male-sterile line NJCMS1A and its maintainer NJCMS1B of soybean. BMC Genomics 2016; 17:24. [PMID: 26729289 PMCID: PMC4700598 DOI: 10.1186/s12864-015-2352-0] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2015] [Accepted: 12/21/2015] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Cytoplasmic male sterility (CMS) provides crucial breeding materials that facilitate hybrid seed production in various crops, and thus plays an important role in the study of hybrid vigor (heterosis), in plants. However, the CMS regulatory network in soybean remains unclear. MicroRNAs (miRNAs) play crucial roles in flower and pollen development by targeting genes that regulate their expression in plants. To identify the miRNAs and their targets that exist in the soybean CMS line NJCMS1A and its maintainer NJCMS1B, high-throughput sequencing and degradome analysis were conducted in this study. RESULTS Two small RNA libraries were constructed from the flower buds of the soybean CMS line NJCMS1A and its maintainer NJCMS1B. A total of 105 new miRNAs present on the other arm of known pre-miRNAs, 23 new miRNA members, 158 novel miRNAs and 160 high-confidence soybean miRNAs were identified using high-throughput sequencing. Among the identified miRNAs, 101 differentially expressed miRNAs with greater than two-fold changes between NJCMS1A and NJCMS1B were discovered. The different expression levels of selected miRNAs were confirmed by stem-loop quantitative real-time PCR. A degradome analysis showed that 856 targets were predicted to be targeted by 296 miRNAs, including a squamosa promoter-binding protein-like transcription factor family protein, a pentatricopeptide repeat-containing protein, and an auxin response factor, which were previously shown to be involved in floral organ or anther development in plants. Additionally, some targets, including a MADS-box transcription factor, NADP-dependent isocitrate dehydrogenase and NADH-ubiquinone oxidoreductase 24 kDa subunit, were identified, and they may have some relationship with the programmed cell death, reactive oxygen species accumulation and energy deficiencies, which might lead to soybean male sterility. CONCLUSIONS The present study is the first to use deep sequencing technology to identify miRNAs and their targets in the flower buds of the soybean CMS line NJCMS1A and its maintainer NJCMS1B. The results revealed that the miRNAs might participate in flower and pollen development, which could facilitate our understanding of the molecular mechanisms behind CMS in soybean.
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Affiliation(s)
- Xianlong Ding
- Soybean Research Institute, National Center for Soybean Improvement, MOA Key Laboratory of Biology and Genetic Improvement of Soybean (General), State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, Jiangsu, 210095, China.
| | - Jiajia Li
- Soybean Research Institute, National Center for Soybean Improvement, MOA Key Laboratory of Biology and Genetic Improvement of Soybean (General), State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, Jiangsu, 210095, China.
| | - Hao Zhang
- Soybean Research Institute, National Center for Soybean Improvement, MOA Key Laboratory of Biology and Genetic Improvement of Soybean (General), State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, Jiangsu, 210095, China.
| | - Tingting He
- Soybean Research Institute, National Center for Soybean Improvement, MOA Key Laboratory of Biology and Genetic Improvement of Soybean (General), State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, Jiangsu, 210095, China.
| | - Shaohuai Han
- Soybean Research Institute, National Center for Soybean Improvement, MOA Key Laboratory of Biology and Genetic Improvement of Soybean (General), State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, Jiangsu, 210095, China.
| | - Yanwei Li
- Soybean Research Institute, National Center for Soybean Improvement, MOA Key Laboratory of Biology and Genetic Improvement of Soybean (General), State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, Jiangsu, 210095, China.
| | - Shouping Yang
- Soybean Research Institute, National Center for Soybean Improvement, MOA Key Laboratory of Biology and Genetic Improvement of Soybean (General), State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, Jiangsu, 210095, China.
| | - Junyi Gai
- Soybean Research Institute, National Center for Soybean Improvement, MOA Key Laboratory of Biology and Genetic Improvement of Soybean (General), State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, Jiangsu, 210095, China.
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10
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Jacobs TB, Lawler NJ, LaFayette PR, Vodkin LO, Parrott WA. Simple gene silencing using the trans-acting siRNA pathway. PLANT BIOTECHNOLOGY JOURNAL 2016; 14:117-27. [PMID: 25816689 DOI: 10.1111/pbi.12362] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/19/2014] [Revised: 02/14/2015] [Accepted: 02/19/2015] [Indexed: 05/27/2023]
Abstract
In plants, particular micro-RNAs (miRNAs) induce the production of a class of small interfering RNAs (siRNA) called trans-acting siRNA (ta-siRNA) that lead to gene silencing. A single miRNA target is sufficient for the production of ta-siRNAs, which target can be incorporated into a vector to induce the production of siRNAs, and ultimately gene silencing. The term miRNA-induced gene silencing (MIGS) has been used to describe such vector systems in Arabidopsis. Several ta-siRNA loci have been identified in soybean, but, prior to this work, few of the inducing miRNAs have been experimentally validated, much less used to silence genes. Nine ta-siRNA loci and their respective miRNA targets were identified, and the abundance of the inducing miRNAs varies dramatically in different tissues. The miRNA targets were experimentally verified by silencing a transgenic GFP gene and two endogenous genes in hairy roots and transgenic plants. Small RNAs were produced in patterns consistent with the utilization of the ta-siRNA pathway. A side-by-side experiment demonstrated that MIGS is as effective at inducing gene silencing as traditional hairpin vectors in soybean hairy roots. Soybean plants transformed with MIGS vectors produced siRNAs and silencing was observed in the T1 generation. These results complement previous reports in Arabidopsis by demonstrating that MIGS is an efficient way to produce siRNAs and induce gene silencing in other species, as shown with soybean. The miRNA targets identified here are simple to incorporate into silencing vectors and offer an effective and efficient alternative to other gene silencing strategies.
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Affiliation(s)
- Thomas B Jacobs
- Institute for Plant Breeding, Genetics and Genomics, University of Georgia, Athens, GA, USA
- Center for Applied Genetic Technologies, University of Georgia, Athens, GA, USA
| | - Noah J Lawler
- Center for Applied Genetic Technologies, University of Georgia, Athens, GA, USA
| | - Peter R LaFayette
- Center for Applied Genetic Technologies, University of Georgia, Athens, GA, USA
- Department of Crop and Soil Sciences, University of Georgia, Athens, GA, USA
| | - Lila O Vodkin
- Department of Crop Sciences, University of Illinois, Urbana, IL, USA
| | - Wayne A Parrott
- Institute for Plant Breeding, Genetics and Genomics, University of Georgia, Athens, GA, USA
- Center for Applied Genetic Technologies, University of Georgia, Athens, GA, USA
- Department of Crop and Soil Sciences, University of Georgia, Athens, GA, USA
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11
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Zhao M, Cai C, Zhai J, Lin F, Li L, Shreve J, Thimmapuram J, Hughes TJ, Meyers BC, Ma J. Coordination of MicroRNAs, PhasiRNAs, and NB-LRR Genes in Response to a Plant Pathogen: Insights from Analyses of a Set of Soybean Rps Gene Near-Isogenic Lines. THE PLANT GENOME 2015; 8:eplantgenome2014.09.0044. [PMID: 33228285 DOI: 10.3835/plantgenome2014.09.0044] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/04/2014] [Accepted: 11/14/2014] [Indexed: 06/11/2023]
Abstract
Disease-related genes, particularly the nucleotide binding site (NB)-leucine-rich repeat (LRR) class of R plant genes can be triggered by microRNAs (miRNAs) to generate phased small interfering RNAs (phasiRNAs), which could reduce the transcript levels of their targets. However, how global changes in NB-LRR transcript levels coordinate with changes in miRNA and phasiRNA levels in defense responses remains largely unknown. Here, we investigated changes in the relative abundance of small RNAs (sRNAs), with a focus on miRNAs and phasiRNAs and their potential targets in response to the pathogen Phytophthora sojae in the susceptible soybean [Glycine max (L.) Merr.] 'Williams' and nine resistant near-isogenic lines (NILs), each carrying a unique resistance to P. sojae (Rps) gene. In total, 369 distinct miRNAs, including 78 new ones, were identified in the 10 soybean lines. The majority of miRNAs were downregulated by the pathogen. Of the 525 NB-LRR genes found in the soybean reference genome, 257 were predicted to be the targets of eight abundant miRNA families and 126 (dubbed phasi-NB-LRRs or pNLs) were predicted to have produced phasiRNAs. Upregulation of 15 phasi-NB-LRRs was associated with downregulation of their corresponding phasiRNAs in the NILs; these phasiRNAs were predicted to regulate 75 additional NB-LRRs in trans. In addition, we identified putative 24-nucleotide (nt) phasiRNAs from transposons, possibly representing a novel general epigenetic mechanism for regulation of transposon activity under biotic stresses. Together, these observations suggest that miRNAs and phasiRNAs play an important role in response to plant pathogens through complex, multiple layers of post-transcriptional regulation.
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Affiliation(s)
- Meixia Zhao
- Dep. of Agronomy, Purdue Univ., West Lafayette, IN, 47907
| | - Chunmei Cai
- College of Life Sciences, Qingdao Agricultural Univ., Chengyang District, Qingdao, 266109, China
| | - Jixian Zhai
- Dep. of Plant and Soil Sciences, and Delaware Biotechnology Institute, Univ. of Delaware, Newark, DE, 19716
| | - Feng Lin
- Dep. of Agronomy, Purdue Univ., West Lafayette, IN, 47907
| | - Linghong Li
- College of Life Sciences, Qingdao Agricultural Univ., Chengyang District, Qingdao, 266109, China
| | - Jacob Shreve
- Bioinformatics Core Facility, Purdue Univ., West Lafayette, IN, 47907
| | | | - Teresa J Hughes
- USDA-ARS, Crop Production and Pest Control Research Unit, West Lafayette, IN, 47907
- Monsanto Company, St. Louis, MO, 63167
| | - Blake C Meyers
- Dep. of Plant and Soil Sciences, and Delaware Biotechnology Institute, Univ. of Delaware, Newark, DE, 19716
| | - Jianxin Ma
- Dep. of Agronomy, Purdue Univ., West Lafayette, IN, 47907
- College of Life Sciences, Qingdao Agricultural Univ., Chengyang District, Qingdao, 266109, China
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12
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Lin Y, Lin L, Lai R, Liu W, Chen Y, Zhang Z, XuHan X, Lai Z. MicroRNA390-Directed TAS3 Cleavage Leads to the Production of tasiRNA-ARF3/4 During Somatic Embryogenesis in Dimocarpus longan Lour. FRONTIERS IN PLANT SCIENCE 2015; 6:1119. [PMID: 26734029 PMCID: PMC4680215 DOI: 10.3389/fpls.2015.01119] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/22/2015] [Accepted: 11/26/2015] [Indexed: 05/18/2023]
Abstract
Trans-acting short-interfering RNAs (tasiRNAs) originate from TAS3 families through microRNA (miRNA) 390-guided cleavage of primary transcripts and target auxin response factors (ARF3/-4), which are involved in the normal development of lateral roots and flowers in plants. However, their roles in embryo development are still unclear. Here, the pathway miR390-TAS3-ARF3/-4 was identified systematically for the first time during somatic embryo development in Dimocarpus longan. We identified the miR390 primary transcript and promoter. The promoter contained cis-acting elements responsive to stimuli such as light, salicylic acid, anaerobic induction, fungal elicitor, circadian control, and heat stress. The longan TAS3 transcript, containing two miR390-binding sites, was isolated; the miR390- guided cleavage site located near the 3' end of the TAS3 transcript was verified. Eight TAS3-tasiRNAs with the 21-nucleotides phase were found among longan small RNA data, further confirming that miR390-directed TAS3 cleavage leads to the production of tasiRNA in longan. Among them, TAS3_5'D5+ and 5'D6+ tasiRNAs were highly abundant, and verified to target ARF3 and -4, implying that miR390-guided TAS3 cleavage with 21-nucleotides phase leading to the production of tasiRNA-ARF is conserved in plants. Pri-miR390 was highly expressed in friable-embryogenic callus (EC), and less expressed in incomplete compact pro-embryogenic cultures, while miR390 showed its lowest expression in EC and highest expression in torpedo-shaped embryos (TEs). DlTAS3 and DlARF4 both exhibited their lowest expressions in EC, and reached their peaks in the globular embryos stage, which were mainly inversely proportional to the expression of miR390, especially at the globular embryos to cotyledonary embryos (CEs) stages. While DlARF3 showed little variation from the EC to TEs stages, and exhibited its lowest expression in the CEs stage. There was a general lack of correlation between the expressions of DlARF3 and miR390. In addition, pri-miR390, DlTAS3, DlARF3 and -4 were up-regulated by 2,4-D in a concentration-dependent manner. They were also preferentially expressed in roots, pulp, and seeds of 'Sijimi' longan, implying their extended roles in the development of longan roots and fruit. This study provided insights into a possible role of miR390-tasiRNAs-ARF in plant somatic embryo development.
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13
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Wong J, Gao L, Yang Y, Zhai J, Arikit S, Yu Y, Duan S, Chan V, Xiong Q, Yan J, Li S, Liu R, Wang Y, Tang G, Meyers BC, Chen X, Ma W. Roles of small RNAs in soybean defense against Phytophthora sojae infection. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2014; 79:928-40. [PMID: 24944042 PMCID: PMC5137376 DOI: 10.1111/tpj.12590] [Citation(s) in RCA: 93] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/02/2013] [Revised: 04/11/2012] [Accepted: 06/11/2014] [Indexed: 05/06/2023]
Abstract
The genus Phytophthora consists of many notorious pathogens of crops and forestry trees. At present, battling Phytophthora diseases is challenging due to a lack of understanding of their pathogenesis. We investigated the role of small RNAs in regulating soybean defense in response to infection by Phytophthora sojae, the second most destructive pathogen of soybean. Small RNAs, including microRNAs (miRNAs) and small interfering RNAs (siRNAs), are universal regulators that repress target gene expression in eukaryotes. We identified known and novel small RNAs that differentially accumulated during P. sojae infection in soybean roots. Among them, miR393 and miR166 were induced by heat-inactivated P. sojae hyphae, indicating that they may be involved in soybean basal defense. Indeed, knocking down the level of mature miR393 led to enhanced susceptibility of soybean to P. sojae; furthermore, the expression of isoflavonoid biosynthetic genes was drastically reduced in miR393 knockdown roots. These data suggest that miR393 promotes soybean defense against P. sojae. In addition to miRNAs, P. sojae infection also resulted in increased accumulation of phased siRNAs (phasiRNAs) that are predominantly generated from canonical resistance genes encoding nucleotide binding-leucine rich repeat proteins and genes encoding pentatricopeptide repeat-containing proteins. This work identifies specific miRNAs and phasiRNAs that regulate defense-associated genes in soybean during Phytophthora infection.
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Affiliation(s)
- James Wong
- Department of Plant Pathology and Microbiology, University of California, Riverside, CA 92521, USA
- Center for Plant Cell Biology, University of California, Riverside, CA 92521, USA
| | - Lei Gao
- Center for Plant Cell Biology, University of California, Riverside, CA 92521, USA
- Department of Botany and Plant Sciences, University of California, Riverside, CA 92521, USA
| | - Yang Yang
- Department of Computer Science and Engineering, Shanghai Maritime University, 1550 Haigang Ave, Lingang New City, Shanghai 201306 China
| | - Jixian Zhai
- Department of Plant & Soil Sciences, University of Delaware, Newark, DE 19716, USA
| | - Siwaret Arikit
- Department of Plant & Soil Sciences, University of Delaware, Newark, DE 19716, USA
| | - Yu Yu
- Center for Plant Cell Biology, University of California, Riverside, CA 92521, USA
- Department of Botany and Plant Sciences, University of California, Riverside, CA 92521, USA
| | - Shuyi Duan
- Department of Plant Pathology and Microbiology, University of California, Riverside, CA 92521, USA
- Department of Plant Pathology, Nanjing Agricultural University, No. 1 Weigang, Nanjing 210095, China
| | - Vicky Chan
- Department of Plant Pathology and Microbiology, University of California, Riverside, CA 92521, USA
| | - Qin Xiong
- Department of Plant Pathology and Microbiology, University of California, Riverside, CA 92521, USA
- Department of Plant Pathology, Nanjing Agricultural University, No. 1 Weigang, Nanjing 210095, China
| | - Jun Yan
- Department of Biological Sciences, Michigan Technological University, Houghton, MI 49931, USA
| | - Shengben Li
- Center for Plant Cell Biology, University of California, Riverside, CA 92521, USA
- Department of Botany and Plant Sciences, University of California, Riverside, CA 92521, USA
| | - Renyi Liu
- Department of Botany and Plant Sciences, University of California, Riverside, CA 92521, USA
| | - Yuanchao Wang
- Department of Plant Pathology, Nanjing Agricultural University, No. 1 Weigang, Nanjing 210095, China
| | - Guiliang Tang
- Department of Biological Sciences, Michigan Technological University, Houghton, MI 49931, USA
| | - Blake C. Meyers
- Department of Computer Science and Engineering, Shanghai Maritime University, 1550 Haigang Ave, Lingang New City, Shanghai 201306 China
| | - Xuemei Chen
- Center for Plant Cell Biology, University of California, Riverside, CA 92521, USA
- Department of Botany and Plant Sciences, University of California, Riverside, CA 92521, USA
- Howard Hughes Medical Institute, 4000 Jones Bridge Road, Chevy Chase, MD 20815, USA
| | - Wenbo Ma
- Department of Plant Pathology and Microbiology, University of California, Riverside, CA 92521, USA
- Center for Plant Cell Biology, University of California, Riverside, CA 92521, USA
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14
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Han YQ, Hu Z, Zheng DF, Gao YM. Analysis of promoters of microRNAs from a Glycine max degradome library. J Zhejiang Univ Sci B 2014; 15:125-32. [PMID: 24510705 PMCID: PMC3924388 DOI: 10.1631/jzus.b1300179] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2013] [Accepted: 08/25/2013] [Indexed: 11/11/2022]
Abstract
OBJECTIVE MicroRNAs (miRNAs) are genome-encoded, small non-coding RNAs that play important functions in development, biotic and abiotic stress responses, and other processes. Our aim was to explore the regulation of miRNA expression. METHODS We used bioinformatics methods to predict the core promoters of 440 miRNAs identified from a soybean (Glycine max) degradome library and to analyze cis-acting elements for 369 miRNAs. RESULTS The prediction results showed that 83.86% of the 440 miRNAs contained promoters in their upstream sequences, and 8.64% (38 loci) in their downstream sequences. The distributions of two core promoter elements, TATA-boxes and transcription start sites (TSSs), were similar. The cis-acting elements were examined to provide clues to the function and regulation of spatiotemporal expression of the miRNAs. Analyses of miRNA cis-elements and targets indicated a potential auxin response factor (ARF)- and gibberellin response factor (GARF)-mediated negative feedback loop for miRNA expression. CONCLUSIONS The features of miRNAs from a Glycine max degradome library obtained here provide insights into the transcription regulation and functions of miRNAs in soybean.
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Affiliation(s)
- Yi-qiang Han
- College of Life Science and Technology, Heilongjiang Bayi Agricultural University, Daqing 163319, China
| | - Zheng Hu
- The National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Dian-feng Zheng
- College of Agronomy, Heilongjiang Bayi Agricultural University, Daqing 163319, China
| | - Ya-mei Gao
- College of Life Science and Technology, Heilongjiang Bayi Agricultural University, Daqing 163319, China
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15
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Ye CY, Xu H, Shen E, Liu Y, Wang Y, Shen Y, Qiu J, Zhu QH, Fan L. Genome-wide identification of non-coding RNAs interacted with microRNAs in soybean. FRONTIERS IN PLANT SCIENCE 2014; 5:743. [PMID: 25566308 PMCID: PMC4274897 DOI: 10.3389/fpls.2014.00743] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/24/2014] [Accepted: 12/05/2014] [Indexed: 05/19/2023]
Abstract
A wide range of RNA species interacting with microRNAs (miRNAs) form a complex gene regulation network and play vital roles in diverse biological processes. In this study, we performed a genome-wide identification of endogenous target mimics (eTMs) for miRNAs and phased-siRNA-producing loci (PHAS) in soybean with a focus on those involved in lipid metabolism. The results showed that a large number of eTMs and PHAS genes could be found in soybean. Additionally, we found that lipid metabolism related genes were potentially regulated by 28 miRNAs, and nine of them were potentially further regulated by a number of eTMs with expression evidence. Thirty-three miRNAs were found to trigger production of phasiRNAs from 49 PHAS genes, which were able to target lipid metabolism related genes. Degradome data supported miRNA- and/or phasiRNA-mediated cleavage of genes involved in lipid metabolism. Most eTMs for miRNAs involved in lipid metabolism and phasiRNAs targeting lipid metabolism related genes showed a tissue-specific expression pattern. Our bioinformatical evidences suggested that lipid metabolism in soybean is potentially regulated by a complex non-coding network, including miRNAs, eTMs, and phasiRNAs, and the results extended our knowledge on functions of non-coding RNAs.
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Affiliation(s)
- Chu-Yu Ye
- Department of Agronomy, Institute of Crop Sciences and Institute of Bioinformatics, College of Agriculture and Biotechnology, Zhejiang UniversityHangzhou, China
| | - Hao Xu
- Guhe InformationHangzhou, China
| | - Enhui Shen
- Department of Agronomy, Institute of Crop Sciences and Institute of Bioinformatics, College of Agriculture and Biotechnology, Zhejiang UniversityHangzhou, China
| | - Yang Liu
- Department of Agronomy, Institute of Crop Sciences and Institute of Bioinformatics, College of Agriculture and Biotechnology, Zhejiang UniversityHangzhou, China
| | - Yu Wang
- Department of Agronomy, Institute of Crop Sciences and Institute of Bioinformatics, College of Agriculture and Biotechnology, Zhejiang UniversityHangzhou, China
| | - Yifei Shen
- Department of Agronomy, Institute of Crop Sciences and Institute of Bioinformatics, College of Agriculture and Biotechnology, Zhejiang UniversityHangzhou, China
| | - Jie Qiu
- Department of Agronomy, Institute of Crop Sciences and Institute of Bioinformatics, College of Agriculture and Biotechnology, Zhejiang UniversityHangzhou, China
| | - Qian-Hao Zhu
- Commonwealth Scientific and Industrial Research Organisation, Agriculture FlagshipCanberra, ACT, Australia
| | - Longjiang Fan
- Department of Agronomy, Institute of Crop Sciences and Institute of Bioinformatics, College of Agriculture and Biotechnology, Zhejiang UniversityHangzhou, China
- *Correspondence: Longjiang Fan, Department of Agronomy, Institute of Crop Sciences and Institute of Bioinformatics, College of Agriculture and Biotechnology, Zhejiang University, 866 Yuhangtang Rd., Hangzhou 310058, China e-mail:
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16
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Rock CD. Trans-acting small interfering RNA4: key to nutraceutical synthesis in grape development? TRENDS IN PLANT SCIENCE 2013; 18:601-10. [PMID: 23993483 PMCID: PMC3818397 DOI: 10.1016/j.tplants.2013.07.006] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/02/2013] [Revised: 07/12/2013] [Accepted: 07/31/2013] [Indexed: 05/19/2023]
Abstract
The facility and versatility of microRNAs (miRNAs) to evolve and change likely underlies how they have become dominant constituents of eukaryotic genomes. In this opinion article I propose that trans-acting small interfering RNA gene 4 (TAS4) evolution may be important for biosynthesis of polyphenolics, arbuscular symbiosis, and bacterial pathogen etiologies. Expression-based and phylogenetic evidence shows that TAS4 targets two novel grape (Vitis vinifera L.) MYB transcription factors (VvMYBA6, VvMYBA7) that spawn phased small interfering RNAs (siRNAs) which probably function in nutraceutical bioflavonoid biosynthesis and fruit development. Characterization of the molecular mechanisms of TAS4 control of plant development and integration into biotic and abiotic stress- and nutrient-signaling regulatory networks has applicability to molecular breeding and the development of strategies for engineering healthier foods.
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Affiliation(s)
- Christopher D Rock
- Department of Biological Sciences, Texas Tech University (TTU), Lubbock, TX 79409-3131, USA.
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17
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Zheng H, Qiyan J, Zhiyong N, Hui Z. Prediction and identification of natural antisense transcripts and their small RNAs in soybean (Glycine max). BMC Genomics 2013; 14:280. [PMID: 23617936 PMCID: PMC3643859 DOI: 10.1186/1471-2164-14-280] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2012] [Accepted: 04/20/2013] [Indexed: 11/12/2022] Open
Abstract
BACKGROUND Natural antisense transcripts (NATs) are a class of RNAs that contain a sequence complementary to other transcripts. NATs occur widely in eukaryotes and play critical roles in post-transcriptional regulation. Soybean NAT sequences are predicted in the PlantNATsDB, but detailed analyses of these NATs remain to be performed. RESULTS A total of 26,216 NATs, including 994 cis-NATs and 25,222 trans-NATs, were predicted in soybean. Each sense transcript had 1-177 antisense transcripts. We identified 21 trans-NATs using RT-PCR amplification. Additionally, we identified 179 cis-NATs and 6,629 trans-NATs that gave rise to small RNAs; these were enriched in the NAT overlapping region. The most abundant small RNAs were 21, 22, and 24 nt in length. The generation of small RNAs was biased to one stand of the NATs, and the degradation of NATs was biased. High-throughput sequencing of the degradome allowed for the global identification of NAT small interfering RNAs (nat-siRNAs) targets. 446 target genes for 165 of these nat-siRNAs were identified. The nat-siRNA target could be one transcript of a given NAT, or from other gene transcripts. We identified five NAT transcripts containing a hairpin structure that is characteristic of pre-miRNA. We identified a total of 86 microRNA (miRNA) targets that had antisense transcripts in soybean. CONCLUSIONS We globally identified nat-siRNAs, and the targets of nat-siRNAs in soybean. It is likely that the cis-NATs, trans-NATs, nat-siRNAs, miRNAs, and miRNA targets form complex regulatory networks.
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Affiliation(s)
- Hu Zheng
- The National Key Facilities for Crop Genetic Resources and Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Jiang Qiyan
- The National Key Facilities for Crop Genetic Resources and Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Ni Zhiyong
- The National Key Facilities for Crop Genetic Resources and Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Zhang Hui
- The National Key Facilities for Crop Genetic Resources and Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
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