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Zhou S, Huang K, Zhou Y, Hu Y, Xiao Y, Chen T, Yin M, Liu Y, Xu M, Jiang X. Degradome sequencing reveals an integrative miRNA-mediated gene interaction network regulating rice seed vigor. BMC PLANT BIOLOGY 2022; 22:269. [PMID: 35650544 PMCID: PMC9158300 DOI: 10.1186/s12870-022-03645-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/30/2022] [Accepted: 05/11/2022] [Indexed: 05/14/2023]
Abstract
BACKGROUND It is well known that seed vigor is essential for agricultural production and rice (Oryza sativa L.) is one of the most important crops in the world. Though we previously reported that miR164c regulates rice seed vigor, but whether and how other miRNAs cooperate with miR164c to regulate seed vigor is still unknown. RESULTS Based on degradome data of six RNA samples isolated from seeds of the wild-type (WT) indica rice cultivar 'Kasalath' as well as two modified lines in 'Kasalath' background (miR164c-silenced line [MIM164c] and miR164c overexpression line [OE164c]), which were subjected to either no aging treatment or an 8-day artificial aging treatment, 1247 different target transcripts potentially cleaved by 421 miRNAs were identified. The miRNA target genes were functionally annotated via GO and KEGG enrichment analyses. By STRING database assay, a miRNA-mediated gene interaction network regulating seed vigor in rice was revealed, which comprised at least four interconnected pathways: the miR5075-mediated oxidoreductase related pathway, the plant hormone related pathway, the miR164e related pathway, and the previously reported RPS27AA related pathway. Knockout and overexpression of the target gene Os02g0817500 of miR5075 decreased and enhanced seed vigor, respectively. By Y2H assay, the proteins encoded by five seed vigor-related genes, Os08g0295100, Os07g0633100, REFA1, OsPER1 and OsGAPC3, were identified to interact with Os02g0817500. CONCLUSIONS miRNAs cooperate to regulate seed vigor in rice via an integrative gene interaction network comprising miRNA target genes and other functional genes. The result provided a basis for fully understanding the molecular mechanisms of seed vigor regulation.
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Affiliation(s)
- Shiqi Zhou
- College of Life Sciences, Hunan Normal University, Changsha, 410081, China
| | - Kerui Huang
- College of Life Sciences, Hunan Normal University, Changsha, 410081, China
- Hunan Province Key Laboratory of Crop Sterile Germplasm Resource Innovation and Application, Changsha, 410081, China
- College of Life and Environmental Sciences, Hunan University of Arts and Science, Changde, 415000, China
| | - Yan Zhou
- College of Life Sciences, Hunan Normal University, Changsha, 410081, China
| | - Yingqian Hu
- College of Life Sciences, Hunan Normal University, Changsha, 410081, China
| | - Yuchao Xiao
- College of Life Sciences, Hunan Normal University, Changsha, 410081, China
| | - Ting Chen
- College of Life Sciences, Hunan Normal University, Changsha, 410081, China
| | - Mengqi Yin
- College of Life Sciences, Hunan Normal University, Changsha, 410081, China
| | - Yan Liu
- College of Life Sciences, Hunan Normal University, Changsha, 410081, China
| | - Mengliang Xu
- College of Life Sciences, Hunan Normal University, Changsha, 410081, China
- Hunan Province Key Laboratory of Crop Sterile Germplasm Resource Innovation and Application, Changsha, 410081, China
| | - Xiaocheng Jiang
- College of Life Sciences, Hunan Normal University, Changsha, 410081, China.
- Hunan Province Key Laboratory of Crop Sterile Germplasm Resource Innovation and Application, Changsha, 410081, China.
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The complete mitochondrial genome of Choroterpes (Euthralus) yixingensis (Ephemeroptera: Leptophlebiidae) and its mitochondrial protein-coding gene expression under imidacloprid stress. Gene 2021; 800:145833. [PMID: 34274477 DOI: 10.1016/j.gene.2021.145833] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2021] [Revised: 07/06/2021] [Accepted: 07/13/2021] [Indexed: 11/21/2022]
Abstract
As one of the most common benthic invertebrates in freshwater, mayflies are very sensitive to changes in water quality and have high requirements for the water environment to allow their nymphs to successfully live and grow. Neonicotinoids, such as imidacloprid, can enter fresh water and pollute the aquatic environment. The present study had two goals: (1) investigate imidacloprid effects on mayfly larvae Choroterpes (Euthralus) yixingensis, and (2) contribute to the phylogenetic status of Ephemeroptera that has always been controversial. Nymphs were collected from Jinhua, China and exposed to different concentrations imidacloprid (5, 10, 20, and 40 μg/L) in the laboratory. Survival of C. yixingensis nymphs decreased as a function of time and imidacloprid concentration with only ~ 55% survival after 72 h exposure to 40 μg/L imidacloprid. After culture under 40 μg/L imidacloprid for 24 h, the steady state transcript levels of mitochondrial COX3, ND4 and ND4L genes were reduced to just 0.07 ± 0.11, 0.30 ± 0.16, and 0.28 ± 0.13 as compared with respective control values (P < 0.01). Steady state transcript levels of ND4 and ND4L were also significantly reduced in a dose-dependent manner (P < 0.05), suggesting that the steady state transcript pattern of these genes in mayfly nymphs can change in response to different levels of environmental contamination. Hence, the mitochondrial protein-coding genes of mayflies could potentially be developed as biomarkers for water ecotoxicity monitoring in the future. In addition, we used the mitochondrial genome sequence of C. yixingensis for an assessment of the phylogenetic tree of Ephemeroptera. The monophyly of Leptophlebiidae was supported and showed that Leptophlebiidae was a sister group to the clade (Baetidae + Caenidae).
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Genomics and transcriptomics analyses provide insights into the cold adaptation strategies of an Antarctic bacterium, Cryobacterium sp. SO1. Polar Biol 2021. [DOI: 10.1007/s00300-021-02883-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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Won JI, Shin J, Park SY, Yoon J, Jeong DH. Global Analysis of the Human RNA Degradome Reveals Widespread Decapped and Endonucleolytic Cleaved Transcripts. Int J Mol Sci 2020; 21:ijms21186452. [PMID: 32899599 PMCID: PMC7555781 DOI: 10.3390/ijms21186452] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2020] [Revised: 08/28/2020] [Accepted: 09/01/2020] [Indexed: 01/20/2023] Open
Abstract
RNA decay is an important regulatory mechanism for gene expression at the posttranscriptional level. Although the main pathways and major enzymes that facilitate this process are well defined, global analysis of RNA turnover remains under-investigated. Recent advances in the application of next-generation sequencing technology enable its use in order to examine various RNA decay patterns at the genome-wide scale. In this study, we investigated human RNA decay patterns using parallel analysis of RNA end-sequencing (PARE-seq) data from XRN1-knockdown HeLa cell lines, followed by a comparison of steady state and degraded mRNA levels from RNA-seq and PARE-seq data, respectively. The results revealed 1103 and 1347 transcripts classified as stable and unstable candidates, respectively. Of the unstable candidates, we found that a subset of the replication-dependent histone transcripts was polyadenylated and rapidly degraded. Additionally, we identified 380 endonucleolytically cleaved candidates by analyzing the most abundant PARE sequence on a transcript. Of these, 41.4% of genes were classified as unstable genes, which implied that their endonucleolytic cleavage might affect their mRNA stability. Furthermore, we identified 1877 decapped candidates, including HSP90B1 and SWI5, having the most abundant PARE sequences at the 5′-end positions of the transcripts. These results provide a useful resource for further analysis of RNA decay patterns in human cells.
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Affiliation(s)
- Jung-Im Won
- Smart Computing Lab., Hallym University, Chuncheon 24252, Korea or (J.-I.W.); (J.S.)
- Center for Innovation in Engineering Education, Hanyang University, Seoul 04763, Korea
| | - JaeMoon Shin
- Smart Computing Lab., Hallym University, Chuncheon 24252, Korea or (J.-I.W.); (J.S.)
- Database Center for Life Science, Joint Support-Center for Data Science Research, Research Organization of Information and Systems, Kashiwa-Shi, Chiba-Ken 277-0871, Japan
| | - So Young Park
- Department of Life Science and Multidisciplinary Genome Institute, Hallym University, Chuncheon 24252, Korea;
| | - JeeHee Yoon
- School of Software, Hallym University, Chuncheon 24252, Korea
- Correspondence: (J.Y.); (D.-H.J.)
| | - Dong-Hoon Jeong
- Department of Life Science and Multidisciplinary Genome Institute, Hallym University, Chuncheon 24252, Korea;
- Correspondence: (J.Y.); (D.-H.J.)
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Early dynamics of photosynthetic Lhcf2 and Lhcf15 transcription and mRNA stabilities in response to herbivory-related decadienal in Phaeodactylum tricornutum. Sci Rep 2020; 10:2029. [PMID: 32029835 PMCID: PMC7005025 DOI: 10.1038/s41598-020-58885-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2019] [Accepted: 01/21/2020] [Indexed: 12/31/2022] Open
Abstract
Abiotic and biotic stresses widely reduce light harvesting complex (LHC) gene expression in higher plants and algae. However, control mechanisms and functions of these changes are not well understood. During herbivory, marine diatom species release oxylipins that impair grazer reproduction and serve as signaling molecules to nearby undamaged diatoms. To examine LHC mRNA regulation by oxylipin exposure, the diatom Phaeodactylum tricornutum was treated with a sublethal concentration of trans,trans-2,4-decadienal (DD) during the light cycle. Transcriptome analyses revealed extensive suppression of LHC mRNAs and a smaller set of up-regulated LHC mRNAs at 3 h. For two divergently regulated LHCF antennae family mRNAs, in vivo 4-thiouracil metabolic labeling was used to distinguish synthesis and degradation rates. Within 3 h of DD exposure, Lhcf2 mRNA levels and transcription were strongly suppressed and its mRNA half-life decreased. In contrast, Lhcf15 mRNA mainly accumulated between 3-9 h, its transcription increased and its mRNA was highly stabilized. Hence, DD-treated cells utilized transcriptional and mRNA stability control mechanisms which were likely major factors in the differing Lhcf2 and Lhcf15 expression patterns. Widespread LHC mRNA regulation and possible effects on photosynthesis may contribute to enhanced fitness in cells impacted by herbivory and other stresses.
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Nakaminami K, Seki M. RNA Regulation in Plant Cold Stress Response. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2019; 1081:23-44. [PMID: 30288702 DOI: 10.1007/978-981-13-1244-1_2] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
In addition to plants, all organisms react to environmental stimuli via the perception of signals and subsequently respond through alterations of gene expression. However, genes/mRNAs are usually not the functional unit themselves, and instead, resultant protein products with individual functions result in various acquired phenotypes. In order to fully characterize the adaptive responses of plants to environmental stimuli, it is essential to determine the level of proteins, in addition to the regulation of mRNA expression. This regulatory step, which is referred to as "mRNA posttranscriptional regulation," occurs subsequent to mRNA transcription and prior to translation. Although these RNA regulatory mechanisms have been well-studied in many organisms, including plants, it is not fully understood how plants respond to environmental stimuli, such as cold stress, via these RNA regulations.A recent study described several RNA regulatory factors in relation to environmental stress responses, including plant cold stress tolerance. In this chapter, the functions of RNA regulatory factors and comprehensive analyses related to the RNA regulations involved in cold stress response are summarized, such as mRNA maturation, including capping, splicing, polyadenylation of mRNA, and the quality control system of mRNA; mRNA degradation, including the decapping step; and mRNA stabilization. In addition, the putative roles of messenger ribonucleoprotein (mRNP) granules, such as processing bodies (PBs) and stress granules (SGs), which are cytoplasmic particles, are described in relation to RNA regulations under stress conditions. These RNA regulatory systems are important for adjusting or fine-tuning and determining the final levels of mRNAs and proteins in order to adapt or respond to environmental stresses. Collectively, these new areas of study revealed that plants possess precise novel regulatory mechanisms which specifically function in the response to cold stress.
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Affiliation(s)
- Kentaro Nakaminami
- Plant Genomic Network Research Team, RIKEN Center for Sustainable Resource Science, Yokohama, Kanagawa, Japan.
| | - Motoaki Seki
- Plant Genomic Network Research Team, RIKEN Center for Sustainable Resource Science, Yokohama, Kanagawa, Japan
- Plant Epigenome Regulation Laboratory, Cluster for Pioneering Research, RIKEN, Wako, Saitama, Japan
- Kihara Institute for Biological Research, Yokohama City University, Yokohama, Kanagawa, Japan
- Core Research for Evolutional Science and Technology (CREST), Japan Science and Technology (JST), Kawaguchi, Saitama, Japan
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Franke KR, Schmidt SA, Park S, Jeong DH, Accerbi M, Green PJ. Analysis of Brachypodium miRNA targets: evidence for diverse control during stress and conservation in bioenergy crops. BMC Genomics 2018; 19:547. [PMID: 30029591 PMCID: PMC6053804 DOI: 10.1186/s12864-018-4911-7] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2018] [Accepted: 07/02/2018] [Indexed: 12/18/2022] Open
Abstract
BACKGROUND Since the proposal of Brachypodium distachyon as a model for the grasses, over 500 Bdi-miRNAs have been annotated in miRBase making Brachypodium second in number only to rice. Other monocots, such as switchgrass, are completely absent from the miRBase database. While a significant number of miRNAs have been identified which are highly conserved across plants, little research has been done with respect to the conservation of miRNA targets. Plant responses to abiotic stresses are regulated by diverse pathways many of which involve miRNAs; however, it can be difficult to identify miRNA guided gene regulation when the miRNA is not the primary regulator of the target mRNA. RESULTS To investigate miRNA target conservation and stress response involvement, a set of PARE (Parallel Analysis of RNA Ends) libraries totaling over two billion reads was constructed and sequenced from Brachypodium, switchgrass, and sorghum representing the first report of RNA degradome data from the latter two species. Analysis of this data provided not only PARE evidence for miRNA guided cleavage of over 7000 predicted target mRNAs in Brachypodium, but also evidence for miRNA guided cleavage of over 1000 homologous transcripts in sorghum and switchgrass. A pipeline was constructed to compare RNA-seq and PARE data made from Brachypodium plants exposed to various abiotic stress conditions. This resulted in the identification of 44 miRNA targets which exhibit stress regulated cleavage. Time course experiments were performed to reveal the relationship between miR393ab, miR169a, miR394ab, and their respective targets throughout the first 36 h of the cold stress response in Brachypodium. CONCLUSIONS Knowledge gained from this study provides considerable insight into the RNA degradomes and the breadth of miRNA target conservation among these three species. Additionally, associations of a number of miRNAs and target mRNAs with the stress responses have been revealed which could aid in the development of stress tolerant transgenic crops.
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Affiliation(s)
- Karl R. Franke
- Department of Biology and Delaware Biotechnology Institute, University of Delaware, 15 Innovation Way, Newark, DE 19711 USA
| | - Skye A. Schmidt
- Department of Plant and Soil Sciences and Delaware Biotechnology Institute, University of Delaware, 15 Innovation Way, Newark, DE 19711 USA
| | - Sunhee Park
- Department of Plant and Soil Sciences and Delaware Biotechnology Institute, University of Delaware, 15 Innovation Way, Newark, DE 19711 USA
| | - Dong-Hoon Jeong
- Department of Life Science, Hallym University, Chuncheon, Republic of Korea
| | - Monica Accerbi
- Department of Plant and Soil Sciences and Delaware Biotechnology Institute, University of Delaware, 15 Innovation Way, Newark, DE 19711 USA
| | - Pamela J. Green
- Department of Plant and Soil Sciences and Delaware Biotechnology Institute, University of Delaware, 15 Innovation Way, Newark, DE 19711 USA
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8
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Crisp PA, Ganguly DR, Smith AB, Murray KD, Estavillo GM, Searle I, Ford E, Bogdanović O, Lister R, Borevitz JO, Eichten SR, Pogson BJ. Rapid Recovery Gene Downregulation during Excess-Light Stress and Recovery in Arabidopsis. THE PLANT CELL 2017; 29:1836-1863. [PMID: 28705956 PMCID: PMC5590493 DOI: 10.1105/tpc.16.00828] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/04/2016] [Revised: 06/22/2017] [Accepted: 07/11/2017] [Indexed: 05/19/2023]
Abstract
Stress recovery may prove to be a promising approach to increase plant performance and, theoretically, mRNA instability may facilitate faster recovery. Transcriptome (RNA-seq, qPCR, sRNA-seq, and PARE) and methylome profiling during repeated excess-light stress and recovery was performed at intervals as short as 3 min. We demonstrate that 87% of the stress-upregulated mRNAs analyzed exhibit very rapid recovery. For instance, HSP101 abundance declined 2-fold every 5.1 min. We term this phenomenon rapid recovery gene downregulation (RRGD), whereby mRNA abundance rapidly decreases promoting transcriptome resetting. Decay constants (k) were modeled using two strategies, linear and nonlinear least squares regressions, with the latter accounting for both transcription and degradation. This revealed extremely short half-lives ranging from 2.7 to 60.0 min for 222 genes. Ribosome footprinting using degradome data demonstrated RRGD loci undergo cotranslational decay and identified changes in the ribosome stalling index during stress and recovery. However, small RNAs and 5'-3' RNA decay were not essential for recovery of the transcripts examined, nor were any of the six excess light-associated methylome changes. We observed recovery-specific gene expression networks upon return to favorable conditions and six transcriptional memory types. In summary, rapid transcriptome resetting is reported in the context of active recovery and cellular memory.
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Affiliation(s)
- Peter A Crisp
- Australian Research Council Centre of Excellence in Plant Energy Biology, Research School of Biology, Australian National University Canberra, Acton ACT 0200, Australia
- Department of Plant and Microbial Biology, University of Minnesota, Saint Paul, Minnesota 55108
| | - Diep R Ganguly
- Australian Research Council Centre of Excellence in Plant Energy Biology, Research School of Biology, Australian National University Canberra, Acton ACT 0200, Australia
| | - Aaron B Smith
- Australian Research Council Centre of Excellence in Plant Energy Biology, Research School of Biology, Australian National University Canberra, Acton ACT 0200, Australia
| | - Kevin D Murray
- Australian Research Council Centre of Excellence in Plant Energy Biology, Research School of Biology, Australian National University Canberra, Acton ACT 0200, Australia
| | - Gonzalo M Estavillo
- Australian Research Council Centre of Excellence in Plant Energy Biology, Research School of Biology, Australian National University Canberra, Acton ACT 0200, Australia
- CSIRO Agriculture and Food, Black Mountain, Canberra ACT 2601, Australia
| | - Iain Searle
- School of Biological Sciences, The University of Adelaide, SA 5005, Australia
| | - Ethan Ford
- Australian Research Council Centre of Excellence in Plant Energy Biology, The University of Western Australia, Perth WA 6009, Australia
| | - Ozren Bogdanović
- Australian Research Council Centre of Excellence in Plant Energy Biology, The University of Western Australia, Perth WA 6009, Australia
- Harry Perkins Institute of Medical Research, Perth WA 6009, Australia
| | - Ryan Lister
- Australian Research Council Centre of Excellence in Plant Energy Biology, The University of Western Australia, Perth WA 6009, Australia
- Harry Perkins Institute of Medical Research, Perth WA 6009, Australia
| | - Justin O Borevitz
- Australian Research Council Centre of Excellence in Plant Energy Biology, Research School of Biology, Australian National University Canberra, Acton ACT 0200, Australia
| | - Steven R Eichten
- Australian Research Council Centre of Excellence in Plant Energy Biology, Research School of Biology, Australian National University Canberra, Acton ACT 0200, Australia
| | - Barry J Pogson
- Australian Research Council Centre of Excellence in Plant Energy Biology, Research School of Biology, Australian National University Canberra, Acton ACT 0200, Australia
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Arae T, Isai S, Sakai A, Mineta K, Yokota Hirai M, Suzuki Y, Kanaya S, Yamaguchi J, Naito S, Chiba Y. Co-ordinated Regulations of mRNA Synthesis and Decay during Cold Acclimation in Arabidopsis Cells. PLANT & CELL PHYSIOLOGY 2017; 58:1090-1102. [PMID: 28444357 DOI: 10.1093/pcp/pcx059] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/05/2016] [Accepted: 04/13/2017] [Indexed: 06/07/2023]
Abstract
Plants possess a cold acclimation system to acquire freezing tolerance through pre-exposure to non-freezing low temperatures. The transcriptional cascade of C-repeat-binding factors (CBFs)/dehydration response element-binding factors (DREBs) is considered a major transcriptional regulatory pathway during cold acclimation. However, little is known regarding the functional significance of mRNA stability regulation in the response of gene expression to cold stress. The actual level of individual mRNAs is determined by a balance between mRNA synthesis and degradation. Therefore, it is important to assess the regulatory steps to increase our understanding of gene regulation. Here, we analyzed temporal changes in mRNA amounts and half-lives in response to cold stress in Arabidopsis cell cultures based on genome-wide analysis. In this mRNA decay array method, mRNA half-life measurements and microarray analyses were combined. In addition, temporal changes in the integrated value of transcription rates were estimated from the above two parameters using a mathematical approach. Our results showed that several cold-responsive genes, including Cold-regulated 15a, were relatively destabilized, whereas the mRNA amounts were increased during cold treatment by accelerating the transcription rate to overcome the destabilization. Considering the kinetics of mRNA synthesis and degradation, this apparently contradictory result supports that mRNA destabilization is advantageous for the swift increase in CBF-responsive genes in response to cold stress.
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Affiliation(s)
- Toshihiro Arae
- Graduate School of Life Science, Hokkaido University, Sapporo, Japan
| | - Shiori Isai
- Graduate School of Life Science, Hokkaido University, Sapporo, Japan
| | - Akira Sakai
- Department of Mathematics, Hokkaido University, Sapporo, Japan
| | - Katsuhiko Mineta
- King Abdullah University of Science and Technology (KAUST), Computational Bioscience Research Center (CBRC), Thuwal, Saudi Arabia
| | | | - Yuya Suzuki
- Graduate School of Life Science, Hokkaido University, Sapporo, Japan
- National Institute of Agrobiological Sciences, NARO, Tsukuba, Japan
| | - Shigehiko Kanaya
- Graduate School of Information Science, Nara Institute of Science and Technology, Ikoma, Japan
| | - Junji Yamaguchi
- Graduate School of Life Science, Hokkaido University, Sapporo, Japan
- Faculty of Science, Hokkaido University, Sapporo, Japan
| | - Satoshi Naito
- Graduate School of Life Science, Hokkaido University, Sapporo, Japan
- Graduate School of Agriculture, Hokkaido University, Sapporo, Japan
| | - Yukako Chiba
- Graduate School of Life Science, Hokkaido University, Sapporo, Japan
- Faculty of Science, Hokkaido University, Sapporo, Japan
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Cao D, Xu H, Zhao Y, Deng X, Liu Y, Soppe WJJ, Lin J. Transcriptome and Degradome Sequencing Reveals Dormancy Mechanisms of Cunninghamia lanceolata Seeds. PLANT PHYSIOLOGY 2016; 172:2347-2362. [PMID: 27760880 PMCID: PMC5129703 DOI: 10.1104/pp.16.00384] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/11/2016] [Accepted: 10/14/2016] [Indexed: 05/05/2023]
Abstract
Seeds with physiological dormancy usually experience primary and secondary dormancy in the nature; however, little is known about the differential regulation of primary and secondary dormancy. We combined multiple approaches to investigate cytological changes, hormonal levels, and gene expression dynamics in Cunninghamia lanceolata seeds during primary dormancy release and secondary dormancy induction. Light microscopy and transmission electron microscopy revealed that protein bodies in the embryo cells coalesced during primary dormancy release and then separated during secondary dormancy induction. Transcriptomic profiling demonstrated that expression of genes negatively regulating gibberellic acid (GA) sensitivity reduced specifically during primary dormancy release, whereas the expression of genes positively regulating abscisic acid (ABA) biosynthesis increased during secondary dormancy induction. Parallel analysis of RNA ends revealed uncapped transcripts for ∼55% of all unigenes. A negative correlation between fold changes in expression levels of uncapped versus capped mRNAs was observed during primary dormancy release. However, this correlation was loose during secondary dormancy induction. Our analyses suggest that the reversible changes in cytology and gene expression during dormancy release and induction are related to ABA/GA balance. Moreover, mRNA degradation functions as a critical posttranscriptional regulator during primary dormancy release. These findings provide a mechanistic framework for understanding physiological dormancy in seeds.
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Affiliation(s)
- Dechang Cao
- Key Laboratory for Genetics and Breeding of Forest Trees and Ornamental Plants of Ministry of Education, College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing 100083, China (D.C., H.X., Y.Z., J.L.)
- Key Laboratory of Plant Resources, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China (X.D., Y.L., J.L.)
- Department of Molecular Ecology, Max Planck Institute for Chemical Ecology, Jena 07745, Germany (D.C.); and
- Department of Plant Breeding and Genetics, Max Planck Institute for Plant Breeding Research, Cologne 50829, Germany (W.J.J.S.)
| | - Huimin Xu
- Key Laboratory for Genetics and Breeding of Forest Trees and Ornamental Plants of Ministry of Education, College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing 100083, China (D.C., H.X., Y.Z., J.L.)
- Key Laboratory of Plant Resources, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China (X.D., Y.L., J.L.)
- Department of Molecular Ecology, Max Planck Institute for Chemical Ecology, Jena 07745, Germany (D.C.); and
- Department of Plant Breeding and Genetics, Max Planck Institute for Plant Breeding Research, Cologne 50829, Germany (W.J.J.S.)
| | - Yuanyuan Zhao
- Key Laboratory for Genetics and Breeding of Forest Trees and Ornamental Plants of Ministry of Education, College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing 100083, China (D.C., H.X., Y.Z., J.L.)
- Key Laboratory of Plant Resources, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China (X.D., Y.L., J.L.)
- Department of Molecular Ecology, Max Planck Institute for Chemical Ecology, Jena 07745, Germany (D.C.); and
- Department of Plant Breeding and Genetics, Max Planck Institute for Plant Breeding Research, Cologne 50829, Germany (W.J.J.S.)
| | - Xin Deng
- Key Laboratory for Genetics and Breeding of Forest Trees and Ornamental Plants of Ministry of Education, College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing 100083, China (D.C., H.X., Y.Z., J.L.)
- Key Laboratory of Plant Resources, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China (X.D., Y.L., J.L.)
- Department of Molecular Ecology, Max Planck Institute for Chemical Ecology, Jena 07745, Germany (D.C.); and
- Department of Plant Breeding and Genetics, Max Planck Institute for Plant Breeding Research, Cologne 50829, Germany (W.J.J.S.)
| | - Yongxiu Liu
- Key Laboratory for Genetics and Breeding of Forest Trees and Ornamental Plants of Ministry of Education, College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing 100083, China (D.C., H.X., Y.Z., J.L.)
- Key Laboratory of Plant Resources, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China (X.D., Y.L., J.L.)
- Department of Molecular Ecology, Max Planck Institute for Chemical Ecology, Jena 07745, Germany (D.C.); and
- Department of Plant Breeding and Genetics, Max Planck Institute for Plant Breeding Research, Cologne 50829, Germany (W.J.J.S.)
| | - Wim J J Soppe
- Key Laboratory for Genetics and Breeding of Forest Trees and Ornamental Plants of Ministry of Education, College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing 100083, China (D.C., H.X., Y.Z., J.L.)
- Key Laboratory of Plant Resources, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China (X.D., Y.L., J.L.)
- Department of Molecular Ecology, Max Planck Institute for Chemical Ecology, Jena 07745, Germany (D.C.); and
- Department of Plant Breeding and Genetics, Max Planck Institute for Plant Breeding Research, Cologne 50829, Germany (W.J.J.S.)
| | - Jinxing Lin
- Key Laboratory for Genetics and Breeding of Forest Trees and Ornamental Plants of Ministry of Education, College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing 100083, China (D.C., H.X., Y.Z., J.L.);
- Key Laboratory of Plant Resources, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China (X.D., Y.L., J.L.);
- Department of Molecular Ecology, Max Planck Institute for Chemical Ecology, Jena 07745, Germany (D.C.); and
- Department of Plant Breeding and Genetics, Max Planck Institute for Plant Breeding Research, Cologne 50829, Germany (W.J.J.S.)
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Exploring drought stress-regulated genes in senna (Cassia angustifolia Vahl.): a transcriptomic approach. Funct Integr Genomics 2016; 17:1-25. [PMID: 27709374 DOI: 10.1007/s10142-016-0523-y] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2016] [Revised: 09/02/2016] [Accepted: 09/05/2016] [Indexed: 01/08/2023]
Abstract
De novo assembly of reads produced by next-generation sequencing (NGS) technologies offers a rapid approach to obtain expressed gene sequences for non-model organisms. Senna (Cassia angustifolia Vahl.) is a drought-tolerant annual undershrub of Caesalpiniaceae, a subfamily of Fabaceae. There are insufficient transcriptomic and genomic data in public databases for understanding the molecular mechanism underlying the drought tolerance of senna. Therefore, the main purpose of this study was to know the transcriptome profile of senna, with special reference to drought stress. RNA from two different stages of leaf development was extracted and sequenced separately using the Illumina technology. A total of 200 million reads were generated, and a de novo assembly of processed reads in the pooled transcriptome using Trinity yielded 43,413 transcripts which were further annotated using NCBI BLAST with "green plant database (txid 33090)," Swiss Prot, Kyoto Encyclopedia of Genes and Genomes (KEGG), Clusters of Orthologous Groups (COG), and Gene Ontology (GO). Out of the total transcripts, 42,280 (95.0 %) were annotated by BLASTX against the green plant database of NCBI. Senna transcriptome showed the highest similarity to Glycine max (41 %), followed by Phaseolus vulgaris (16 %), Cicer arietinum (15 %), and Medicago trancatula (5 %). The highest number of GO terms were enriched for the molecular functions category; of these "catalytic activity" (GO: 0003824) (25.10 %) and "binding activity" (GO: 0005488) (20.10 %) were most abundantly represented. We used InterProscan to see protein similarity at domain level; a total of 33,256 transcripts were annotated against the Pfam domains. The transcripts were assigned with various KEGG pathways. Coding DNA sequences (CDS) encoding various drought stress-regulated pathways such as signaling factors, protein-modifying/degrading enzymes, biosynthesis of phytohormone, phytohormone signaling, osmotically active compounds, free radical scavengers, chlorophyll metabolism, leaf cuticular wax, polyamines, and protective proteins were identified through BLASTX search. The lucine-rich repeat kinase family was the most abundantly found group of protein kinases. Orphan, bHLH, and bZIP family TFs were the most abundantly found in senna. Six genes encoding MYC2 transcription factor, 9-cis-epoxycarotenoid dioxygenase (NCED), l -ascorbate peroxidase (APX), aminocyclopropane carboxylate oxidase (ACO), abscisic acid 8'-hydroxylase (ABA), and WRKY transcription factor were confirmed through reverse transcriptase-PCR (RT-PCR) and Sanger sequencing for the first time in senna. The potential drought stress-related transcripts identified in this study provide a good start for further investigation into the drought adaptation in senna. Additionally, our transcriptome sequences are the valuable resource for accelerated genomics-assisted genetic improvement programs and facilitate manipulation of biochemical pathways for developing drought-tolerant genotypes of crop plants.
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Suzuki N, Devireddy AR, Inupakutika MA, Baxter A, Miller G, Song L, Shulaev E, Azad RK, Shulaev V, Mittler R. Ultra-fast alterations in mRNA levels uncover multiple players in light stress acclimation in plants. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2015; 84:760-72. [PMID: 26408339 PMCID: PMC5019327 DOI: 10.1111/tpj.13039] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/04/2015] [Revised: 09/12/2015] [Accepted: 09/15/2015] [Indexed: 05/19/2023]
Abstract
The acclimation of plants to changes in light intensity requires rapid responses at several different levels. These include biochemical and biophysical responses as well as alterations in the steady-state level of different transcripts and proteins. Recent studies utilizing promoter::reporter constructs suggested that transcriptional responses to changes in light intensity could occur within seconds, rates for which changes in mRNA expression are not routinely measured or functionally studied. To identify and characterize rapid changes in the steady-state level of different transcripts in response to light stress we performed RNA sequencing analysis of Arabidopsis thaliana plants subjected to light stress. Here we report that mRNA accumulation of 731 transcripts occurs as early as 20-60 sec following light stress application, and that at least five of these early response transcripts play an important biological role in the acclimation of plants to light stress. More than 20% of transcripts accumulating in plants within 20-60 sec of initiation of light stress are H2 O2 - and ABA-response transcripts, and the accumulation of several of these transcripts is inhibited by transcriptional inhibitors. In accordance with the association of rapid response transcripts with H2 O2 and ABA signaling, a mutant impaired in ABA sensing (abi-1) was found to be more tolerant to light stress, and the response of several of the rapid response transcripts was altered in mutants impaired in reactive oxygen metabolism. Our findings reveal that transcriptome reprogramming in plants could occur within seconds of initiation of abiotic stress and that this response could invoke known as well as unknown proteins and pathways.
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Affiliation(s)
- Nobuhiro Suzuki
- Department of Materials and Life Sciences, Faculty of Science and Technology, Sophia University, 7-1 Kioi-cho, Chiyoda-ku, 102-8554, Tokyo, Japan
| | - Amith R Devireddy
- Department of Biological Sciences, University of North Texas, Denton, TX, 76203, USA
| | - Madhuri A Inupakutika
- Department of Biological Sciences, University of North Texas, Denton, TX, 76203, USA
| | - Aaron Baxter
- Department of Biological Sciences, University of North Texas, Denton, TX, 76203, USA
| | - Gad Miller
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Life Sciences Building (204) Room 211, Ramat-Gan, 5290002, Israel
| | - Luhua Song
- Department of Biological Sciences, University of North Texas, Denton, TX, 76203, USA
| | - Elena Shulaev
- Department of Biological Sciences, University of North Texas, Denton, TX, 76203, USA
| | - Rajeev K Azad
- Department of Biological Sciences, University of North Texas, Denton, TX, 76203, USA
- Department of Mathematics, University of North Texas, Denton, TX, 76203, USA
| | - Vladimir Shulaev
- Department of Biological Sciences, University of North Texas, Denton, TX, 76203, USA
| | - Ron Mittler
- Department of Biological Sciences, University of North Texas, Denton, TX, 76203, USA
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Yi F, Chen J, Yu J. Global analysis of uncapped mRNA changes under drought stress and microRNA-dependent endonucleolytic cleavages in foxtail millet. BMC PLANT BIOLOGY 2015; 15:241. [PMID: 26444665 PMCID: PMC4594888 DOI: 10.1186/s12870-015-0632-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/14/2015] [Accepted: 09/30/2015] [Indexed: 05/20/2023]
Abstract
BACKGROUND mRNA degradation plays an important role in the determination of mRNA abundance and can quickly regulate gene expression. The production of uncapped mRNAs, an important mechanism of mRNA degradation, can be initiated by decapping enzymes, endonucleases or small RNAs such as microRNAs (miRNAs). Little is known, however, about the role of uncapped mRNAs in plants under environmental stress. RESULTS Using a novel approach called parallel analysis of RNA ends (PARE), we performed a global study of uncapped mRNAs under drought stress in foxtail millet (Setaria italica [L.] P. Beauv.). When both gene degradation (PARE) and gene transcription (RNA-sequencing) data were considered, four types of mRNA decay patterns were identified under drought stress. In addition, 385 miRNA-target interactions were identified in the PARE data using PAREsnip. The PARE analysis also suggested that two miRNA hairpin processing mechanisms--loop-last and loop-first processing--operate in foxtail millet, with both miR319 and miR156 gene families undergoing precise processing via the unusual loop-first mechanism. Finally, we found 11 C4 photosynthesis-related enzymes encoded by drought-responsive genes. CONCLUSIONS We performed a global analysis of mRNA degradation under drought stress and uncovered diverse drought-response mechanisms in foxtail millet. This information will deepen our understanding of mRNA expression under stressful environmental conditions in gramineous plants. In addition, PARE analysis identified many miRNA targets and revealed miRNA-precursor processing modes in foxtail millet.
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Affiliation(s)
- Fei Yi
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing, 100193, China.
| | - Jian Chen
- State Key Laboratory of Agrobiotechnology, College of Agriculture and Biotechnology, China Agricultural University, Beijing, 100193, China.
| | - Jingjuan Yu
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing, 100193, China.
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14
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Browning KS, Bailey-Serres J. Mechanism of cytoplasmic mRNA translation. THE ARABIDOPSIS BOOK 2015; 13:e0176. [PMID: 26019692 PMCID: PMC4441251 DOI: 10.1199/tab.0176] [Citation(s) in RCA: 152] [Impact Index Per Article: 16.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
Protein synthesis is a fundamental process in gene expression that depends upon the abundance and accessibility of the mRNA transcript as well as the activity of many protein and RNA-protein complexes. Here we focus on the intricate mechanics of mRNA translation in the cytoplasm of higher plants. This chapter includes an inventory of the plant translational apparatus and a detailed review of the translational processes of initiation, elongation, and termination. The majority of mechanistic studies of cytoplasmic translation have been carried out in yeast and mammalian systems. The factors and mechanisms of translation are for the most part conserved across eukaryotes; however, some distinctions are known to exist in plants. A comprehensive understanding of the complex translational apparatus and its regulation in plants is warranted, as the modulation of protein production is critical to development, environmental plasticity and biomass yield in diverse ecosystems and agricultural settings.
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Affiliation(s)
- Karen S. Browning
- Department of Molecular Biosciences and Institute for Cell and Molecular Biology, University of Texas at Austin, Austin TX 78712-0165
- Both authors contributed equally to this work
| | - Julia Bailey-Serres
- Department of Botany and Plant Sciences and Center for Plant Cell Biology, University of California, Riverside, CA, 92521 USA
- Both authors contributed equally to this work
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15
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Gutierrez-Beltran E, Moschou PN, Smertenko AP, Bozhkov PV. Tudor staphylococcal nuclease links formation of stress granules and processing bodies with mRNA catabolism in Arabidopsis. THE PLANT CELL 2015; 27:926-43. [PMID: 25736060 PMCID: PMC4558657 DOI: 10.1105/tpc.114.134494] [Citation(s) in RCA: 105] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/25/2014] [Revised: 02/03/2015] [Accepted: 02/16/2015] [Indexed: 05/18/2023]
Abstract
Tudor Staphylococcal Nuclease (TSN or Tudor-SN; also known as SND1) is an evolutionarily conserved protein involved in the transcriptional and posttranscriptional regulation of gene expression in animals. Although TSN was found to be indispensable for normal plant development and stress tolerance, the molecular mechanisms underlying these functions remain elusive. Here, we show that Arabidopsis thaliana TSN is essential for the integrity and function of cytoplasmic messenger ribonucleoprotein (mRNP) complexes called stress granules (SGs) and processing bodies (PBs), sites of posttranscriptional gene regulation during stress. TSN associates with SGs following their microtubule-dependent assembly and plays a scaffolding role in both SGs and PBs. The enzymatically active tandem repeat of four SN domains is crucial for targeting TSN to the cytoplasmic mRNA complexes and is sufficient for the cytoprotective function of TSN during stress. Furthermore, our work connects the cytoprotective function of TSN with its positive role in stress-induced mRNA decapping. While stress led to a pronounced increase in the accumulation of uncapped mRNAs in wild-type plants, this increase was abrogated in TSN knockout plants. Taken together, our results establish TSN as a key enzymatic component of the catabolic machinery responsible for the processing of mRNAs in the cytoplasmic mRNP complexes during stress.
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Affiliation(s)
- Emilio Gutierrez-Beltran
- Department of Plant Biology, Uppsala BioCenter, Swedish University of Agricultural Sciences and Linnean Center for Plant Biology, SE-75007 Uppsala, Sweden
| | - Panagiotis N Moschou
- Department of Plant Biology, Uppsala BioCenter, Swedish University of Agricultural Sciences and Linnean Center for Plant Biology, SE-75007 Uppsala, Sweden
| | - Andrei P Smertenko
- Institute of Biological Chemistry, Washington State University, Pullman, Washington 99164 Institute for Global Food Security, Queen's University Belfast, Belfast BT9 5BN, United Kingdom
| | - Peter V Bozhkov
- Department of Plant Biology, Uppsala BioCenter, Swedish University of Agricultural Sciences and Linnean Center for Plant Biology, SE-75007 Uppsala, Sweden
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Schmidt SA, Foley PL, Jeong DH, Rymarquis LA, Doyle F, Tenenbaum SA, Belasco JG, Green PJ. Identification of SMG6 cleavage sites and a preferred RNA cleavage motif by global analysis of endogenous NMD targets in human cells. Nucleic Acids Res 2014; 43:309-23. [PMID: 25429978 PMCID: PMC4288159 DOI: 10.1093/nar/gku1258] [Citation(s) in RCA: 81] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023] Open
Abstract
In metazoans, cleavage by the endoribonuclease SMG6 is often the first degradative event in non-sense-mediated mRNA decay (NMD). However, the exact sites of SMG6 cleavage have yet to be determined for any endogenous targets, and most evidence as to the identity of SMG6 substrates is indirect. Here, we use Parallel Analysis of RNA Ends to specifically identify the 5′ termini of decay intermediates whose production is dependent on SMG6 and the universal NMD factor UPF1. In this manner, the SMG6 cleavage sites in hundreds of endogenous NMD targets in human cells have been mapped at high resolution. In addition, a preferred sequence motif spanning most SMG6 cleavage sites has been discovered and validated by mutational analysis. For many SMG6 substrates, depletion of SMG6 resulted in the accumulation of decapped transcripts, an effect indicative of competition between SMG6-dependent and SMG6-independent NMD pathways. These findings provide key insights into the mechanisms by which mRNAs targeted by NMD are degraded.
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Affiliation(s)
- Skye A Schmidt
- Delaware Biotechnology Institute and Department of Plant and Soil Sciences, University of Delaware, Newark, DE 19711, USA
| | - Patricia L Foley
- Kimmel Center for Biology and Medicine at the Skirball Institute and Department of Microbiology, New York University School of Medicine, New York, NY 10016, USA
| | - Dong-Hoon Jeong
- Delaware Biotechnology Institute and Department of Plant and Soil Sciences, University of Delaware, Newark, DE 19711, USA
| | - Linda A Rymarquis
- Delaware Biotechnology Institute and Department of Plant and Soil Sciences, University of Delaware, Newark, DE 19711, USA
| | - Francis Doyle
- Department of Life Science, Hallym University, Chuncheon, Gangwon, Republic of Korea
| | - Scott A Tenenbaum
- Department of Life Science, Hallym University, Chuncheon, Gangwon, Republic of Korea
| | - Joel G Belasco
- Kimmel Center for Biology and Medicine at the Skirball Institute and Department of Microbiology, New York University School of Medicine, New York, NY 10016, USA
| | - Pamela J Green
- Delaware Biotechnology Institute and Department of Plant and Soil Sciences, University of Delaware, Newark, DE 19711, USA
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Mousavi S, Alisoltani A, Shiran B, Fallahi H, Ebrahimie E, Imani A, Houshmand S. De novo transcriptome assembly and comparative analysis of differentially expressed genes in Prunus dulcis Mill. in response to freezing stress. PLoS One 2014; 9:e104541. [PMID: 25122458 PMCID: PMC4133227 DOI: 10.1371/journal.pone.0104541] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2014] [Accepted: 07/13/2014] [Indexed: 11/18/2022] Open
Abstract
Almond (Prunus dulcis Mill.), one of the most important nut crops, requires chilling during winter to develop fruiting buds. However, early spring chilling and late spring frost may damage the reproductive tissues leading to reduction in the rate of productivity. Despite the importance of transcriptional changes and regulation, little is known about the almond’s transcriptome under the cold stress conditions. In the current reserch, we used RNA-seq technique to study the response of the reporuductive tissues of almond (anther and ovary) to frost stress. RNA sequencing resulted in more than 20 million reads from anther and ovary tissues of almond, individually. About 40,000 contigs were assembled and annotated denovo in each tissue. Profile of gene expression in ovary showed significant alterations in 5,112 genes, whereas in anther 6,926 genes were affected by freezing stress. Around two thousands of these genes were common altered genes in both ovary and anther libraries. Gene ontology indicated the involvement of differentially expressed (DE) genes, responding to freezing stress, in metabolic and cellular processes. qRT-PCR analysis verified the expression pattern of eight genes randomley selected from the DE genes. In conclusion, the almond gene index assembled in this study and the reported DE genes can provide great insights on responses of almond and other Prunus species to abiotic stresses. The obtained results from current research would add to the limited available information on almond and Rosaceae. Besides, the findings would be very useful for comparative studies as the number of DE genes reported here is much higher than that of any previous reports in this plant.
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Affiliation(s)
- Sadegh Mousavi
- Department of Plant Breeding and Biotechnology, Faculty of Agriculture, Shahrekord University, Shahrekord, Iran
| | - Arghavan Alisoltani
- Department of Plant Breeding and Biotechnology, Faculty of Agriculture, Shahrekord University, Shahrekord, Iran
| | - Behrouz Shiran
- Department of Plant Breeding and Biotechnology, Faculty of Agriculture, Shahrekord University, Shahrekord, Iran
- Institute of Biotechnology, Shahrekord University, Shahrekord, Iran
- * E-mail:
| | - Hossein Fallahi
- Department of Biology, School of Sciences, Razi University, Bagh-e-Abrisham Kermanshah, Iran
| | - Esameil Ebrahimie
- Department of Crop Production and Plant Breeding, Faculty of Agriculture, Shiraz University, Shiraz, Iran
- School of Molecular and Biomedical Science, The University of Adelaide, Adelaide, Australia
| | - Ali Imani
- Department of Horticulture, Seed and Plant Improvement Institute (SPII), Karaj, Iran
| | - Saadollah Houshmand
- Department of Plant Breeding and Biotechnology, Faculty of Agriculture, Shahrekord University, Shahrekord, Iran
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Parallel analysis of RNA ends enhances global investigation of microRNAs and target RNAs of Brachypodium distachyon. Genome Biol 2013; 14:R145. [PMID: 24367943 PMCID: PMC4053937 DOI: 10.1186/gb-2013-14-12-r145] [Citation(s) in RCA: 59] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2013] [Accepted: 12/24/2013] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The wild grass Brachypodium distachyon has emerged as a model system for temperate grasses and biofuel plants. However, the global analysis of miRNAs, molecules known to be key for eukaryotic gene regulation, has been limited in B. distachyon to studies examining a few samples or that rely on computational predictions. Similarly an in-depth global analysis of miRNA-mediated target cleavage using parallel analysis of RNA ends (PARE) data is lacking in B. distachyon. RESULTS B. distachyon small RNAs were cloned and deeply sequenced from 17 libraries that represent different tissues and stresses. Using a computational pipeline, we identified 116 miRNAs including not only conserved miRNAs that have not been reported in B. distachyon, but also non-conserved miRNAs that were not found in other plants. To investigate miRNA-mediated cleavage function, four PARE libraries were constructed from key tissues and sequenced to a total depth of approximately 70 million sequences. The roughly 5 million distinct genome-matched sequences that resulted represent an extensive dataset for analyzing small RNA-guided cleavage events. Analysis of the PARE and miRNA data provided experimental evidence for miRNA-mediated cleavage of 264 sites in predicted miRNA targets. In addition, PARE analysis revealed that differentially expressed miRNAs in the same family guide specific target RNA cleavage in a correspondingly tissue-preferential manner. CONCLUSIONS B. distachyon miRNAs and target RNAs were experimentally identified and analyzed. Knowledge gained from this study should provide insights into the roles of miRNAs and the regulation of their targets in B. distachyon and related plants.
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