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Wang J, Guo T, Zhang X, Guo J, Meng X, Yan S, Wang Y, Xiao Y, Xu W, Wei X, Ding K, Zhang J, Mi Y, Wu S, Chen J, Huang Y, Ren S, Hou J. Comprehensive investigation in oncogenic functions and immunological roles of NCBP2 and its validation in prostate cancer. Transl Oncol 2024; 47:102049. [PMID: 38964031 PMCID: PMC11283080 DOI: 10.1016/j.tranon.2024.102049] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2023] [Revised: 06/06/2024] [Accepted: 07/01/2024] [Indexed: 07/06/2024] Open
Abstract
BACKGROUND Nuclear cap-binding protein 2 (NCBP2), as the component of the cap-binding complex, participates in a number of biological processes, including pre-mRNA splicing, transcript export, translation regulation and other gene expression steps. However, the role of NCBP2 on the tumor cells and immune microenvironment remains unclear. To systematically analyze and validate functions of NCBP2, we performed a pan-cancer analysis using multiple approaches. METHODS The data in this study were derived from sequencing, mutation, and methylation data in the TCGA cohort, normal sample sequencing data in the GTEx project, and cell line expression profile data in the CCLE database. RESULTS Survival analyses including the Cox proportional-hazards model and log-rank test revealed the poor prognostic role of NCBP2 in multiple tumors. We further validated the oncogenic ability of NCBP2 in prostate cancer cell lines, organoids and tumor-bearing mice. A negative correlation was observed between NCBP2 expression and immune score by the ESTIMATE algorithm. Simultaneously, the NCBP2-induced immunosuppressive microenvironment might be related to the decline in CD8+T cells and the increase in regulatory T cells and neutrophils, examined by flow cytometry experiments for NCBP2 overexpressed tumor-bearing mice. CONCLUSION This research offered strong proof supporting NCBP2 as the prognostic marker and the therapeutic target in the future.
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Affiliation(s)
- Jian Wang
- Department of Urology, The First Affiliated Hospital of Soochow University, Suzhou, China; Department of Urology, Shanghai Changzheng Hospital, Shanghai, China; Department of Urology, Shanghai Changhai Hospital, Shanghai, China; Department of Urology, Affiliated Hospital of Jiangnan University, Wuxi, China
| | - Tao Guo
- Department of Urology, The First Affiliated Hospital of Soochow University, Suzhou, China
| | - Xiaomin Zhang
- Department of Urology, Shanghai Changhai Hospital, Shanghai, China
| | - Jiacheng Guo
- CAS Key Laboratory of Tissue Microenvironment and Tumor, Shanghai Institute of Nutrition and Health, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai, China
| | - Xiangyu Meng
- Department of Urology, The First Affiliated Hospital of Nanjing Medical University, Nanjing China
| | - Shi Yan
- Department of Urology, Shanghai Changhai Hospital, Shanghai, China
| | - Ye Wang
- Department of Urology, Shanghai Changzheng Hospital, Shanghai, China
| | - Yutian Xiao
- Department of Urology, Shanghai Changhai Hospital, Shanghai, China
| | - Weidong Xu
- Department of Urology, Shanghai Changzheng Hospital, Shanghai, China
| | - Xuedong Wei
- Department of Urology, The First Affiliated Hospital of Soochow University, Suzhou, China
| | - Keke Ding
- Department of Urology, The First Affiliated Hospital of Soochow University, Suzhou, China
| | - Jun Zhang
- Department of Urology, The First Affiliated Hospital of Soochow University, Suzhou, China
| | - Yuanyuan Mi
- Department of Urology, Affiliated Hospital of Jiangnan University, Wuxi, China
| | - Sheng Wu
- Department of Urology, Affiliated Hospital of Jiangnan University, Wuxi, China
| | - Jie Chen
- Department of Urology, Shanghai Changzheng Hospital, Shanghai, China.
| | - Yuhua Huang
- Department of Urology, The First Affiliated Hospital of Soochow University, Suzhou, China.
| | - Shancheng Ren
- Department of Urology, Shanghai Changzheng Hospital, Shanghai, China.
| | - Jianquan Hou
- Department of Urology, The First Affiliated Hospital of Soochow University, Suzhou, China.
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Zhang W, Wang H, Guo Y, Hao X, Li Y, He W, Zhao X, Cai S, Song X. Functional Validation of Different Alternative Splicing Variants of the Chrysanthemum lavandulifolium ClNUM1 Gene in Tobacco. Curr Issues Mol Biol 2024; 46:5242-5256. [PMID: 38920986 PMCID: PMC11201747 DOI: 10.3390/cimb46060314] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2024] [Revised: 05/10/2024] [Accepted: 05/17/2024] [Indexed: 06/27/2024] Open
Abstract
The Asteraceae are widely distributed throughout the world, with diverse functions and large genomes. Many of these genes remain undiscovered and unstudied. In this study, we discovered a new gene ClNUM1 in Chrysanthemum lavandulifolium and studied its function. In this study, bioinformatics, RT-qPCR, paraffin sectioning, and tobacco transgenics were utilized to bioinformatically analyze and functionally study the three variable splice variants of the unknown gene ClNUM1 cloned from C. lavandulifolium. The results showed that ClNUM1.1 and ClNUM1.2 had selective 3' splicing and selective 5' splicing, and ClNUM1.3 had selective 5' splicing. When the corresponding transgenic tobacco plants were subjected to abiotic stress treatment, in the tobacco seedlings, the ClNUM1.1 gene and the ClNUM1.2 gene enhanced salt and low-temperature tolerance and the ClNUM1.3 gene enhanced low-temperature tolerance; in mature tobacco plants, the ClNUM1.1 gene was able to enhance salt and low-temperature tolerance, and the ClNUM1.2 and ClNUM1.3 genes were able to enhance low-temperature tolerance. In summary, there are differences in the functions of the different splice variants and the different seedling stages of transgenic tobacco, but all of them enhanced the resistance of tobacco to a certain extent. The analysis and functional characterization of the ClNUM1 gene provided new potential genes and research directions for abiotic resistance breeding in Chrysanthemum.
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Affiliation(s)
| | | | | | | | | | | | | | | | - Xuebin Song
- College of Landscape Architecture and Forestry, Qingdao Agricultural University, Qingdao 266109, China; (W.Z.); (H.W.); (Y.G.); (X.H.); (Y.L.); (W.H.); (X.Z.); (S.C.)
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Cheng W, Hong C, Zeng F, Liu N, Gao H. Sequence variations affect the 5' splice site selection of plant introns. PLANT PHYSIOLOGY 2023; 193:1281-1296. [PMID: 37394939 DOI: 10.1093/plphys/kiad375] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/16/2023] [Revised: 05/31/2023] [Accepted: 06/04/2023] [Indexed: 07/04/2023]
Abstract
Introns are noncoding sequences spliced out of pre-mRNAs by the spliceosome to produce mature mRNAs. The 5' ends of introns mostly begin with GU and have a conserved sequence motif of AG/GUAAGU that could base-pair with the core sequence of U1 snRNA of the spliceosome. Intriguingly, ∼ 1% of introns in various eukaryotic species begin with GC. This occurrence could cause misannotation of genes; however, the underlying splicing mechanism is unclear. We analyzed the sequences around the intron 5' splice site (ss) in Arabidopsis (Arabidopsis thaliana) and found sequences at the GC intron ss are much more stringent than those of GT introns. Mutational analysis at various positions of the intron 5' ss revealed that although mutations impair base pairing, different mutations at the same site can have different effects, suggesting that steric hindrance also affects splicing. Moreover, mutations of 5' ss often activate a hidden ss nearby. Our data suggest that the 5' ss is selected via a competition between the major ss and the nearby minor ss. This work not only provides insights into the splicing mechanism of intron 5' ss but also improves the accuracy of gene annotation and the study of the evolution of intron 5' ss.
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Affiliation(s)
- Wenzhen Cheng
- National Engineering Research Center of Tree Breeding and Ecological Restoration, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, China
| | - Conghao Hong
- National Engineering Research Center of Tree Breeding and Ecological Restoration, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, China
| | - Fang Zeng
- National Engineering Research Center of Tree Breeding and Ecological Restoration, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, China
| | - Nan Liu
- National Engineering Research Center of Tree Breeding and Ecological Restoration, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, China
| | - Hongbo Gao
- National Engineering Research Center of Tree Breeding and Ecological Restoration, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, China
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Jozwiak M, Bielewicz D, Szweykowska-Kulinska Z, Jarmolowski A, Bajczyk M. SERRATE: a key factor in coordinated RNA processing in plants. TRENDS IN PLANT SCIENCE 2023; 28:841-853. [PMID: 37019716 DOI: 10.1016/j.tplants.2023.03.009] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/02/2022] [Revised: 02/17/2023] [Accepted: 03/09/2023] [Indexed: 06/17/2023]
Abstract
The SERRATE (SE) protein is involved in the processing of RNA polymerase II (RNAPII) transcripts. It is associated with different complexes engaged in different aspects of plant RNA metabolism, including assemblies involved in transcription, splicing, polyadenylation, miRNA biogenesis, and RNA degradation. SE stability and interactome properties can be influenced by phosphorylation. SE exhibits an intriguing liquid-liquid phase separation property that may be important in the assembly of different RNA-processing bodies. Therefore, we propose that SE seems to participate in the coordination of different RNA-processing steps and can direct the fate of transcripts, targeting them for processing or degradation when they cannot be properly processed or are synthesized in excess.
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Affiliation(s)
- Monika Jozwiak
- Department of Gene Expression, Institute of Molecular Biology and Biotechnology, Adam Mickiewicz University, Poznan, Poland
| | - Dawid Bielewicz
- Center for Advanced Technology, Adam Mickiewicz University, Poznan, Poland
| | - Zofia Szweykowska-Kulinska
- Department of Gene Expression, Institute of Molecular Biology and Biotechnology, Adam Mickiewicz University, Poznan, Poland
| | - Artur Jarmolowski
- Department of Gene Expression, Institute of Molecular Biology and Biotechnology, Adam Mickiewicz University, Poznan, Poland.
| | - Mateusz Bajczyk
- Department of Gene Expression, Institute of Molecular Biology and Biotechnology, Adam Mickiewicz University, Poznan, Poland.
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Sybilska E, Daszkowska-Golec A. Alternative splicing in ABA signaling during seed germination. FRONTIERS IN PLANT SCIENCE 2023; 14:1144990. [PMID: 37008485 PMCID: PMC10060653 DOI: 10.3389/fpls.2023.1144990] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/15/2023] [Accepted: 03/02/2023] [Indexed: 06/19/2023]
Abstract
Seed germination is an essential step in a plant's life cycle. It is controlled by complex physiological, biochemical, and molecular mechanisms and external factors. Alternative splicing (AS) is a co-transcriptional mechanism that regulates gene expression and produces multiple mRNA variants from a single gene to modulate transcriptome diversity. However, little is known about the effect of AS on the function of generated protein isoforms. The latest reports indicate that alternative splicing (AS), the relevant mechanism controlling gene expression, plays a significant role in abscisic acid (ABA) signaling. In this review, we present the current state of the art about the identified AS regulators and the ABA-related changes in AS during seed germination. We show how they are connected with the ABA signaling and the seed germination process. We also discuss changes in the structure of the generated AS isoforms and their impact on the functionality of the generated proteins. Also, we point out that the advances in sequencing technology allow for a better explanation of the role of AS in gene regulation by more accurate detection of AS events and identification of full-length splicing isoforms.
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6
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Wang L, Xu F, Yu F. Two environmental signal-driven RNA metabolic processes: Alternative splicing and translation. PLANT, CELL & ENVIRONMENT 2023; 46:718-732. [PMID: 36609800 DOI: 10.1111/pce.14537] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/18/2022] [Revised: 12/29/2022] [Accepted: 01/06/2023] [Indexed: 06/17/2023]
Abstract
Plants live in fixed locations and have evolved adaptation mechanisms that integrate multiple responses to various environmental signals. Among the different components of these response pathways, receptors/sensors represent nodes that recognise environmental signals. Additionally, RNA metabolism plays an essential role in the regulation of gene expression and protein synthesis. With the development of RNA biotechnology, recent advances have been made in determining the roles of RNA metabolism in response to different environmental signals-especially the roles of alternative splicing and translation. In this review, we discuss recent progress in research on how the environmental adaptation mechanisms in plants are affected at the posttranscriptional level. These findings improve our understanding of the mechanism through which plants adapt to environmental changes by regulating the posttranscriptional level and are conducive for breeding stress-tolerant plants to cope with dynamic and rapidly changing environments.
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Affiliation(s)
- Long Wang
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Biology, Hunan Key Laboratory of Plant Functional Genomics and Developmental Regulation, Hunan University, Changsha, China
| | - Fan Xu
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Biology, Hunan Key Laboratory of Plant Functional Genomics and Developmental Regulation, Hunan University, Changsha, China
| | - Feng Yu
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Biology, Hunan Key Laboratory of Plant Functional Genomics and Developmental Regulation, Hunan University, Changsha, China
- State Key Laboratory of Hybrid Rice, Hunan Hybrid Rice Research Center, Changsha, China
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7
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Li J, Gao X, Chen X, Fan Z, Zhang Y, Wang Z, Shi J, Wang C, Zhang H, Wang L, Zhao Q. Comparative transcriptome responses of leaf and root tissues to salt stress in wheat strains with different salinity tolerances. Front Genet 2023; 14:1015599. [PMID: 36911411 PMCID: PMC9996022 DOI: 10.3389/fgene.2023.1015599] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2022] [Accepted: 02/07/2023] [Indexed: 02/25/2023] Open
Abstract
Background: Salinity stress is a major adverse environmental factor that can limit crop yield and restrict normal land use. The selection of salt-tolerant strains and elucidation of the underlying mechanisms by plant breeding scientists are urgently needed to increase agricultural production in arid and semi-arid regions. Results: In this study, we selected the salt-tolerant wheat (Triticum aestivum) strain ST9644 as a model to study differences in expression patterns between salt-tolerant and salt-sensitive strains. High-throughput RNA sequencing resulted in more than 359.10 Gb of clean data from 54 samples, with an average of 6.65 Gb per sample. Compared to the IWGSC reference annotation, we identified 50,096 new genes, 32,923 of which have functional annotations. Comparisons of abundances between salt-tolerant and salt-sensitive strains revealed 3,755, 5,504, and 4,344 genes that were differentially expressed at 0, 6, and 24 h, respectively, in root tissue under salt stress. KEGG pathway analysis of these genes showed that they were enriched for phenylpropanoid biosynthesis (ko00940), cysteine and methionine metabolism (ko00270), and glutathione metabolism (ko00480). We also applied weighted gene co-expression network analysis (WGCNA) analysis to determine the time course of root tissue response to salt stress and found that the acute response lasts >6 h and ends before 12 h. We also identified key alternative splicing factors showing different splicing patterns in salt-sensitive and salt-tolerant strains; however, only few of them were differentially expressed in the two groups. Conclusion: Our results offer a better understanding of wheat salt tolerance and improve wheat breeding.
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Affiliation(s)
- Jianfeng Li
- Institute of Nuclear and Biological Technologies, Xinjiang Academy of Agricultural Sciences, Urummqi, China
| | - Xin Gao
- Institute of Nuclear and Biological Technologies, Xinjiang Academy of Agricultural Sciences, Urummqi, China
| | - Xunji Chen
- Institute of Nuclear and Biological Technologies, Xinjiang Academy of Agricultural Sciences, Urummqi, China
| | - Zheru Fan
- Institute of Nuclear and Biological Technologies, Xinjiang Academy of Agricultural Sciences, Urummqi, China
| | - Yueqiang Zhang
- Institute of Nuclear and Biological Technologies, Xinjiang Academy of Agricultural Sciences, Urummqi, China
| | - Zhong Wang
- Institute of Nuclear and Biological Technologies, Xinjiang Academy of Agricultural Sciences, Urummqi, China
| | - Jia Shi
- Institute of Nuclear and Biological Technologies, Xinjiang Academy of Agricultural Sciences, Urummqi, China
| | - Chunsheng Wang
- Institute of Nuclear and Biological Technologies, Xinjiang Academy of Agricultural Sciences, Urummqi, China
| | - Hongzhi Zhang
- Institute of Nuclear and Biological Technologies, Xinjiang Academy of Agricultural Sciences, Urummqi, China
| | - Lihong Wang
- Institute of Nuclear and Biological Technologies, Xinjiang Academy of Agricultural Sciences, Urummqi, China
| | - Qi Zhao
- Institute of Nuclear and Biological Technologies, Xinjiang Academy of Agricultural Sciences, Urummqi, China
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8
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Wyrzykowska A, Bielewicz D, Plewka P, Sołtys‐Kalina D, Wasilewicz‐Flis I, Marczewski W, Jarmolowski A, Szweykowska‐Kulinska Z. The MYB33, MYB65, and MYB101 transcription factors affect Arabidopsis and potato responses to drought by regulating the ABA signaling pathway. PHYSIOLOGIA PLANTARUM 2022; 174:e13775. [PMID: 36050907 PMCID: PMC9828139 DOI: 10.1111/ppl.13775] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/23/2022] [Revised: 08/18/2022] [Accepted: 08/30/2022] [Indexed: 06/15/2023]
Abstract
Drought is one of the main climate threats limiting crop production. Potato is one of the four most important food crop species worldwide and is sensitive to water shortage. The CBP80 gene was shown to affect Arabidopsis and potato responses to drought by regulating the level of microRNA159 and, consequently, the levels of the MYB33 and MYB101 transcription factors (TFs). Here, we show that three MYB TFs, MYB33, MYB65, and MYB101, are involved in plant responses to water shortage. Their downregulation in Arabidopsis causes stomatal hyposensitivity to abscisic acid (ABA), leading to reduced tolerance to drought. Transgenic Arabidopsis and potato plants overexpressing these genes, with a mutated recognition site in miR159, show hypersensitivity to ABA and relatively high tolerance to drought conditions. Thus, the MYB33, MYB65, and MYB101 genes may be potential targets for innovative breeding to obtain crops with relatively high tolerance to drought.
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Affiliation(s)
- Anna Wyrzykowska
- Department of Gene Expression, Institute of Molecular Biology and Biotechnology, Faculty of BiologyAdam Mickiewicz UniversityPoznańWielkopolskiePoland
| | - Dawid Bielewicz
- Department of Gene Expression, Institute of Molecular Biology and Biotechnology, Faculty of BiologyAdam Mickiewicz UniversityPoznańWielkopolskiePoland
| | - Patrycja Plewka
- Department of Gene Expression, Institute of Molecular Biology and Biotechnology, Faculty of BiologyAdam Mickiewicz UniversityPoznańWielkopolskiePoland
| | - Dorota Sołtys‐Kalina
- Plant Breeding and Acclimatization Institute – National Research InstituteMłochówMasovian VoivodeshipPoland
| | - Iwona Wasilewicz‐Flis
- Plant Breeding and Acclimatization Institute – National Research InstituteMłochówMasovian VoivodeshipPoland
| | - Waldemar Marczewski
- Plant Breeding and Acclimatization Institute – National Research InstituteMłochówMasovian VoivodeshipPoland
| | - Artur Jarmolowski
- Department of Gene Expression, Institute of Molecular Biology and Biotechnology, Faculty of BiologyAdam Mickiewicz UniversityPoznańWielkopolskiePoland
| | - Zofia Szweykowska‐Kulinska
- Department of Gene Expression, Institute of Molecular Biology and Biotechnology, Faculty of BiologyAdam Mickiewicz UniversityPoznańWielkopolskiePoland
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9
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Zhang H, Li X, Song R, Zhan Z, Zhao F, Li Z, Jiang D. Cap-binding complex assists RNA polymerase II transcription in plant salt stress response. PLANT, CELL & ENVIRONMENT 2022; 45:2780-2793. [PMID: 35773782 DOI: 10.1111/pce.14388] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/05/2022] [Revised: 05/14/2022] [Accepted: 06/17/2022] [Indexed: 06/15/2023]
Abstract
Adaptive response to stress involves an extensive reprogramming of gene expression. Under stressful conditions, the induction of efficient changes in messenger RNA (mRNA) production is crucial for maximized plant survival. Transcription and pre-mRNA processing are two closely related steps in mRNA biogenesis, yet how they are controlled in plant stress response remains elusive. Here, we show that the Arabidopsis nuclear cap-binding complex (CBC) component CBP20 directly interacts with ELF7, a subunit of the transcription elongation factor RNA Pol II-associated factor 1 complex (PAF1c) to promote RNA Pol II transcription in plant response to salt stress. CBP20 and ELF7 coregulate the expression of a large number of genes including those crucial for salt tolerance. Both CBP20 and ELF7 are required for enhanced RNA Pol II elongation at salt-activated genes. Though CBP20 also regulates intron splicing, this function is largely independent of ELF7. Our study reveals the function of an RNA processing regulator CBC in assisting efficient RNA Pol II transcription and pinpoints the complex roles of CBC on mRNA production in plant salt stress resistance.
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Affiliation(s)
- Huairen Zhang
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, The Innovative Academy for Seed Design, Chinese Academy of Sciences, Beijing, China
| | - Xiaoyi Li
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, The Innovative Academy for Seed Design, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Ruitian Song
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, The Innovative Academy for Seed Design, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Zhenping Zhan
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, The Innovative Academy for Seed Design, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Fengyue Zhao
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, The Innovative Academy for Seed Design, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Zicong Li
- Ministry of Education Key Laboratory of Plant Development and Environmental Adaption Biology, School of Life Sciences, Shandong University, Qingdao, China
| | - Danhua Jiang
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, The Innovative Academy for Seed Design, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
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10
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Cai Y, Zhang W, Fu Y, Shan Z, Xu J, Wang P, Kong F, Jin J, Yan H, Ge X, Wang Y, You X, Chen J, Li X, Chen W, Chen X, Ma J, Tang X, Zhang J, Bao Y, Jiang L, Wang H, Wan J. Du13 encodes a C 2 H 2 zinc-finger protein that regulates Wx b pre-mRNA splicing and microRNA biogenesis in rice endosperm. PLANT BIOTECHNOLOGY JOURNAL 2022; 20:1387-1401. [PMID: 35560858 PMCID: PMC9241381 DOI: 10.1111/pbi.13821] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/16/2020] [Revised: 01/27/2022] [Accepted: 03/10/2022] [Indexed: 05/07/2023]
Abstract
Amylose content is a crucial physicochemical property responsible for the eating and cooking quality of rice (Oryza sativa L.) grain and is mainly controlled by the Waxy (Wx) gene. Previous studies have identified several Dull genes that modulate the expression of the Wxb allele in japonica rice by affecting the splicing efficiency of the Wxb pre-mRNA. Here, we uncover dual roles for a novel Dull gene in pre-mRNA splicing and microRNA processing. We isolated the dull mutant, du13, with a dull endosperm and low amylose content. Map-based cloning showed that Du13 encodes a C2 H2 zinc-finger protein. Du13 coordinates with the nuclear cap-binding complex to regulate the splicing of Wxb transcripts in rice endosperm. Moreover, Du13 also regulates alternative splicing of other protein-coding transcripts and affects the biogenesis of a subset of microRNAs. Our results reveal an evolutionarily conserved link between pre-mRNA splicing and microRNA biogenesis in rice endosperm. Our findings also provide new insights into the functions of Dull genes in rice and expand our knowledge of microRNA biogenesis in monocots.
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Affiliation(s)
- Yue Cai
- State Key Laboratory for Crop Genetics and Germplasm EnhancementJiangsu Plant Gene Engineering Research CenterNanjing Agricultural UniversityNanjingChina
| | - Wenwei Zhang
- State Key Laboratory for Crop Genetics and Germplasm EnhancementJiangsu Plant Gene Engineering Research CenterNanjing Agricultural UniversityNanjingChina
| | - Yushuang Fu
- State Key Laboratory for Crop Genetics and Germplasm EnhancementJiangsu Plant Gene Engineering Research CenterNanjing Agricultural UniversityNanjingChina
| | - Zhuangzhuang Shan
- State Key Laboratory for Crop Genetics and Germplasm EnhancementJiangsu Plant Gene Engineering Research CenterNanjing Agricultural UniversityNanjingChina
| | - Jiahuan Xu
- State Key Laboratory for Crop Genetics and Germplasm EnhancementJiangsu Plant Gene Engineering Research CenterNanjing Agricultural UniversityNanjingChina
| | - Peng Wang
- State Key Laboratory for Crop Genetics and Germplasm EnhancementJiangsu Plant Gene Engineering Research CenterNanjing Agricultural UniversityNanjingChina
| | - Fei Kong
- State Key Laboratory for Crop Genetics and Germplasm EnhancementJiangsu Plant Gene Engineering Research CenterNanjing Agricultural UniversityNanjingChina
| | - Jie Jin
- State Key Laboratory for Crop Genetics and Germplasm EnhancementJiangsu Plant Gene Engineering Research CenterNanjing Agricultural UniversityNanjingChina
| | - Haigang Yan
- State Key Laboratory for Crop Genetics and Germplasm EnhancementJiangsu Plant Gene Engineering Research CenterNanjing Agricultural UniversityNanjingChina
| | - Xinyuan Ge
- State Key Laboratory for Crop Genetics and Germplasm EnhancementJiangsu Plant Gene Engineering Research CenterNanjing Agricultural UniversityNanjingChina
| | - Yongxiang Wang
- State Key Laboratory for Crop Genetics and Germplasm EnhancementJiangsu Plant Gene Engineering Research CenterNanjing Agricultural UniversityNanjingChina
| | - Xiaoman You
- State Key Laboratory for Crop Genetics and Germplasm EnhancementJiangsu Plant Gene Engineering Research CenterNanjing Agricultural UniversityNanjingChina
| | - Jie Chen
- State Key Laboratory for Crop Genetics and Germplasm EnhancementJiangsu Plant Gene Engineering Research CenterNanjing Agricultural UniversityNanjingChina
| | - Xin Li
- State Key Laboratory for Crop Genetics and Germplasm EnhancementJiangsu Plant Gene Engineering Research CenterNanjing Agricultural UniversityNanjingChina
| | - Weiwei Chen
- State Key Laboratory for Crop Genetics and Germplasm EnhancementJiangsu Plant Gene Engineering Research CenterNanjing Agricultural UniversityNanjingChina
| | - Xingang Chen
- State Key Laboratory for Crop Genetics and Germplasm EnhancementJiangsu Plant Gene Engineering Research CenterNanjing Agricultural UniversityNanjingChina
| | - Jing Ma
- State Key Laboratory for Crop Genetics and Germplasm EnhancementJiangsu Plant Gene Engineering Research CenterNanjing Agricultural UniversityNanjingChina
| | - Xiaojie Tang
- State Key Laboratory for Crop Genetics and Germplasm EnhancementJiangsu Plant Gene Engineering Research CenterNanjing Agricultural UniversityNanjingChina
| | - Jie Zhang
- State Key Laboratory for Crop Genetics and Germplasm EnhancementJiangsu Plant Gene Engineering Research CenterNanjing Agricultural UniversityNanjingChina
| | - Yiqun Bao
- College of Life SciencesNanjing Agricultural UniversityNanjingChina
| | - Ling Jiang
- State Key Laboratory for Crop Genetics and Germplasm EnhancementJiangsu Plant Gene Engineering Research CenterNanjing Agricultural UniversityNanjingChina
| | - Haiyang Wang
- National Key Facility for Crop Gene Resources and Genetic ImprovementInstitute of Crop ScienceChinese Academy of Agricultural SciencesBeijingChina
| | - Jianmin Wan
- State Key Laboratory for Crop Genetics and Germplasm EnhancementJiangsu Plant Gene Engineering Research CenterNanjing Agricultural UniversityNanjingChina
- National Key Facility for Crop Gene Resources and Genetic ImprovementInstitute of Crop ScienceChinese Academy of Agricultural SciencesBeijingChina
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11
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Zhang Q, Zhang W, Wei J, Gao Z, Guan J, Cui Z, Wang X. SKIP Regulates ABA Signaling through Alternative Splicing in Arabidopsis. PLANT & CELL PHYSIOLOGY 2022; 63:494-507. [PMID: 35134199 DOI: 10.1093/pcp/pcac014] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/26/2021] [Revised: 01/10/2022] [Accepted: 02/01/2022] [Indexed: 06/14/2023]
Abstract
Abscisic acid (ABA) plays key roles in plant development and responses to abiotic stresses. A wide number of transcriptional and posttranslational regulatory mechanisms of ABA signaling are known; however, less is known about the regulatory roles of alternative splicing. In this work, we found that SKIP, a splicing factor, positively regulates ABA signaling. SKIP binds to the pre-mRNA of ABA signaling-related genes, such as PYL7, PYL8, ABI1, HAB1 and ABI5, to regulate their splicing. The precursor mRNA alternative splicing of several PYL receptors, PP2C phosphatases and ABF transcriptional factors is disrupted by the skip-1 mutation. The abnormal alternative splicing in skip-1 represses the expression of ABA-positive regulators, including PYLs and ABFs, and activates the expression of ABA-negative regulators, such as PP2Cs, which confers ABA hyposensitive phenotype of skip-1. We also found that ABA-mediated genome-wide alternative splicing and differential gene expression are changed by the skip-1 mutation. The number of the differential splicing events is increased by skip-1; however, the number of differential expressed genes in response to ABA is reduced by skip-1. Our results reveal a principle on how a splicing factor regulates ABA signaling and ABA-mediated genome-wide alternative splicing.
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Affiliation(s)
- Qi Zhang
- Rice Research Institute, Shenyang Agricultural University, Shenyang 110866, China
| | - Wei Zhang
- Rice Research Institute, Shenyang Agricultural University, Shenyang 110866, China
- Biotechnology Research Institute, Heilongjiang Academy of Agricultural Sciences, Harbin 150086, China
| | - Jianbo Wei
- Rice Research Institute, Shenyang Agricultural University, Shenyang 110866, China
| | - Zhaoxu Gao
- Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing 100871, China
| | - Jianing Guan
- Rice Research Institute, Shenyang Agricultural University, Shenyang 110866, China
| | - Zhibo Cui
- Rice Research Institute, Shenyang Agricultural University, Shenyang 110866, China
| | - Xiaoxue Wang
- Rice Research Institute, Shenyang Agricultural University, Shenyang 110866, China
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12
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Rambout X, Maquat LE. The nuclear cap-binding complex as choreographer of gene transcription and pre-mRNA processing. Genes Dev 2021; 34:1113-1127. [PMID: 32873578 PMCID: PMC7462061 DOI: 10.1101/gad.339986.120] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
In this review, Rambout and Maquat discuss known roles of the nuclear cap-binding complex (CBC) during the transcription of genes that encode proteins, stitching together past studies from diverse groups to describe the continuum of CBC-mediated checks and balances in eukaryotic cells. The largely nuclear cap-binding complex (CBC) binds to the 5′ caps of RNA polymerase II (RNAPII)-synthesized transcripts and serves as a dynamic interaction platform for a myriad of RNA processing factors that regulate gene expression. While influence of the CBC can extend into the cytoplasm, here we review the roles of the CBC in the nucleus, with a focus on protein-coding genes. We discuss differences between CBC function in yeast and mammals, covering the steps of transcription initiation, release of RNAPII from pausing, transcription elongation, cotranscriptional pre-mRNA splicing, transcription termination, and consequences of spurious transcription. We describe parameters known to control the binding of generic or gene-specific cofactors that regulate CBC activities depending on the process(es) targeted, illustrating how the CBC is an ever-changing choreographer of gene expression.
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Affiliation(s)
- Xavier Rambout
- Department of Biochemistry and Biophysics, School of Medicine and Dentistry, University of Rochester, Rochester, New York 14642, USA.,Center for RNA Biology, University of Rochester, Rochester, New York 14642, USA
| | - Lynne E Maquat
- Department of Biochemistry and Biophysics, School of Medicine and Dentistry, University of Rochester, Rochester, New York 14642, USA.,Center for RNA Biology, University of Rochester, Rochester, New York 14642, USA
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13
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Li Y, Guo Q, Liu P, Huang J, Zhang S, Yang G, Wu C, Zheng C, Yan K. Dual roles of the serine/arginine-rich splicing factor SR45a in promoting and interacting with nuclear cap-binding complex to modulate the salt-stress response in Arabidopsis. THE NEW PHYTOLOGIST 2021; 230:641-655. [PMID: 33421141 DOI: 10.1111/nph.17175] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/02/2020] [Accepted: 12/23/2020] [Indexed: 05/23/2023]
Abstract
Alternative splicing (AS) is emerging as a critical co-transcriptional regulation for plants in response to environmental stresses. Although multiple splicing factors have been linked to the salt-sensitive signaling network, the molecular mechanism remains unclear. We discovered that a conserved serine/arginine-rich (SR)-like protein, SR45a, as a component of the spliceosome, was involved in post-transcriptional regulation of salinity tolerance in Arabidopsis thaliana. Furthermore, SR45a was required for the AS and messenger RNA (mRNA) maturation of several salt-tolerance genes. Two alternatively spliced variants of SR45a were induced by salt stress, full-length SR45a-1a and the truncated isoform SR45a-1b, respectively. Lines with overexpression of SR45a-1a and SR45a-1b exhibited hypersensitive to salt stress. Our data indicated that SR45a directly interacted with the cap-binding complex (CBC) subunit cap-binding protein 20 (CBP20) which mediated salt-stress responses. Instead of binding to other spliceosome components, SR45a-1b promoted the association of SR45a-1a with CBP20, therefore mediating salt-stress signal transduction pathways. Additionally, the mutations in SR45a and CBP20 led to different salt-stress phenotypes. Together, these results provide the evidence that SR45a-CBP20 acts as a regulatory complex to regulate the plant response to salt stress, through a regulatory mechanism to fine-tune the splicing factors, especially in stressful conditions.
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Affiliation(s)
- Ying Li
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Taian, Shandong, 271018, China
| | - Qianhuan Guo
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Taian, Shandong, 271018, China
| | - Peng Liu
- Donald Danforth Plant Science Center, St Louis, MO, 63132, USA
| | - Jinguang Huang
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Taian, Shandong, 271018, China
| | - Shizhong Zhang
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Taian, Shandong, 271018, China
| | - Guodong Yang
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Taian, Shandong, 271018, China
| | - Changai Wu
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Taian, Shandong, 271018, China
| | - Chengchao Zheng
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Taian, Shandong, 271018, China
| | - Kang Yan
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Taian, Shandong, 271018, China
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14
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Ma Y, Zhang S, Bi C, Mei C, Jiang SC, Wang XF, Lu ZJ, Zhang DP. Arabidopsis exoribonuclease USB1 interacts with the PPR-domain protein SOAR1 to negatively regulate abscisic acid signaling. JOURNAL OF EXPERIMENTAL BOTANY 2020; 71:5837-5851. [PMID: 32969475 PMCID: PMC7541913 DOI: 10.1093/jxb/eraa315] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/19/2019] [Accepted: 09/23/2020] [Indexed: 05/27/2023]
Abstract
Signaling by the phytohormone abscisic acid (ABA) involves pre-mRNA splicing, a key process of post-transcriptional regulation of gene expression. However, the regulatory mechanism of alternative pre-mRNA splicing in ABA signaling remains largely unknown. We previously identified a pentatricopeptide repeat protein SOAR1 (suppressor of the ABAR-overexpressor 1) as a crucial player downstream of ABAR (putative ABA receptor) in ABA signaling. In this study, we identified a SOAR1 interaction partner USB1, which is an exoribonuclease catalyzing U6 production for spliceosome assembly. We reveal that together USB1 and SOAR1 negatively regulate ABA signaling in early seedling development. USB1 and SOAR1 are both required for the splicing of transcripts of numerous genes, including those involved in ABA signaling pathways, suggesting that USB1 and SOAR1 collaborate to regulate ABA signaling by affecting spliceosome assembly. These findings provide important new insights into the mechanistic control of alternative pre-mRNA splicing in the regulation of ABA-mediated plant responses to environmental cues.
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Affiliation(s)
- Yu Ma
- MOE Key Lab of Bioinformatics, Center for Plant Biology, School of Life Sciences,Tsinghua University, Beijing, China
| | - Shang Zhang
- MOE Key Lab of Bioinformatics, Center for Plant Biology, School of Life Sciences,Tsinghua University, Beijing, China
| | - Chao Bi
- MOE Key Lab of Bioinformatics, Center for Plant Biology, School of Life Sciences,Tsinghua University, Beijing, China
| | - Chao Mei
- MOE Key Lab of Bioinformatics, Center for Plant Biology, School of Life Sciences,Tsinghua University, Beijing, China
| | - Shang-Chuan Jiang
- MOE Key Lab of Bioinformatics, Center for Plant Biology, School of Life Sciences,Tsinghua University, Beijing, China
| | - Xiao-Fang Wang
- MOE Key Lab of Bioinformatics, Center for Plant Biology, School of Life Sciences,Tsinghua University, Beijing, China
| | - Zhi John Lu
- MOE Key Lab of Bioinformatics, Center for Plant Biology, School of Life Sciences,Tsinghua University, Beijing, China
| | - Da-Peng Zhang
- MOE Key Lab of Bioinformatics, Center for Plant Biology, School of Life Sciences,Tsinghua University, Beijing, China
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15
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Arabidopsis thaliana cbp80, c2h2, and flk Knockout Mutants Accumulate Increased Amounts of Circular RNAs. Cells 2020; 9:cells9091937. [PMID: 32825779 PMCID: PMC7564263 DOI: 10.3390/cells9091937] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2020] [Revised: 08/17/2020] [Accepted: 08/18/2020] [Indexed: 11/17/2022] Open
Abstract
Circular RNAs (circRNAs) are the products of the non-canonical splicing of pre-mRNAs. In contrast to humans and animals, our knowledge of the biogenesis and function of circRNAs in plants is very scarce. To identify proteins involved in plant circRNA generation, we characterized the transcriptomes of 18 Arabidopsis thaliana knockout mutants for genes related to splicing. The vast majority (>90%) of circRNAs were formed in more than one variant; only a small fraction of circRNAs was mutant-specific. Five times more circRNA types were identified in cbp80 and three times more in c2h2 mutants than in the wild-type. We also discovered that in cbp80, c2h2 and flk mutants, the accumulation of circRNAs was significantly increased. The increased accumulation of circular transcripts was not accompanied by corresponding changes in the accumulation of linear transcripts. Our results indicate that one of the roles of CBP80, C2H2 and FLK in splicing is to ensure the proper order of the exons. In the absence of one of the above-mentioned factors, the process might be altered, leading to the production of circular transcripts. This suggests that the transition toward circRNA production can be triggered by factors sequestering these proteins. Consequently, the expression of linear transcripts might be regulated through circRNA production.
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16
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First Come, First Served: Sui Generis Features of the First Intron. PLANTS 2020; 9:plants9070911. [PMID: 32707681 PMCID: PMC7411622 DOI: 10.3390/plants9070911] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/31/2020] [Revised: 07/15/2020] [Accepted: 07/17/2020] [Indexed: 02/07/2023]
Abstract
Most of the transcribed genes in eukaryotic cells are interrupted by intervening sequences called introns that are co-transcriptionally removed from nascent messenger RNA through the process of splicing. In Arabidopsis, 79% of genes contain introns and more than 60% of intron-containing genes undergo alternative splicing (AS), which ostensibly is considered to increase protein diversity as one of the intrinsic mechanisms for fitness to the varying environment or the internal developmental program. In addition, recent findings have prevailed in terms of overlooked intron functions. Here, we review recent progress in the underlying mechanisms of intron function, in particular by focusing on unique features of the first intron that is located in close proximity to the transcription start site. The distinct deposition of epigenetic marks and nucleosome density on the first intronic DNA sequence, the impact of the first intron on determining the transcription start site and elongation of its own expression (called intron-mediated enhancement, IME), translation control in 5′-UTR, and the new mechanism of the trans-acting function of the first intron in regulating gene expression at the post-transcriptional level are summarized.
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17
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Abstract
To investigate factors influencing pre-mRNA splicing in plants, we conducted a forward genetic screen using an alternatively-spliced GFP reporter gene in Arabidopsis thaliana. This effort generated a collection of sixteen mutants impaired in various splicing-related proteins, many of which had not been recovered in any prior genetic screen or implicated in splicing in plants. The factors are predicted to act at different steps of the spliceosomal cycle, snRNP biogenesis pathway, transcription, and mRNA transport. We have described eleven of the mutants in recent publications. Here we present the final five mutants, which are defective, respectively, in RNA-BINDING PROTEIN 45D (rbp45d), DIGEORGE SYNDROME CRITICAL REGION 14 (dgcr14), CYCLIN-DEPENDENT KINASE G2 (cdkg2), INTERACTS WITH SPT6 (iws1) and CAP BINDING PROTEIN 80 (cbp80). We provide RNA-sequencing data and analyses of differential gene expression and alternative splicing patterns for the cbp80 mutant and for several previously published mutants, including smfa and new alleles of cwc16a, for which such information was not yet available. Sequencing of small RNAs from the cbp80 mutant highlighted the necessity of wild-type CBP80 for processing of microRNA (miRNA) precursors into mature miRNAs. Redundancy tests of paralogs encoding several of the splicing factors revealed their functional non-equivalence in the GFP reporter gene system. We discuss the cumulative findings and their implications for the regulation of pre-mRNA splicing efficiency and alternative splicing in plants. The mutant collection provides a unique resource for further studies on a coherent set of splicing factors and their roles in gene expression, alternative splicing and plant development.
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18
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Li H, Siddiqui O, Zhang H, Guan Y. Joint learning improves protein abundance prediction in cancers. BMC Biol 2019; 17:107. [PMID: 31870366 PMCID: PMC6929375 DOI: 10.1186/s12915-019-0730-9] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2019] [Accepted: 12/04/2019] [Indexed: 12/20/2022] Open
Abstract
BACKGROUND The classic central dogma in biology is the information flow from DNA to mRNA to protein, yet complicated regulatory mechanisms underlying protein translation often lead to weak correlations between mRNA and protein abundances. This is particularly the case in cancer samples and when evaluating the same gene across multiple samples. RESULTS Here, we report a method for predicting proteome from transcriptome, using a training dataset provided by NCI-CPTAC and TCGA, consisting of transcriptome and proteome data from 77 breast and 105 ovarian cancer samples. First, we establish a generic model capturing the correlation between mRNA and protein abundance of a single gene. Second, we build a gene-specific model capturing the interdependencies among multiple genes in a regulatory network. Third, we create a cross-tissue model by joint learning the information of shared regulatory networks and pathways across cancer tissues. Our method ranked first in the NCI-CPTAC DREAM Proteogenomics Challenge, and the predictive performance is close to the accuracy of experimental replicates. Key functional pathways and network modules controlling the proteomic abundance in cancers were revealed, in particular metabolism-related genes. CONCLUSIONS We present a method to predict proteome from transcriptome, leveraging data from different cancer tissues to build a trans-tissue model, and suggest how to integrate information from multiple cancers to provide a foundation for further research.
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Affiliation(s)
- Hongyang Li
- Department of Computational Medicine and Bioinformatics, University of Michigan, 100 Washtenaw Avenue, Ann Arbor, MI, 48109, USA.
| | - Omer Siddiqui
- Department of Computational Medicine and Bioinformatics, University of Michigan, 100 Washtenaw Avenue, Ann Arbor, MI, 48109, USA
| | - Hongjiu Zhang
- Department of Computational Medicine and Bioinformatics, University of Michigan, 100 Washtenaw Avenue, Ann Arbor, MI, 48109, USA
| | - Yuanfang Guan
- Department of Computational Medicine and Bioinformatics, University of Michigan, 100 Washtenaw Avenue, Ann Arbor, MI, 48109, USA. .,Department of Internal Medicine, University of Michigan, 100 Washtenaw Avenue, Ann Arbor, MI, 48109, USA.
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Highly ABA-Induced 1 (HAI1)-Interacting protein HIN1 and drought acclimation-enhanced splicing efficiency at intron retention sites. Proc Natl Acad Sci U S A 2019; 116:22376-22385. [PMID: 31611386 PMCID: PMC6825267 DOI: 10.1073/pnas.1906244116] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
The Highly ABA-Induced 1 (HAI1) protein phosphatase is a central component of drought-related signaling. A screen for HAI1-interacting proteins identified HAI1-Interactor 1 (HIN1), a nuclear protein of unknown function which could be dephosphorylated by HAI1 in vitro. HIN1 colocalization and interaction with serine-arginine rich (SR) splicing factors and appearance of nuclear speckle-localized HIN1 during low water potential (ψw) stress suggested a pre-mRNA splicing-related function. RNA sequencing of Arabidopsis Col-0 wild type identified more than 500 introns where moderate severity low ψw altered intron retention (IR) frequency. Surprisingly, nearly 90% of these had increased splicing efficiency (decreased IR) during stress. For one-third of these introns, ectopic HIN1 expression (35S:HIN1) in unstressed plants mimicked the increased splicing efficiency seen in stress-treated wild type. HIN1 bound to a GAA-repeat, Exonic Splicing Enhancer-like RNA motif enriched in flanking sequence around HIN1-regulated introns. Genes with stress and HIN1-affected splicing efficiency were enriched for abiotic stress and signaling-related functions. The 35S:HIN1 plants had enhanced growth maintenance during low ψw, while hin1 mutants had reduced growth, further indicating the role of HIN1 in drought response. HIN1 is annotated as an MYB/SANT domain protein but has limited homology to other MYB/SANT proteins and is not related to known yeast or metazoan RNA-binding proteins or splicing regulators. Together these data identify HIN1 as a plant-specific RNA-binding protein, show a specific effect of drought acclimation to promote splicing efficiency of IR-prone introns, and also discover HAI1-HIN1 interaction and dephosphorylation that connects stress signaling to splicing regulation.
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20
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Gu J, Xia Z, Luo Y, Jiang X, Qian B, Xie H, Zhu JK, Xiong L, Zhu J, Wang ZY. Spliceosomal protein U1A is involved in alternative splicing and salt stress tolerance in Arabidopsis thaliana. Nucleic Acids Res 2019; 46:1777-1792. [PMID: 29228330 PMCID: PMC5829640 DOI: 10.1093/nar/gkx1229] [Citation(s) in RCA: 47] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2016] [Accepted: 11/30/2017] [Indexed: 12/14/2022] Open
Abstract
Soil salinity is a significant threat to sustainable agricultural production worldwide. Plants must adjust their developmental and physiological processes to cope with salt stress. Although the capacity for adaptation ultimately depends on the genome, the exceptional versatility in gene regulation provided by the spliceosome-mediated alternative splicing (AS) is essential in these adaptive processes. However, the functions of the spliceosome in plant stress responses are poorly understood. Here, we report the in-depth characterization of a U1 spliceosomal protein, AtU1A, in controlling AS of pre-mRNAs under salt stress and salt stress tolerance in Arabidopsis thaliana. The atu1a mutant was hypersensitive to salt stress and accumulated more reactive oxygen species (ROS) than the wild-type under salt stress. RNA-seq analysis revealed that AtU1A regulates AS of many genes, presumably through modulating recognition of 5′ splice sites. We showed that AtU1A is associated with the pre-mRNA of the ROS detoxification-related gene ACO1 and is necessary for the regulation of ACO1 AS. ACO1 is important for salt tolerance because ectopic expression of ACO1 in the atu1a mutant can partially rescue its salt hypersensitive phenotype. Our findings highlight the critical role of AtU1A as a regulator of pre-mRNA processing and salt tolerance in plants.
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Affiliation(s)
- Jinbao Gu
- Hainan Key Laboratory for Sustainable Utilization of Tropical Bioresource, Institute of Tropical Agriculture and Forestry, Hainan University, Haikou, Hainan 570228, China
| | - Zhiqiang Xia
- Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, Hainan 571101, China
| | - Yuehua Luo
- Hainan Key Laboratory for Sustainable Utilization of Tropical Bioresource, Institute of Tropical Agriculture and Forestry, Hainan University, Haikou, Hainan 570228, China
| | - Xingyu Jiang
- Hainan Key Laboratory for Sustainable Utilization of Tropical Bioresource, Institute of Tropical Agriculture and Forestry, Hainan University, Haikou, Hainan 570228, China
| | - Bilian Qian
- Department of Plant Science and Landscape Architecture, University of Maryland, College Park, MD 20742, USA
| | - He Xie
- Tobacco Breeding and Biotechnology Research Center, Yunnan Academy of Tobacco Agricultural Sciences, Kunming 650021, China
| | - Jian-Kang Zhu
- Department of Horticulture and Landscape Architecture, Purdue University, West Lafayette, IN 47906, USA.,Shanghai Center for Plant Stress Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200032, China
| | - Liming Xiong
- King Abdullah University of Science and Technology (KAUST), Biological and Environmental Sciences & Engineering Division, Thuwal 23955-6900, Saudi Arabia
| | - Jianhua Zhu
- Department of Plant Science and Landscape Architecture, University of Maryland, College Park, MD 20742, USA
| | - Zhen-Yu Wang
- Hainan Key Laboratory for Sustainable Utilization of Tropical Bioresource, Institute of Tropical Agriculture and Forestry, Hainan University, Haikou, Hainan 570228, China
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22
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Song X, Li Y, Cao X, Qi Y. MicroRNAs and Their Regulatory Roles in Plant-Environment Interactions. ANNUAL REVIEW OF PLANT BIOLOGY 2019; 70:489-525. [PMID: 30848930 DOI: 10.1146/annurev-arplant-050718-100334] [Citation(s) in RCA: 366] [Impact Index Per Article: 73.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/19/2023]
Abstract
MicroRNAs (miRNAs) are 20-24 nucleotide noncoding RNAs abundant in plants and animals. The biogenesis of plant miRNAs involves transcription of miRNA genes, processing of primary miRNA transcripts by DICER-LIKE proteins into mature miRNAs, and loading of mature miRNAs into ARGONAUTE proteins to form miRNA-induced silencing complex (miRISC). By targeting complementary sequences, miRISC negatively regulates gene expression, thereby coordinating plant development and plant-environment interactions. In this review, we present and discuss recent updates on the mechanisms and regulation of miRNA biogenesis, miRISC assembly and actions as well as the regulatory roles of miRNAs in plant developmental plasticity, abiotic/biotic responses, and symbiotic/parasitic interactions. Finally, we suggest future directions for plant miRNA research.
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Affiliation(s)
- Xianwei Song
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research, CAS Center for Excellence in Molecular Plant Sciences, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China;
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100039, China
| | - Yan Li
- Center for Plant Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China;
- Tsinghua-Peking Center for Life Sciences, Beijing 100084, China
| | - Xiaofeng Cao
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research, CAS Center for Excellence in Molecular Plant Sciences, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China;
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100039, China
| | - Yijun Qi
- Center for Plant Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China;
- Tsinghua-Peking Center for Life Sciences, Beijing 100084, China
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23
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Chen SL, Rooney TJ, Hu AR, Beard HS, Garrett WM, Mangalath LM, Powers JJ, Cooper B, Zhang XN. Quantitative Proteomics Reveals a Role for SERINE/ARGININE-Rich 45 in Regulating RNA Metabolism and Modulating Transcriptional Suppression via the ASAP Complex in Arabidopsis thaliana. FRONTIERS IN PLANT SCIENCE 2019; 10:1116. [PMID: 31608083 PMCID: PMC6761909 DOI: 10.3389/fpls.2019.01116] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/29/2019] [Accepted: 08/14/2019] [Indexed: 05/12/2023]
Abstract
Pre-mRNA alternative splicing is a conserved mechanism for eukaryotic cells to leverage existing genetic resources to create a diverse pool of protein products. It is regulated in coordination with other events in RNA metabolism such as transcription, polyadenylation, RNA transport, and nonsense-mediated decay via protein networks. SERINE/ARGININE-RICH 45 (SR45) is thought to be a neutral splicing regulator. It is orthologous to a component of the apoptosis and splicing-associated protein (ASAP) complex functioning to regulate RNA metabolism at multiple levels. Within this context, we try to understand why the sr45-1 mutant Arabidopsis has malformed flowers, delayed flowering time, and increased disease resistance. Prior studies revealed increased expression for some disease resistance genes and the flowering suppressor Flowering Locus C (FLC) in sr45-1 mutants and a physical association between SR45 and reproductive process-related RNAs. Here, we used Tandem Mass Tag-based quantitative mass spectrometry to compare the protein abundance from inflorescence between Arabidopsis wild-type (Col-0) and sr45-1 mutant plants. A total of 7,206 proteins were quantified, of which 227 proteins exhibited significantly different accumulation. Only a small percentage of these proteins overlapped with the dataset of RNAs with altered expression. The proteomics results revealed that the sr45-1 mutant had increased amounts of enzymes for glucosinolate biosynthesis which are important for disease resistance. Furthermore, the mutant inflorescence had a drastically reduced amount of the Sin3-associated protein 18 (SAP18), a second ASAP complex component, despite no significant reduction in SAP18 RNA. The third ASAP component protein, ACINUS, also had lower abundance without significant RNA changes in the sr45-1 mutant. To test the effect of SR45 on SAP18, a SAP18-GFP fusion protein was overproduced in transgenic Arabidopsis Col-0 and sr45-1 plants. SAP18-GFP has less accumulation in the nucleus, the site of activity for the ASAP complex, without SR45. Furthermore, transgenic sr45-1 mutants overproducing SAP18-GFP expressed even more FLC and had a more severe flowering delay than non-transgenic sr45-1 mutants. These results suggest that SR45 is required to maintain the wild-type level of SAP18 protein accumulation in the nucleus and that FLC-regulated flowering time is regulated by the correct expression and localization of the ASAP complex.
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Affiliation(s)
- Samuel L. Chen
- Bioinformatics Program, St. Bonaventure University, St. Bonaventure, NY, United States
| | - Timothy J. Rooney
- Biochemistry Program, St. Bonaventure University, St. Bonaventure, NY, United States
| | - Anna R. Hu
- Biochemistry Program, St. Bonaventure University, St. Bonaventure, NY, United States
| | - Hunter S. Beard
- Soybean Genomics and Improvement Laboratory, USDA-ARS, Beltsville, MD, United States
| | - Wesley M. Garrett
- Animal Biosciences & Biotechnology Laboratory, USDA-ARS, Beltsville, MD, United States
| | - Leann M. Mangalath
- Department of Biology, St. Bonaventure University, St. Bonaventure, NY, United States
| | - Jordan J. Powers
- Biochemistry Program, St. Bonaventure University, St. Bonaventure, NY, United States
| | - Bret Cooper
- Soybean Genomics and Improvement Laboratory, USDA-ARS, Beltsville, MD, United States
| | - Xiao-Ning Zhang
- Biochemistry Program, St. Bonaventure University, St. Bonaventure, NY, United States
- Department of Biology, St. Bonaventure University, St. Bonaventure, NY, United States
- *Correspondence: Xiao-Ning Zhang,
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24
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Abstract
Assembly of the barley genome and extensive use of RNA-seq has resulted in an abundance of gene expression data and the recognition of wide-scale production of alternatively spliced transcripts. Here, we describe in detail a high-resolution reverse transcription-PCR based panel (HR RT-PCR) that confirms the accuracy of alternatively spliced transcripts from RNA-seq and allows quantification of changes in the proportion of splice isoforms between different experimental conditions, time points, tissues, genotypes, ecotypes, and treatments. By validating a selection of barley genes, use of the panel gives confidence or otherwise to the genome-wide global changes in alternatively spliced transcripts reported by RNA-seq. This simple assay can readily be applied to perform detailed transcript isoform analysis for any gene in any species.
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25
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de Francisco Amorim M, Willing EM, Szabo EX, Francisco-Mangilet AG, Droste-Borel I, Maček B, Schneeberger K, Laubinger S. The U1 snRNP Subunit LUC7 Modulates Plant Development and Stress Responses via Regulation of Alternative Splicing. THE PLANT CELL 2018; 30:2838-2854. [PMID: 30309899 PMCID: PMC6305971 DOI: 10.1105/tpc.18.00244] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/28/2018] [Revised: 09/11/2018] [Accepted: 10/05/2018] [Indexed: 05/21/2023]
Abstract
Introns are removed by the spliceosome, a large macromolecular complex composed of five ribonucleoprotein subcomplexes (U snRNPs). The U1 snRNP, which binds to 5' splice sites, plays an essential role in early steps of the splicing reaction. Here, we show that Arabidopsis thaliana LETHAL UNLESS CBC7 (LUC7) proteins, which are encoded by a three-member gene family in Arabidopsis, are important for plant development and stress resistance. We show that LUC7 is a U1 snRNP accessory protein by RNA immunoprecipitation experiments and LUC7 protein complex purifications. Transcriptome analyses revealed that LUC7 proteins are not only important for constitutive splicing, but also affect hundreds of alternative splicing events. Interestingly, LUC7 proteins specifically promote splicing of a subset of terminal introns. Splicing of LUC7-dependent introns is a prerequisite for nuclear export, and some splicing events are modulated by stress in a LUC7-dependent manner. Taken together, our results highlight the importance of the U1 snRNP component LUC7 in splicing regulation and suggest a previously unrecognized role of a U1 snRNP accessory factor in terminal intron splicing.
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Affiliation(s)
- Marcella de Francisco Amorim
- Centre for Plant Molecular Biology (ZMBP), University of Tuebingen, 72076 Tuebingen, Germany
- Chemical Genomics Centre of the Max Planck Society, 44227 Dortmund, Germany
- Max Planck Institute for Developmental Biology, 72076 Tuebingen, Germany
| | - Eva-Maria Willing
- Max Planck Institute for Plant Breeding Research, 50829 Cologne, Germany
| | - Emese X Szabo
- Centre for Plant Molecular Biology (ZMBP), University of Tuebingen, 72076 Tuebingen, Germany
- Chemical Genomics Centre of the Max Planck Society, 44227 Dortmund, Germany
- Max Planck Institute for Developmental Biology, 72076 Tuebingen, Germany
- Carl von Ossietzky University, 26129 Oldenburg, Germany
| | - Anchilie G Francisco-Mangilet
- Centre for Plant Molecular Biology (ZMBP), University of Tuebingen, 72076 Tuebingen, Germany
- Chemical Genomics Centre of the Max Planck Society, 44227 Dortmund, Germany
- Max Planck Institute for Developmental Biology, 72076 Tuebingen, Germany
- Carl von Ossietzky University, 26129 Oldenburg, Germany
| | | | - Boris Maček
- Proteome Centre, University of Tuebingen, 72076 Tuebingen, Germany
| | | | - Sascha Laubinger
- Centre for Plant Molecular Biology (ZMBP), University of Tuebingen, 72076 Tuebingen, Germany
- Chemical Genomics Centre of the Max Planck Society, 44227 Dortmund, Germany
- Max Planck Institute for Developmental Biology, 72076 Tuebingen, Germany
- Carl von Ossietzky University, 26129 Oldenburg, Germany
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26
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Bazin J, Romero N, Rigo R, Charon C, Blein T, Ariel F, Crespi M. Nuclear Speckle RNA Binding Proteins Remodel Alternative Splicing and the Non-coding Arabidopsis Transcriptome to Regulate a Cross-Talk Between Auxin and Immune Responses. FRONTIERS IN PLANT SCIENCE 2018; 9:1209. [PMID: 30186296 PMCID: PMC6111844 DOI: 10.3389/fpls.2018.01209] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/16/2018] [Accepted: 07/27/2018] [Indexed: 05/25/2023]
Abstract
Nuclear speckle RNA binding proteins (NSRs) act as regulators of alternative splicing (AS) and auxin-regulated developmental processes such as lateral root formation in Arabidopsis thaliana. These proteins were shown to interact with specific alternatively spliced mRNA targets and at least with one structured lncRNA, named Alternative Splicing Competitor RNA. Here, we used genome-wide analysis of RNAseq to monitor the NSR global role on multiple tiers of gene expression, including RNA processing and AS. NSRs affect AS of 100s of genes as well as the abundance of lncRNAs particularly in response to auxin. Among them, the FPA floral regulator displayed alternative polyadenylation and differential expression of antisense COOLAIR lncRNAs in nsra/b mutants. This may explains the early flowering phenotype observed in nsra and nsra/b mutants. GO enrichment analysis of affected lines revealed a novel link of NSRs with the immune response pathway. A RIP-seq approach on an NSRa fusion protein in mutant background identified that lncRNAs are privileged direct targets of NSRs in addition to specific AS mRNAs. The interplay of lncRNAs and AS mRNAs in NSR-containing complexes may control the crosstalk between auxin and the immune response pathway.
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Affiliation(s)
- Jérémie Bazin
- CNRS, INRA, Institute of Plant Sciences Paris-Saclay IPS2, Univ Paris Sud, Univ Evry, Univ Paris-Diderot, Sorbonne Paris-Cite, Universite Paris-Saclay, Orsay, France
| | - Natali Romero
- CNRS, INRA, Institute of Plant Sciences Paris-Saclay IPS2, Univ Paris Sud, Univ Evry, Univ Paris-Diderot, Sorbonne Paris-Cite, Universite Paris-Saclay, Orsay, France
| | - Richard Rigo
- CNRS, INRA, Institute of Plant Sciences Paris-Saclay IPS2, Univ Paris Sud, Univ Evry, Univ Paris-Diderot, Sorbonne Paris-Cite, Universite Paris-Saclay, Orsay, France
| | - Celine Charon
- CNRS, INRA, Institute of Plant Sciences Paris-Saclay IPS2, Univ Paris Sud, Univ Evry, Univ Paris-Diderot, Sorbonne Paris-Cite, Universite Paris-Saclay, Orsay, France
| | - Thomas Blein
- CNRS, INRA, Institute of Plant Sciences Paris-Saclay IPS2, Univ Paris Sud, Univ Evry, Univ Paris-Diderot, Sorbonne Paris-Cite, Universite Paris-Saclay, Orsay, France
| | - Federico Ariel
- CNRS, INRA, Institute of Plant Sciences Paris-Saclay IPS2, Univ Paris Sud, Univ Evry, Univ Paris-Diderot, Sorbonne Paris-Cite, Universite Paris-Saclay, Orsay, France
- Instituto de Agrobiotecnologıa del Litoral, CONICET, Universidad Nacional del Litoral, Santa Fe, Argentina
| | - Martin Crespi
- CNRS, INRA, Institute of Plant Sciences Paris-Saclay IPS2, Univ Paris Sud, Univ Evry, Univ Paris-Diderot, Sorbonne Paris-Cite, Universite Paris-Saclay, Orsay, France
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27
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Cheng L, Wang Y, Liu Y, Zhang Q, Gao H, Zhang F. Comparative proteomics illustrates the molecular mechanism of potato (Solanum tuberosum L.) tuberization inhibited by exogenous gibberellins in vitro. PHYSIOLOGIA PLANTARUM 2018; 163:103-123. [PMID: 29135031 DOI: 10.1111/ppl.12670] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/08/2017] [Revised: 10/31/2017] [Accepted: 11/08/2017] [Indexed: 05/24/2023]
Abstract
Among the multiple environmental signals and hormonal factors regulating potato tuberization, gibberellins (GAs) are important components of the signaling pathways in these processes. To understand the GAs-signaling response mechanism of potato tuberization, a comparative proteomics approach was applied to analyze proteome change of potato tuberization in vitro subjected to a range of exogenous GA3 treatments (0, 0.01, 0.1 and 1.0 μM) using two-dimensional gel electrophoresis. Quantitative image analyses showed that a total of 37 protein spots have their abundance significantly altered more than 2-fold. Among these proteins, 13 proteins were up-regulated, 13 proteins were down-regulated, one protein was absent and 10 proteins were induced after treatment by exogenous GA3 . The MALDI-TOF/TOF MS analyses led to the identification of differentially abundant proteins that are mainly involved in bioenergy and metabolism, storage, signaling, cell defense and rescue, transcription, chaperones, transport. Furthermore, the comparative analysis of GA3 -responsive proteome allowed for general elucidation of underlying molecular mechanisms of potato tuberization inhibited by exogenous GA3 . Most of these cellular processes were not conducive to the transition from stolon elongation to tuber formation, including a blockage of starch and storage protein accumulation, the accelerated carbohydrate catabolism, a blockage of JA biosynthesis but an elevated endogenous GAs level, the amplification of GA3 signal transduction by other signaling pathways, and the regulation of cellular RNA metabolism for controlling tuberization. Our results firstly integrated physiology and proteome data to provide new insights into GA3 -signaling response mechanisms of potato tuberization in vitro.
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Affiliation(s)
- Lixiang Cheng
- College of Agronomy, Gansu Provincial Key Laboratory of Aridland Crop Science, Gansu Key Laboratory of Crop Improvement & Germplasm Enhancement, Gansu Agricultural University, Lanzhou, China
| | - Yuping Wang
- College of Agronomy, Gansu Provincial Key Laboratory of Aridland Crop Science, Gansu Key Laboratory of Crop Improvement & Germplasm Enhancement, Gansu Agricultural University, Lanzhou, China
| | - Yueshan Liu
- College of Agronomy, Gansu Provincial Key Laboratory of Aridland Crop Science, Gansu Key Laboratory of Crop Improvement & Germplasm Enhancement, Gansu Agricultural University, Lanzhou, China
| | - Qingquan Zhang
- College of Agronomy, Gansu Provincial Key Laboratory of Aridland Crop Science, Gansu Key Laboratory of Crop Improvement & Germplasm Enhancement, Gansu Agricultural University, Lanzhou, China
| | - Huihui Gao
- College of Agronomy, Gansu Provincial Key Laboratory of Aridland Crop Science, Gansu Key Laboratory of Crop Improvement & Germplasm Enhancement, Gansu Agricultural University, Lanzhou, China
| | - Feng Zhang
- College of Agronomy, Gansu Provincial Key Laboratory of Aridland Crop Science, Gansu Key Laboratory of Crop Improvement & Germplasm Enhancement, Gansu Agricultural University, Lanzhou, China
- College of Life Science and Technology, Gansu Agricultural University, Lanzhou, China
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28
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Pieczynski M, Kruszka K, Bielewicz D, Dolata J, Szczesniak M, Karlowski W, Jarmolowski A, Szweykowska-Kulinska Z. A Role of U12 Intron in Proper Pre-mRNA Splicing of Plant Cap Binding Protein 20 Genes. FRONTIERS IN PLANT SCIENCE 2018; 9:475. [PMID: 29755485 PMCID: PMC5932401 DOI: 10.3389/fpls.2018.00475] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/12/2018] [Accepted: 03/27/2018] [Indexed: 05/30/2023]
Abstract
The nuclear cap-binding complex (CBC) is composed of two cap-binding proteins: CBP20 and CBP80. The CBP20 gene structure is highly conserved across land plant species. All studied CBP20 genes contain eight exons and seven introns, with the fourth intron belonging to the U12 class. This highly conserved U12 intron always divides the plant CBP20 gene into two parts: one part encodes the core domain containing the RNA binding domain (RBD), and the second part encodes the tail domain with a nuclear localization signal (NLS). In this study, we investigate the importance of the U12 intron in the Arabidopsis thaliana CBP20 gene by moving it to different intron locations of the gene. Relocation of the U12 intron resulted in a significant decrease in the U12 intron splicing efficiency and the accumulation of wrongly processed transcripts. These results suggest that moving the U12 intron to any other position of the A. thaliana CBP20 gene disturbs splicing, leading to substantial downregulation of the level of properly spliced mRNA and CBP20 protein. Moreover, the replacement of the U12 intron with a U2 intron leads to undesired alternative splicing events, indicating that the proper localization of the U12 intron in the CBP20 gene secures correct CBP20 pre-mRNA maturation and CBP20 protein levels in a plant. Surprisingly, our results also show that the efficiency of U12 splicing depends on intron length. In conclusion, our study emphasizes the importance of proper U12 intron localization in plant CBP20 genes for correct pre-mRNA processing.
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Affiliation(s)
- Marcin Pieczynski
- Department of Gene Expression, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University in Poznan, Poznan, Poland
| | - Katarzyna Kruszka
- Department of Gene Expression, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University in Poznan, Poznan, Poland
| | - Dawid Bielewicz
- Department of Gene Expression, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University in Poznan, Poznan, Poland
| | - Jakub Dolata
- Department of Gene Expression, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University in Poznan, Poznan, Poland
| | - Michal Szczesniak
- Department of Integrative Genomics, Institute of Anthropology, Faculty of Biology, Adam Mickiewicz University in Poznan, Poznan, Poland
| | - Wojciech Karlowski
- Department of Computational Biology, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University in Poznan, Poznan, Poland
| | - Artur Jarmolowski
- Department of Gene Expression, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University in Poznan, Poznan, Poland
| | - Zofia Szweykowska-Kulinska
- Department of Gene Expression, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University in Poznan, Poznan, Poland
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29
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Laloum T, Martín G, Duque P. Alternative Splicing Control of Abiotic Stress Responses. TRENDS IN PLANT SCIENCE 2018; 23:140-150. [PMID: 29074233 DOI: 10.1016/j.tplants.2017.09.019] [Citation(s) in RCA: 281] [Impact Index Per Article: 46.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/23/2017] [Revised: 09/25/2017] [Accepted: 09/26/2017] [Indexed: 05/20/2023]
Abstract
Alternative splicing, which generates multiple transcripts from the same gene, is an important modulator of gene expression that can increase proteome diversity and regulate mRNA levels. In plants, this post-transcriptional mechanism is markedly induced in response to environmental stress, and recent studies have identified alternative splicing events that allow rapid adjustment of the abundance and function of key stress-response components. In agreement, plant mutants defective in splicing factors are severely impaired in their response to abiotic stress. Notably, mounting evidence indicates that alternative splicing regulates stress responses largely by targeting the abscisic acid (ABA) pathway. We review here current understanding of post-transcriptional control of plant stress tolerance via alternative splicing and discuss research challenges for the near future.
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Affiliation(s)
- Tom Laloum
- Instituto Gulbenkian de Ciência, 2780-156 Oeiras, Portugal
| | - Guiomar Martín
- Instituto Gulbenkian de Ciência, 2780-156 Oeiras, Portugal
| | - Paula Duque
- Instituto Gulbenkian de Ciência, 2780-156 Oeiras, Portugal.
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30
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Daszkowska-Golec A. Emerging Roles of the Nuclear Cap-Binding Complex in Abiotic Stress Responses. PLANT PHYSIOLOGY 2018; 176:242-253. [PMID: 29142023 PMCID: PMC5761810 DOI: 10.1104/pp.17.01017] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/24/2017] [Accepted: 10/23/2017] [Indexed: 05/26/2023]
Abstract
Plant nuclear CBC consisted of two subunits (CBP20 and CBP80) is involved in both conserved processes related to RNA metabolism and simultaneously in extremely dynamic plant stress response.
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Affiliation(s)
- Agata Daszkowska-Golec
- Department of Genetics, Faculty of Biology and Environmental Protection, University of Silesia in Katowice, 40-032 Katowice, Poland
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31
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Xie S, Zhang X, Zhou Z, Li X, Huang Y, Zhang J, Weng J. Identification of genes alternatively spliced in developing maize endosperm. PLANT BIOLOGY (STUTTGART, GERMANY) 2018; 20:59-66. [PMID: 28945323 DOI: 10.1111/plb.12631] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/02/2017] [Accepted: 09/17/2017] [Indexed: 06/07/2023]
Abstract
The process of alternative splicing is critical for the regulation of growth and development of plants. Thus far, little is known about the role of alternative splicing in the regulation of maize (Zea mays L.) endosperm development. RNA sequencing (RNA-seq) data of endosperms from two maize inbred lines, Mo17 and Ji419, at 15 and 25 days after pollination (DAP), respectively, were used to identify genes that were alternatively spliced during endosperm development. Intron retention (IR) in GRMZM2G005887 was further validated using PCR and re-sequencing technologies. In total, 49,000 alternatively spliced events and ca. 20,000 alternatively spliced genes were identified in the two maize inbred lines. Of these, 30 genes involved in amino acid biosynthesis and starch biosynthesis were identified, with IR occurring only in a specific sample, and were significantly co-expressed with ten well-known genes related to maize endosperm development. Moreover, IR in GRMZM2G005887, which encodes a cysteine synthase, was confirmed to occur only in the endosperm of Mo17 at 15 DAP, resulting in the retention of a 121-bp fragment in its 5' untranslated region. Two cis-acting regulatory elements, CAAT-box and TATA-box were observed in the retained fragment in Mo17 at 15 DAP; this could regulate the expression of this gene and influence endosperm development. The results suggest that the 30 genes with IR identified herein might be associated with maize endosperm development, and are likely to play important roles in the developing maize endosperm.
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Affiliation(s)
- S Xie
- College of Life Science, Sichuan Agricultural University, Ya'an, China
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - X Zhang
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Z Zhou
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - X Li
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Y Huang
- College of Agronomy, Sichuan Agricultural University, Chengdu, China
| | - J Zhang
- College of Life Science, Sichuan Agricultural University, Ya'an, China
| | - J Weng
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, China
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32
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miRNA mediated regulation of NAC transcription factors in plant development and environment stress response. ACTA ACUST UNITED AC 2017. [DOI: 10.1016/j.plgene.2017.05.013] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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33
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Zhang R, Calixto CPG, Marquez Y, Venhuizen P, Tzioutziou NA, Guo W, Spensley M, Entizne JC, Lewandowska D, Ten Have S, Frei Dit Frey N, Hirt H, James AB, Nimmo HG, Barta A, Kalyna M, Brown JWS. A high quality Arabidopsis transcriptome for accurate transcript-level analysis of alternative splicing. Nucleic Acids Res 2017; 45:5061-5073. [PMID: 28402429 PMCID: PMC5435985 DOI: 10.1093/nar/gkx267] [Citation(s) in RCA: 169] [Impact Index Per Article: 24.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2016] [Accepted: 04/04/2017] [Indexed: 12/30/2022] Open
Abstract
Alternative splicing generates multiple transcript and protein isoforms from the same gene and thus is important in gene expression regulation. To date, RNA-sequencing (RNA-seq) is the standard method for quantifying changes in alternative splicing on a genome-wide scale. Understanding the current limitations of RNA-seq is crucial for reliable analysis and the lack of high quality, comprehensive transcriptomes for most species, including model organisms such as Arabidopsis, is a major constraint in accurate quantification of transcript isoforms. To address this, we designed a novel pipeline with stringent filters and assembled a comprehensive Reference Transcript Dataset for Arabidopsis (AtRTD2) containing 82,190 non-redundant transcripts from 34 212 genes. Extensive experimental validation showed that AtRTD2 and its modified version, AtRTD2-QUASI, for use in Quantification of Alternatively Spliced Isoforms, outperform other available transcriptomes in RNA-seq analysis. This strategy can be implemented in other species to build a pipeline for transcript-level expression and alternative splicing analyses.
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Affiliation(s)
- Runxuan Zhang
- Informatics and Computational Sciences, The James Hutton Institute, Invergowrie, Dundee DD2 5DA, UK
| | - Cristiane P G Calixto
- Plant Sciences Division, College of Life Sciences, University of Dundee, Invergowrie, Dundee DD2 5DA, UK
| | - Yamile Marquez
- Max F. Perutz Laboratories, Medical University of Vienna, Dr. Bohrgasse 9/3, 1030 Vienna, Austria
| | - Peter Venhuizen
- Max F. Perutz Laboratories, Medical University of Vienna, Dr. Bohrgasse 9/3, 1030 Vienna, Austria
| | - Nikoleta A Tzioutziou
- Plant Sciences Division, College of Life Sciences, University of Dundee, Invergowrie, Dundee DD2 5DA, UK
| | - Wenbin Guo
- Informatics and Computational Sciences, The James Hutton Institute, Invergowrie, Dundee DD2 5DA, UK.,Plant Sciences Division, College of Life Sciences, University of Dundee, Invergowrie, Dundee DD2 5DA, UK
| | - Mark Spensley
- The Donnelly Centre, University of Toronto, 160 College Street, Toronto, Ontario, Canada
| | - Juan Carlos Entizne
- Plant Sciences Division, College of Life Sciences, University of Dundee, Invergowrie, Dundee DD2 5DA, UK
| | - Dominika Lewandowska
- Cell and Molecular Sciences, The James Hutton Institute, Invergowrie, Dundee DD2 5DA, UK
| | - Sara Ten Have
- Centre for Gene Regulation and Expression, School of Life Sciences, University of Dundee, Dundee, UK
| | | | - Heribert Hirt
- Institute of Plant Sciences Paris Saclay, INRA-CNRS-UEVE, Orsay 91405, France
| | - Allan B James
- Institute of Molecular, Cell and Systems Biology, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow G12 8QQ, UK
| | - Hugh G Nimmo
- Institute of Molecular, Cell and Systems Biology, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow G12 8QQ, UK
| | - Andrea Barta
- Max F. Perutz Laboratories, Medical University of Vienna, Dr. Bohrgasse 9/3, 1030 Vienna, Austria
| | - Maria Kalyna
- Department of Applied Genetics and Cell Biology, University of Natural Resources and Life Sciences - BOKU, Muthgasse 18, 1190 Vienna, Austria
| | - John W S Brown
- Plant Sciences Division, College of Life Sciences, University of Dundee, Invergowrie, Dundee DD2 5DA, UK.,Cell and Molecular Sciences, The James Hutton Institute, Invergowrie, Dundee DD2 5DA, UK
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34
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Knop K, Stepien A, Barciszewska-Pacak M, Taube M, Bielewicz D, Michalak M, Borst JW, Jarmolowski A, Szweykowska-Kulinska Z. Active 5' splice sites regulate the biogenesis efficiency of Arabidopsis microRNAs derived from intron-containing genes. Nucleic Acids Res 2017; 45:2757-2775. [PMID: 27907902 PMCID: PMC5389571 DOI: 10.1093/nar/gkw895] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2016] [Revised: 08/31/2016] [Accepted: 09/28/2016] [Indexed: 01/06/2023] Open
Abstract
Arabidopsis, miR402 that is encoded within the first intron of a protein-coding gene At1g77230, is induced by heat stress. Its upregulation correlates with splicing inhibition and intronic proximal polyA site selection. It suggests that miR402 is not processed from an intron, but rather from a shorter transcript after selection of the proximal polyA site within this intron. Recently, introns and active 5΄ splice sites (5΄ss’) have been shown to stimulate the accumulation of miRNAs encoded within the first exons of intron-containing MIR genes. In contrast, we have observed the opposite effect of splicing inhibition on intronic miR402 production. Transient expression experiments performed in tobacco leaves revealed a significant accumulation of the intronic mature miR402 when the 5΄ss of the miR402-hosting intron was inactivated. In contrast, when the miR402 stem-loop structure was moved into the first exon, mutation of the first-intron 5΄ss resulted in a decrease in the miRNA level. Thus, the 5΄ss controls the efficiency of miRNA biogenesis. We also show that the SERRATE protein (a key component of the plant microprocessor) colocalizes and interacts with several U1 snRNP auxiliary proteins. We postulate that SERRATE-spliceosome connections have a direct effect on miRNA maturation.
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Affiliation(s)
- Katarzyna Knop
- Department of Gene Expression, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University, Umultowska 89, Poznan 61-614, Poland
| | - Agata Stepien
- Department of Gene Expression, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University, Umultowska 89, Poznan 61-614, Poland
| | - Maria Barciszewska-Pacak
- Department of Gene Expression, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University, Umultowska 89, Poznan 61-614, Poland
| | - Michal Taube
- Department of Gene Expression, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University, Umultowska 89, Poznan 61-614, Poland
| | - Dawid Bielewicz
- Department of Gene Expression, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University, Umultowska 89, Poznan 61-614, Poland
| | - Michal Michalak
- Department of Molecular and Cellular Biology, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University, Umultowska 89, Poznan, 61-614, Poland
| | - Jan W Borst
- Laboratory of Biochemistry and Microspectroscopy Centre, Wageningen University, Stippeneng 4 Wageningen 6708, The Netherlands
| | - Artur Jarmolowski
- Department of Gene Expression, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University, Umultowska 89, Poznan 61-614, Poland
| | - Zofia Szweykowska-Kulinska
- Department of Gene Expression, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University, Umultowska 89, Poznan 61-614, Poland
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35
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Stepien A, Knop K, Dolata J, Taube M, Bajczyk M, Barciszewska-Pacak M, Pacak A, Jarmolowski A, Szweykowska-Kulinska Z. Posttranscriptional coordination of splicing and miRNA biogenesis in plants. WILEY INTERDISCIPLINARY REVIEWS-RNA 2016; 8. [DOI: 10.1002/wrna.1403] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/02/2015] [Revised: 09/30/2016] [Accepted: 10/08/2016] [Indexed: 12/20/2022]
Affiliation(s)
- Agata Stepien
- Department of Gene Expression, Institute of Molecular Biology and Biotechnology, Faculty of Biology; Adam Mickiewicz University; Poznan Poland
| | - Katarzyna Knop
- Department of Gene Expression, Institute of Molecular Biology and Biotechnology, Faculty of Biology; Adam Mickiewicz University; Poznan Poland
| | - Jakub Dolata
- Department of Gene Expression, Institute of Molecular Biology and Biotechnology, Faculty of Biology; Adam Mickiewicz University; Poznan Poland
| | - Michal Taube
- Department of Gene Expression, Institute of Molecular Biology and Biotechnology, Faculty of Biology; Adam Mickiewicz University; Poznan Poland
| | - Mateusz Bajczyk
- Department of Gene Expression, Institute of Molecular Biology and Biotechnology, Faculty of Biology; Adam Mickiewicz University; Poznan Poland
| | - Maria Barciszewska-Pacak
- Department of Gene Expression, Institute of Molecular Biology and Biotechnology, Faculty of Biology; Adam Mickiewicz University; Poznan Poland
| | - Andrzej Pacak
- Department of Gene Expression, Institute of Molecular Biology and Biotechnology, Faculty of Biology; Adam Mickiewicz University; Poznan Poland
| | - Artur Jarmolowski
- Department of Gene Expression, Institute of Molecular Biology and Biotechnology, Faculty of Biology; Adam Mickiewicz University; Poznan Poland
| | - Zofia Szweykowska-Kulinska
- Department of Gene Expression, Institute of Molecular Biology and Biotechnology, Faculty of Biology; Adam Mickiewicz University; Poznan Poland
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36
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Yu X, Willmann MR, Anderson SJ, Gregory BD. Genome-Wide Mapping of Uncapped and Cleaved Transcripts Reveals a Role for the Nuclear mRNA Cap-Binding Complex in Cotranslational RNA Decay in Arabidopsis. THE PLANT CELL 2016; 28:2385-2397. [PMID: 27758893 PMCID: PMC5134982 DOI: 10.1105/tpc.16.00456] [Citation(s) in RCA: 58] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/08/2016] [Revised: 08/02/2016] [Accepted: 10/07/2016] [Indexed: 05/19/2023]
Abstract
RNA turnover is necessary for controlling proper mRNA levels posttranscriptionally. In general, RNA degradation is via exoribonucleases that degrade RNA either from the 5' end to the 3' end, such as XRN4, or in the opposite direction by the multisubunit exosome complex. Here, we use genome-wide mapping of uncapped and cleaved transcripts to reveal the global landscape of cotranslational mRNA decay in the Arabidopsis thaliana transcriptome. We found that this process leaves a clear three nucleotide periodicity in open reading frames. This pattern of cotranslational degradation is especially evident near the ends of open reading frames, where we observe accumulation of cleavage events focused 16 to 17 nucleotides upstream of the stop codon because of ribosomal pausing during translation termination. Following treatment of Arabidopsis plants with the translation inhibitor cycloheximide, cleavage events accumulate 13 to 14 nucleotides upstream of the start codon where initiating ribosomes have been stalled with these sequences in their P site. Further analysis in xrn4 mutant plants indicates that cotranslational RNA decay is XRN4 dependent. Additionally, studies in plants lacking CAP BINDING PROTEIN80/ABA HYPERSENSITIVE1, the largest subunit of the nuclear mRNA cap binding complex, reveal a role for this protein in cotranslational decay. In total, our results demonstrate the global prevalence and features of cotranslational RNA decay in a plant transcriptome.
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Affiliation(s)
- Xiang Yu
- Department of Biology, University of Pennsylvania, Philadelphia, Pennsylvania 19104
| | - Matthew R Willmann
- Department of Biology, University of Pennsylvania, Philadelphia, Pennsylvania 19104
| | - Stephen J Anderson
- Department of Biology, University of Pennsylvania, Philadelphia, Pennsylvania 19104
- Biology Graduate Group, University of Pennsylvania, Philadelphia, Pennsylvania 19104
| | - Brian D Gregory
- Department of Biology, University of Pennsylvania, Philadelphia, Pennsylvania 19104
- Biology Graduate Group, University of Pennsylvania, Philadelphia, Pennsylvania 19104
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37
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Simpson CG, Fuller J, Calixto CPG, McNicol J, Booth C, Brown JWS, Staiger D. Monitoring Alternative Splicing Changes in Arabidopsis Circadian Clock Genes. Methods Mol Biol 2016; 1398:119-32. [PMID: 26867620 DOI: 10.1007/978-1-4939-3356-3_11] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Posttranscriptional control makes an important contribution to circadian regulation of gene expression. In higher plants, alternative splicing is particularly prevalent upon abiotic and biotic stress and in the circadian system. Here we describe in detail a high-resolution reverse transcription-PCR based panel (HR RT-PCR) to monitor alternative splicing events. The use of the panel allows the quantification of changes in the proportion of splice isoforms between different samples, e.g., different time points, different tissues, genotypes, ecotypes, or treatments.
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Affiliation(s)
- Craig G Simpson
- Cell and Molecular Sciences, The James Hutton Institute, Invergowrie, DD2 5DA, Scotland, UK.
| | - John Fuller
- Cell and Molecular Sciences, The James Hutton Institute, Invergowrie, DD2 5DA, Scotland, UK
| | - Cristiane P G Calixto
- Division of Plant Sciences, University of Dundee at The James Hutton Institute, Dundee, DD2 5DA, UK
| | - Jim McNicol
- Biomathematics and Statistics Scotland, Invergowrie, DD2 5DA, Scotland, UK
| | - Clare Booth
- Cell and Molecular Sciences, The James Hutton Institute, Invergowrie, DD2 5DA, Scotland, UK
| | - John W S Brown
- Cell and Molecular Sciences, The James Hutton Institute, Invergowrie, DD2 5DA, Scotland, UK.,Division of Plant Sciences, University of Dundee at The James Hutton Institute, Dundee, DD2 5DA, UK
| | - Dorothee Staiger
- Molecular Cell Physiology, Faculty of Biology, Bielefeld University, Universitaetsstrasse 25, Bielefeld, D-33615, Germany
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38
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Zhang R, Calixto CPG, Tzioutziou NA, James AB, Simpson CG, Guo W, Marquez Y, Kalyna M, Patro R, Eyras E, Barta A, Nimmo HG, Brown JWS. AtRTD - a comprehensive reference transcript dataset resource for accurate quantification of transcript-specific expression in Arabidopsis thaliana. THE NEW PHYTOLOGIST 2015; 208:96-101. [PMID: 26111100 PMCID: PMC4744958 DOI: 10.1111/nph.13545] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/19/2015] [Accepted: 06/05/2015] [Indexed: 05/02/2023]
Abstract
RNA-sequencing (RNA-seq) allows global gene expression analysis at the individual transcript level. Accurate quantification of transcript variants generated by alternative splicing (AS) remains a challenge. We have developed a comprehensive, nonredundant Arabidopsis reference transcript dataset (AtRTD) containing over 74 000 transcripts for use with algorithms to quantify AS transcript isoforms in RNA-seq. The AtRTD was formed by merging transcripts from TAIR10 and novel transcripts identified in an AS discovery project. We have estimated transcript abundance in RNA-seq data using the transcriptome-based alignment-free programmes Sailfish and Salmon and have validated quantification of splicing ratios from RNA-seq by high resolution reverse transcription polymerase chain reaction (HR RT-PCR). Good correlations between splicing ratios from RNA-seq and HR RT-PCR were obtained demonstrating the accuracy of abundances calculated for individual transcripts in RNA-seq. The AtRTD is a resource that will have immediate utility in analysing Arabidopsis RNA-seq data to quantify differential transcript abundance and expression.
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Affiliation(s)
- Runxuan Zhang
- Informatics and Computational SciencesThe James Hutton InstituteInvergowrieDundeeDD2 5DAUK
| | - Cristiane P. G. Calixto
- Plant Sciences DivisionCollege of Life SciencesUniversity of DundeeInvergowrieDundeeDD2 5DAUK
| | - Nikoleta A. Tzioutziou
- Plant Sciences DivisionCollege of Life SciencesUniversity of DundeeInvergowrieDundeeDD2 5DAUK
| | - Allan B. James
- Institute of Molecular, Cell and Systems BiologyCollege of Medical, Veterinary and Life SciencesUniversity of GlasgowGlasgowG12 8QQUK
| | - Craig G. Simpson
- Cell and Molecular SciencesThe James Hutton InstituteInvergowrieDundeeDD2 5DAUK
| | - Wenbin Guo
- Informatics and Computational SciencesThe James Hutton InstituteInvergowrieDundeeDD2 5DAUK
- Plant Sciences DivisionCollege of Life SciencesUniversity of DundeeInvergowrieDundeeDD2 5DAUK
| | - Yamile Marquez
- Max F. Perutz LaboratoriesMedical University of ViennaDr Bohrgasse 9/31030ViennaAustria
| | - Maria Kalyna
- Department of Applied Genetics and Cell BiologyUniversity of Natural Resources and Life SciencesMuthgasse 181190ViennaAustria
| | - Rob Patro
- Computer Science Department1422 Computer ScienceStony Brook UniversityStony BrookNY11794‐4400USA
| | - Eduardo Eyras
- Computational GenomicsUniversitat Pompeu Fabra08002BarcelonaSpain
- Catalan Institution of Research and Advanced Studies (ICREA)08010BarcelonaSpain
| | - Andrea Barta
- Max F. Perutz LaboratoriesMedical University of ViennaDr Bohrgasse 9/31030ViennaAustria
| | - Hugh G. Nimmo
- Institute of Molecular, Cell and Systems BiologyCollege of Medical, Veterinary and Life SciencesUniversity of GlasgowGlasgowG12 8QQUK
| | - John W. S. Brown
- Plant Sciences DivisionCollege of Life SciencesUniversity of DundeeInvergowrieDundeeDD2 5DAUK
- Cell and Molecular SciencesThe James Hutton InstituteInvergowrieDundeeDD2 5DAUK
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39
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Zhan X, Qian B, Cao F, Wu W, Yang L, Guan Q, Gu X, Wang P, Okusolubo TA, Dunn SL, Zhu JK, Zhu J. An Arabidopsis PWI and RRM motif-containing protein is critical for pre-mRNA splicing and ABA responses. Nat Commun 2015; 6:8139. [PMID: 26404089 DOI: 10.1038/ncomms9139] [Citation(s) in RCA: 75] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2014] [Accepted: 07/22/2015] [Indexed: 01/21/2023] Open
Abstract
The phytohormone abscisic acid (ABA) is important for growth, development and stress responses in plants. Recent research has identified ABA receptors and signalling components that regulate seed germination and stomatal closure. However, proteins that regulate ABA signalling remain poorly understood. Here we use a forward-genetic screen to identify rbm25-1 and rbm25-2, two Arabidopsis mutants with increased sensitivity to growth inhibition by ABA. Using RNA-seq, we found that RBM25 controls the splicing of many pre-mRNAs. The protein phosphatase 2C HAB1, a critical component in ABA signalling, shows a dramatic defect in pre-mRNA splicing in rbm25 mutants. Ectopic expression of a HAB1 complementary DNA derived from wild-type mRNAs partially suppresses the rbm25-2 mutant phenotype. We suggest that RNA splicing is of particular importance for plant response to ABA and that the splicing factor RBM25 has a critical role in this response.
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Affiliation(s)
- Xiangqiang Zhan
- Shanghai Center for Plant Stress Biology, Shanghai Institutes of Biological Sciences, Chinese Academy of Sciences, Shanghai 200032, China
| | - Bilian Qian
- Department of Plant Science and Landscape Architecture, University of Maryland, 2121 Plant Sciences Building, College Park, Maryland 20742, USA
| | - Fengqiu Cao
- Shanghai Center for Plant Stress Biology, Shanghai Institutes of Biological Sciences, Chinese Academy of Sciences, Shanghai 200032, China
| | - Wenwu Wu
- Shanghai Center for Plant Stress Biology, Shanghai Institutes of Biological Sciences, Chinese Academy of Sciences, Shanghai 200032, China
| | - Lan Yang
- Shanghai Center for Plant Stress Biology, Shanghai Institutes of Biological Sciences, Chinese Academy of Sciences, Shanghai 200032, China
| | - Qingmei Guan
- Department of Plant Science and Landscape Architecture, University of Maryland, 2121 Plant Sciences Building, College Park, Maryland 20742, USA
| | - Xianbin Gu
- Department of Plant Science and Landscape Architecture, University of Maryland, 2121 Plant Sciences Building, College Park, Maryland 20742, USA
| | - Pengcheng Wang
- Department of Horticulture and Landscape Architecture, Purdue University, West Lafayette, Indiana 47907, USA
| | - Temiloluwa A Okusolubo
- Department of Plant Science and Landscape Architecture, University of Maryland, 2121 Plant Sciences Building, College Park, Maryland 20742, USA
| | - Stephanie L Dunn
- Department of Plant Science and Landscape Architecture, University of Maryland, 2121 Plant Sciences Building, College Park, Maryland 20742, USA
| | - Jian-Kang Zhu
- Shanghai Center for Plant Stress Biology, Shanghai Institutes of Biological Sciences, Chinese Academy of Sciences, Shanghai 200032, China.,Department of Horticulture and Landscape Architecture, Purdue University, West Lafayette, Indiana 47907, USA
| | - Jianhua Zhu
- Department of Plant Science and Landscape Architecture, University of Maryland, 2121 Plant Sciences Building, College Park, Maryland 20742, USA
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40
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Chen T, Cui P, Xiong L. The RNA-binding protein HOS5 and serine/arginine-rich proteins RS40 and RS41 participate in miRNA biogenesis in Arabidopsis. Nucleic Acids Res 2015; 43:8283-98. [PMID: 26227967 PMCID: PMC4787832 DOI: 10.1093/nar/gkv751] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2014] [Accepted: 07/11/2015] [Indexed: 12/28/2022] Open
Abstract
MicroRNAs are a class of small regulatory RNAs that are generated from primary miRNA (pri-miRNA) transcripts with a stem-loop structure. Accuracy of the processing of pri-miRNA into mature miRNA in plants can be enhanced by SERRATE (SE) and HYPONASTIC LEAVES 1 (HYL1). HYL1 activity is regulated by the FIERY2 (FRY2)/RNA polymerase II C-terminal domain phosphatase-like 1 (CPL1). Here, we discover that HIGH OSMOTIC STRESS GENE EXPRESSION 5 (HOS5) and two serine/arginine-rich splicing factors RS40 and RS41, previously shown to be involved in pre-mRNA splicing, affect the biogenesis of a subset of miRNA. These proteins are required for correct miRNA strand selection and the maintenance of miRNA levels. FRY2 dephosphorylates HOS5 whose phosphorylation status affects its subnuclear localization. HOS5 and the RS proteins bind both intronless and intron-containing pri-miRNAs. Importantly, all of these splicing-related factors directly interact with both HYL1 and SE in nuclear splicing speckles. Our results indicate that these splicing factors are directly involved in the biogenesis of a group of miRNA.
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Affiliation(s)
- Tao Chen
- Division of Biological and Environmental Sciences and Engineering, King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia
| | - Peng Cui
- Division of Biological and Environmental Sciences and Engineering, King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia
| | - Liming Xiong
- Division of Biological and Environmental Sciences and Engineering, King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia
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41
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Abstract
Alternative pre-messenger RNA splicing in higher plants emerges as an important layer of regulation upon exposure to exogenous and endogenous cues. Accordingly, mutants defective in RNA-binding proteins predicted to function in the splicing process show severe phenotypic alterations. Among those are developmental defects, impaired responses to pathogen threat or abiotic stress factors, and misregulation of the circadian timing system. A suite of splicing factors has been identified in the model plant Arabidopsis thaliana. Here we summarize recent insights on how defects in these splicing factors impair plant performance.
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42
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Zielezinski A, Dolata J, Alaba S, Kruszka K, Pacak A, Swida-Barteczka A, Knop K, Stepien A, Bielewicz D, Pietrykowska H, Sierocka I, Sobkowiak L, Lakomiak A, Jarmolowski A, Szweykowska-Kulinska Z, Karlowski WM. mirEX 2.0 - an integrated environment for expression profiling of plant microRNAs. BMC PLANT BIOLOGY 2015; 15:144. [PMID: 26141515 PMCID: PMC4490709 DOI: 10.1186/s12870-015-0533-2] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/22/2015] [Accepted: 05/23/2015] [Indexed: 05/19/2023]
Abstract
BACKGROUND MicroRNAs are the key post-transcriptional regulators of gene expression in development and stress responses. Thus, precisely quantifying the level of each particular microRNA is of utmost importance when studying the biology of any organism. DESCRIPTION The mirEX 2.0 web portal ( http://www.combio.pl/mirex ) provides a comprehensive platform for the exploration of microRNA expression data based on quantitative Real Time PCR and NGS sequencing experiments, covering various developmental stages, from wild-type to mutant plants. The portal includes mature and pri-miRNA expression levels detected in three plant species (Arabidopsis thaliana, Hordeum vulgare and Pellia endiviifolia), and in A. thaliana miRNA biogenesis pathway mutants. In total, the database contains information about the expression of 461 miRNAs representing 268 families. The data can be explored through the use of advanced web tools, including (i) a graphical query builder system allowing a combination of any given species, developmental stages and tissues, (ii) a modular presentation of the results in the form of thematic windows, and (iii) a number of user-friendly utilities such as a community-building discussion system and extensive tutorial documentation (e.g., tooltips, exemplary videos and presentations). All data contained within the mirEX 2.0 database can be downloaded for use in further applications in a context-based way from the result windows or from a dedicated web page. CONCLUSIONS The mirEX 2.0 portal provides the plant research community with easily accessible data and powerful tools for application in multi-conditioned analyses of miRNA expression from important plant species in different biological and developmental backgrounds.
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Affiliation(s)
- Andrzej Zielezinski
- Department of Computational Biology, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University, Umultowska 89, 61-614, Poznan, Poland.
| | - Jakub Dolata
- Department of Gene Expression, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University, Umultowska 89, 61-614, Poznan, Poland.
| | - Sylwia Alaba
- Department of Computational Biology, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University, Umultowska 89, 61-614, Poznan, Poland.
| | - Katarzyna Kruszka
- Department of Gene Expression, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University, Umultowska 89, 61-614, Poznan, Poland.
| | - Andrzej Pacak
- Department of Gene Expression, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University, Umultowska 89, 61-614, Poznan, Poland.
| | - Aleksandra Swida-Barteczka
- Department of Gene Expression, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University, Umultowska 89, 61-614, Poznan, Poland.
| | - Katarzyna Knop
- Department of Gene Expression, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University, Umultowska 89, 61-614, Poznan, Poland.
| | - Agata Stepien
- Department of Gene Expression, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University, Umultowska 89, 61-614, Poznan, Poland.
| | - Dawid Bielewicz
- Department of Gene Expression, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University, Umultowska 89, 61-614, Poznan, Poland.
| | - Halina Pietrykowska
- Department of Gene Expression, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University, Umultowska 89, 61-614, Poznan, Poland.
| | - Izabela Sierocka
- Department of Gene Expression, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University, Umultowska 89, 61-614, Poznan, Poland.
| | - Lukasz Sobkowiak
- Department of Gene Expression, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University, Umultowska 89, 61-614, Poznan, Poland.
| | - Alicja Lakomiak
- Department of Gene Expression, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University, Umultowska 89, 61-614, Poznan, Poland.
| | - Artur Jarmolowski
- Department of Gene Expression, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University, Umultowska 89, 61-614, Poznan, Poland.
| | - Zofia Szweykowska-Kulinska
- Department of Computational Biology, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University, Umultowska 89, 61-614, Poznan, Poland.
- Department of Gene Expression, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University, Umultowska 89, 61-614, Poznan, Poland.
| | - Wojciech M Karlowski
- Department of Computational Biology, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University, Umultowska 89, 61-614, Poznan, Poland.
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43
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Filichkin S, Priest HD, Megraw M, Mockler TC. Alternative splicing in plants: directing traffic at the crossroads of adaptation and environmental stress. CURRENT OPINION IN PLANT BIOLOGY 2015; 24:125-35. [PMID: 25835141 DOI: 10.1016/j.pbi.2015.02.008] [Citation(s) in RCA: 133] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/13/2015] [Revised: 02/19/2015] [Accepted: 02/20/2015] [Indexed: 05/20/2023]
Abstract
In recent years, high-throughput sequencing-based analysis of plant transcriptomes has suggested that up to ∼60% of plant gene loci encode alternatively spliced mature transcripts. These studies have also revealed that alternative splicing in plants can be regulated by cell type, developmental stage, the environment, and the circadian clock. Alternative splicing is coupled to RNA surveillance and processing mechanisms, including nonsense mediated decay. Recently, non-protein-coding transcripts have also been shown to undergo alternative splicing. These discoveries collectively describe a robust system of post-transcriptional regulatory feedback loops which influence RNA abundance. In this review, we summarize recent studies describing the specific roles alternative splicing and RNA surveillance play in plant adaptation to environmental stresses and the regulation of the circadian clock.
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Affiliation(s)
- Sergei Filichkin
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR 97331, USA; Center for Genome Research and Biocomputing, Oregon State University, Corvallis, OR 97331, USA.
| | - Henry D Priest
- Division of Biology and Biomedical Sciences, Washington University, Saint Louis, MO 63130, USA; Donald Danforth Plant Science Center, Saint Louis, MO 63132, USA
| | - Molly Megraw
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR 97331, USA; Center for Genome Research and Biocomputing, Oregon State University, Corvallis, OR 97331, USA
| | - Todd C Mockler
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR 97331, USA; Center for Genome Research and Biocomputing, Oregon State University, Corvallis, OR 97331, USA; Division of Biology and Biomedical Sciences, Washington University, Saint Louis, MO 63130, USA; Donald Danforth Plant Science Center, Saint Louis, MO 63132, USA.
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44
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Xie M, Zhang S, Yu B. microRNA biogenesis, degradation and activity in plants. Cell Mol Life Sci 2015; 72:87-99. [PMID: 25209320 PMCID: PMC11113746 DOI: 10.1007/s00018-014-1728-7] [Citation(s) in RCA: 99] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2014] [Revised: 08/13/2014] [Accepted: 09/04/2014] [Indexed: 12/11/2022]
Abstract
microRNAs (miRNAs) are important regulators of gene expression. After excised from primary miRNA transcript by dicer-like1 (DCL1, an RNAse III enzyme), miRNAs bind and guide their effector protein named argonaute 1 (AGO1) to silence the expression of target RNAs containing their complementary sequences in plants. miRNA levels and activities are tightly controlled to ensure their functions in various biological processes such as development, metabolism and responses to abiotic and biotic stresses. Studies have identified many factors that involve in miRNA accumulation and activities. Characterization of these factors in turn greatly improves our understanding of the processes related to miRNAs. Here, we review recent progress of mechanisms underlying miRNA expression and functions in plants.
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Affiliation(s)
- Meng Xie
- Center for Plant Science Innovation and School of Biological Sciences, University of Nebraska-Lincoln, Lincoln, NE 68588–0660 USA
| | - Shuxin Zhang
- Center for Plant Science Innovation and School of Biological Sciences, University of Nebraska-Lincoln, Lincoln, NE 68588–0660 USA
| | - Bin Yu
- Center for Plant Science Innovation and School of Biological Sciences, University of Nebraska-Lincoln, Lincoln, NE 68588–0660 USA
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45
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Simpson CG, Lewandowska D, Liney M, Davidson D, Chapman S, Fuller J, McNicol J, Shaw P, Brown JWS. Arabidopsis PTB1 and PTB2 proteins negatively regulate splicing of a mini-exon splicing reporter and affect alternative splicing of endogenous genes differentially. THE NEW PHYTOLOGIST 2014; 203:424-436. [PMID: 24749484 DOI: 10.1111/nph.12821] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/28/2013] [Accepted: 03/14/2013] [Indexed: 06/03/2023]
Abstract
This paper examines the function of Arabidopsis thaliana AtPTB1 and AtPTB2 as plant splicing factors. The effect on splicing of overexpression of AtPTB1 and AtPTB2 was analysed in an in vivo protoplast transient expression system with a novel mini-exon splicing reporter. A range of mutations in pyrimidine-rich sequences were compared with and without AtPTB and NpU2AF65 overexpression. Splicing analyses of constructs in protoplasts and RNA from overexpression lines used high-resolution reverse transcription polymerase chain reaction (RT-PCR). AtPTB1 and AtPTB2 reduced inclusion/splicing of the potato invertase mini-exon splicing reporter, indicating that these proteins can repress plant intron splicing. Mutation of the polypyrimidine tract and closely associated Cytosine and Uracil-rich (CU-rich) sequences, upstream of the mini-exon, altered repression by AtPTB1 and AtPTB2. Coexpression of a plant orthologue of U2AF65 alleviated the splicing repression of AtPTB1. Mutation of a second CU-rich upstream of the mini-exon 3' splice site led to a decline in mini-exon splicing, indicating the presence of a splicing enhancer sequence. Finally, RT-PCR of AtPTB overexpression lines with c. 90 known alternative splicing (AS) events showed that AtPTBs significantly altered AS of over half the events. AtPTB1 and AtPTB2 are splicing factors that influence alternative splicing. This occurs in the potato invertase mini-exon via the polypyrimidine tract and associated pyrimidine-rich sequence.
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Affiliation(s)
- Craig G Simpson
- Cell and Molecular Sciences, The James Hutton Institute, Invergowrie, Dundee, DD2 5DA, UK
| | - Dominika Lewandowska
- Cell and Molecular Sciences, The James Hutton Institute, Invergowrie, Dundee, DD2 5DA, UK
| | - Michele Liney
- Cell and Molecular Sciences, The James Hutton Institute, Invergowrie, Dundee, DD2 5DA, UK
| | - Diane Davidson
- Cell and Molecular Sciences, The James Hutton Institute, Invergowrie, Dundee, DD2 5DA, UK
| | - Sean Chapman
- Cell and Molecular Sciences, The James Hutton Institute, Invergowrie, Dundee, DD2 5DA, UK
| | - John Fuller
- Cell and Molecular Sciences, The James Hutton Institute, Invergowrie, Dundee, DD2 5DA, UK
| | - Jim McNicol
- Biomathematics and Statistics Scotland, Invergowrie, Dundee, DD2 5DA, UK
| | - Paul Shaw
- Information and Computational Sciences, The James Hutton Institute, Invergowrie, Dundee, DD2 5DA, UK
| | - John W S Brown
- Cell and Molecular Sciences, The James Hutton Institute, Invergowrie, Dundee, DD2 5DA, UK
- Division of Plant Sciences, University of Dundee at JHI, Invergowrie, Dundee, DD2 5DA, UK
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46
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Abstract
The 7mG (7-methylguanosine cap) formed on mRNA is fundamental to eukaryotic gene expression. Protein complexes recruited to 7mG mediate key processing events throughout the lifetime of the transcript. One of the most important mediators of 7mG functions is CBC (cap-binding complex). CBC has a key role in several gene expression mechanisms, including transcription, splicing, transcript export and translation. Gene expression can be regulated by signalling pathways which influence CBC function. The aim of the present review is to discuss the mechanisms by which CBC mediates and co-ordinates multiple gene expression events.
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47
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Gonatopoulos-Pournatzis T, Cowling VH. Cap-binding complex (CBC). Biochem J 2014. [PMID: 24354960 DOI: 10.1042/bj2013121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
The 7mG (7-methylguanosine cap) formed on mRNA is fundamental to eukaryotic gene expression. Protein complexes recruited to 7mG mediate key processing events throughout the lifetime of the transcript. One of the most important mediators of 7mG functions is CBC (cap-binding complex). CBC has a key role in several gene expression mechanisms, including transcription, splicing, transcript export and translation. Gene expression can be regulated by signalling pathways which influence CBC function. The aim of the present review is to discuss the mechanisms by which CBC mediates and co-ordinates multiple gene expression events.
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Affiliation(s)
| | - Victoria H Cowling
- *MRC Protein Phosphorylation Unit, College of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, U.K
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48
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Szweykowska-Kulinska Z, Jarmolowski A, Vazquez F. The crosstalk between plant microRNA biogenesis factors and the spliceosome. PLANT SIGNALING & BEHAVIOR 2013; 8:e26955. [PMID: 24300047 PMCID: PMC4091587 DOI: 10.4161/psb.26955] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/03/2013] [Accepted: 10/25/2013] [Indexed: 05/18/2023]
Abstract
Many of the plant microRNA (miRNA) genes contain introns. The miRNA-containing hairpin loop structure is predominantly located within the first exon of such pri-miRNAs. We have shown that the downstream intron and its splicing are important for the regulation of the processing of these pri-miRNAs. The 5' splice site in MIR genes is essential in the process of miRNA biogenesis. We postulate that the presence of yet undefined interactions between U1 snRNP and the pri-miRNA processing machinery leads to an increase in the efficiency of miRNA biogenesis. The 5' splice site also decreases the accessibility of the polyadenylation machinery to the pri-miRNA polyA signal located within the same intron. It is likely that the spliceosome assembly controls the length and structure of MIR primary transcripts, and regulates mature miRNA levels. The emerging picture shows that introns, splicing, and/or alternative splicing have highly relevant roles in regulating the miRNA levels in very specific conditions that contribute to proper plant response to stress conditions.
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Affiliation(s)
- Zofia Szweykowska-Kulinska
- Department of Gene Expression; Institute of Molecular Biology and Biotechnology; Adam Mickiewicz University; Poznan, Poland
- Correspondence to: Zofia Szweykowska-Kulinska,
| | - Artur Jarmolowski
- Department of Gene Expression; Institute of Molecular Biology and Biotechnology; Adam Mickiewicz University; Poznan, Poland
| | - Franck Vazquez
- Department of Environmental Sciences; University of Basel; Zurich-Basel Plant Science Center; Part of the Swiss Plant Science Web; Basel, Switzerland
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Raczynska KD, Stepien A, Kierzkowski D, Kalak M, Bajczyk M, McNicol J, Simpson CG, Szweykowska-Kulinska Z, Brown JWS, Jarmolowski A. The SERRATE protein is involved in alternative splicing in Arabidopsis thaliana. Nucleic Acids Res 2013; 42:1224-44. [PMID: 24137006 PMCID: PMC3902902 DOI: 10.1093/nar/gkt894] [Citation(s) in RCA: 64] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
How alternative splicing (AS) is regulated in plants has not yet been elucidated. Previously, we have shown that the nuclear cap-binding protein complex (AtCBC) is involved in AS in Arabidopsis thaliana. Here we show that both subunits of AtCBC (AtCBP20 and AtCBP80) interact with SERRATE (AtSE), a protein involved in the microRNA biogenesis pathway. Moreover, using a high-resolution reverse transcriptase-polymerase chain reaction AS system we have found that AtSE influences AS in a similar way to the cap-binding complex (CBC), preferentially affecting selection of 5′ splice site of first introns. The AtSE protein acts in cooperation with AtCBC: many changes observed in the mutant lacking the correct SERRATE activity were common to those observed in the cbp mutants. Interestingly, significant changes in AS of some genes were also observed in other mutants of plant microRNA biogenesis pathway, hyl1-2 and dcl1-7, but a majority of them did not correspond to the changes observed in the se-1 mutant. Thus, the role of SERRATE in AS regulation is distinct from that of HYL1 and DCL1, and is similar to the regulation of AS in which CBC is involved.
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Affiliation(s)
- Katarzyna Dorota Raczynska
- Department of Gene Expression, Institute of Molecular Biology and Biotechnology, Adam Mickiewicz University, Poznan, Poland, Department of Molecular and Cellular Biology, Institute of Molecular Biology and Biotechnology, Adam Mickiewicz University, Poznan, Poland, Max Planck Institute for Plant Breading Research, 50829, Germany, Biomathematics and Statistics Scotland (BioSS), James Hutton Institute, Dundee DD2 5DA, Scotland, UK, Cell and Molecular Sciences, James Hutton Institute, Dundee DD2 5DA, Scotland, UK and Division of Plant Sciences, University of Dundee at the James Hutton Institute, Dundee DD2 5DA, Scotland, UK
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Staiger D, Brown JWS. Alternative splicing at the intersection of biological timing, development, and stress responses. THE PLANT CELL 2013. [PMID: 24179132 DOI: 10.1105/tcp.113.117523] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
High-throughput sequencing for transcript profiling in plants has revealed that alternative splicing (AS) affects a much higher proportion of the transcriptome than was previously assumed. AS is involved in most plant processes and is particularly prevalent in plants exposed to environmental stress. The identification of mutations in predicted splicing factors and spliceosomal proteins that affect cell fate, the circadian clock, plant defense, and tolerance/sensitivity to abiotic stress all point to a fundamental role of splicing/AS in plant growth, development, and responses to external cues. Splicing factors affect the AS of multiple downstream target genes, thereby transferring signals to alter gene expression via splicing factor/AS networks. The last two to three years have seen an ever-increasing number of examples of functional AS. At a time when the identification of AS in individual genes and at a global level is exploding, this review aims to bring together such examples to illustrate the extent and importance of AS, which are not always obvious from individual publications. It also aims to ensure that plant scientists are aware that AS is likely to occur in the genes that they study and that dynamic changes in AS and its consequences need to be considered routinely.
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Affiliation(s)
- Dorothee Staiger
- Molecular Cell Physiology, Bielefeld University, D33615 Bielefeld, Germany
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