1
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Mangilet AF, Weber J, Schüler S, Adler M, Mjema EY, Heilmann P, Herold A, Renneberg M, Nagel L, Droste-Borel I, Streicher S, Schmutzer T, Rot G, Macek B, Schmidtke C, Laubinger S. The Arabidopsis U1 snRNP regulates mRNA 3'-end processing. NATURE PLANTS 2024:10.1038/s41477-024-01796-8. [PMID: 39313562 DOI: 10.1038/s41477-024-01796-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/22/2023] [Accepted: 08/27/2024] [Indexed: 09/25/2024]
Abstract
The removal of introns by the spliceosome is a key gene regulatory mechanism in eukaryotes, with the U1 snRNP subunit playing a crucial role in the early stages of splicing. Studies in metazoans show that the U1 snRNP also conducts splicing-independent functions, but the lack of genetic tools and knowledge about U1 snRNP-associated proteins have limited the study of such splicing-independent functions in plants. Here we describe an RNA-centric approach that identified more than 200 proteins associated with the Arabidopsis U1 snRNP and revealed a tight link to mRNA cleavage and polyadenylation factors. Interestingly, we found that the U1 snRNP protects mRNAs against premature cleavage and polyadenylation within introns-a mechanism known as telescripting in metazoans-while also influencing alternative polyadenylation site selection in 3'-UTRs. Overall, our work provides a comprehensive view of U1 snRNP interactors and reveals novel functions in regulating mRNA 3'-end processing in Arabidopsis, laying the groundwork for understanding non-canonical functions of plant U1 snRNPs.
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Affiliation(s)
- Anchilie F Mangilet
- Institute of Biology and Environmental Sciences, University of Oldenburg, Oldenburg, Germany
- Max Planck Institute for Plant Breeding Research (MPIPZ), Cologne, Germany
| | - Joachim Weber
- Institute of Biology and Environmental Sciences, University of Oldenburg, Oldenburg, Germany
- Institute of Biology, Department of Genetics, Martin Luther University Halle-Wittenberg, Halle (Saale), Germany
| | - Sandra Schüler
- Institute of Biology and Environmental Sciences, University of Oldenburg, Oldenburg, Germany
- Institute of Biology, Department of Genetics, Martin Luther University Halle-Wittenberg, Halle (Saale), Germany
| | - Manon Adler
- Institute of Biology and Environmental Sciences, University of Oldenburg, Oldenburg, Germany
- Institute of Biology, Department of Genetics, Martin Luther University Halle-Wittenberg, Halle (Saale), Germany
| | - Eneza Yoeli Mjema
- Institute of Biology and Environmental Sciences, University of Oldenburg, Oldenburg, Germany
- Institute of Biology, Department of Genetics, Martin Luther University Halle-Wittenberg, Halle (Saale), Germany
| | - Paula Heilmann
- Institute of Biology, Department of Genetics, Martin Luther University Halle-Wittenberg, Halle (Saale), Germany
| | - Angie Herold
- Institute of Biology, Department of Genetics, Martin Luther University Halle-Wittenberg, Halle (Saale), Germany
| | - Monique Renneberg
- Institute of Biology, Department of Genetics, Martin Luther University Halle-Wittenberg, Halle (Saale), Germany
| | - Luise Nagel
- Institute of Biology, Department of Genetics, Martin Luther University Halle-Wittenberg, Halle (Saale), Germany
| | | | - Samuel Streicher
- Institute of Agricultural and Nutritional Sciences, Martin Luther University Halle-Wittenberg, Halle (Saale), Germany
| | - Thomas Schmutzer
- Institute of Agricultural and Nutritional Sciences, Martin Luther University Halle-Wittenberg, Halle (Saale), Germany
| | - Gregor Rot
- Institute of Molecular Life Sciences of the University of Zurich and Swiss Institute of Bioinformatics, Zurich, Switzerland
| | - Boris Macek
- Proteome Center, University of Tuebingen, Tuebingen, Germany
| | - Cornelius Schmidtke
- Institute of Biology, Department of Genetics, Martin Luther University Halle-Wittenberg, Halle (Saale), Germany
| | - Sascha Laubinger
- Institute of Biology and Environmental Sciences, University of Oldenburg, Oldenburg, Germany.
- Institute of Biology, Department of Genetics, Martin Luther University Halle-Wittenberg, Halle (Saale), Germany.
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2
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Wang L, Chen H, Zhuang Y, Chen K, Zhang C, Cai T, Yang Q, Fu H, Chen X, Chitkineni A, Wang X, Varshney RK, Zhuang W. Multiple strategies, including 6mA methylation, affecting plant alternative splicing in allopolyploid peanut. PLANT BIOTECHNOLOGY JOURNAL 2024; 22:1681-1702. [PMID: 38294334 PMCID: PMC11123434 DOI: 10.1111/pbi.14296] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/29/2023] [Revised: 11/28/2023] [Accepted: 01/11/2024] [Indexed: 02/01/2024]
Abstract
Alternative splicing (AS), an important post-transcriptional regulation mechanism in eukaryotes, can significantly increase transcript diversity and contribute to gene expression regulation and many other complicated developmental processes. While plant gene AS events are well described, few studies have investigated the comprehensive regulation machinery of plant AS. Here, we use multi-omics to analyse peanut AS events. Using long-read isoform sequencing, 146 464 full-length non-chimeric transcripts were obtained, resulting in annotation corrections for 1782 genes and the identification of 4653 new loci. Using Iso-Seq RNA sequences, 271 776 unique splice junctions were identified, 82.49% of which were supported by transcriptome data. We characterized 50 977 polyadenylation sites for 23 262 genes, 12 369 of which had alternative polyadenylation sites. AS allows differential regulation of the same gene by miRNAs at the isoform level coupled with polyadenylation. In addition, we identified many long non-coding RNAs and fusion transcripts. There is a suppressed effect of 6mA on AS and gene expression. By analysis of chromatin structures, the genes located in the boundaries of topologically associated domains, proximal chromosomal telomere regions, inter- or intra-chromosomal loops were found to have more unique splice isoforms, higher expression, lower 6mA and more transposable elements (TEs) in their gene bodies than the other genes, indicating that chromatin interaction, 6mA and TEs play important roles in AS and gene expression. These results greatly refine the peanut genome annotation and contribute to the study of gene expression and regulation in peanuts. This work also showed AS is associated with multiple strategies for gene regulation.
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Affiliation(s)
- Lihui Wang
- Center for Legume Plant Genetics and System Biology, College of Plant ProtectionFujian Agriculture and Forestry UniversityFuzhouFujianChina
| | - Hua Chen
- Center for Legume Plant Genetics and System Biology, College of AgronomyFujian Agriculture and Forestry UniversityFuzhouFujianChina
| | - Yuhui Zhuang
- Center for Legume Plant Genetics and System Biology, College of Life ScienceFujian Agriculture and Forestry UniversityFuzhouFujianChina
| | - Kun Chen
- Center for Legume Plant Genetics and System Biology, College of Plant ProtectionFujian Agriculture and Forestry UniversityFuzhouFujianChina
| | - Chong Zhang
- Center for Legume Plant Genetics and System Biology, College of AgronomyFujian Agriculture and Forestry UniversityFuzhouFujianChina
| | - Tiecheng Cai
- Center for Legume Plant Genetics and System Biology, College of AgronomyFujian Agriculture and Forestry UniversityFuzhouFujianChina
| | - Qiang Yang
- Center for Legume Plant Genetics and System Biology, College of AgronomyFujian Agriculture and Forestry UniversityFuzhouFujianChina
| | - Huiwen Fu
- Center for Legume Plant Genetics and System Biology, College of Plant ProtectionFujian Agriculture and Forestry UniversityFuzhouFujianChina
| | - Xiangyu Chen
- Crop Research InstituteFujian Academy of Agricultural SciencesFuzhouFujianChina
| | - Annapurna Chitkineni
- Centre for Crop & Food Innovation, State Agricultural Biotechnology CentreFood Futures Institute, Murdoch UniversityMurdochWestern AustraliaAustralia
| | - Xiyin Wang
- North China University of Science and TechnologyTangshanChina
| | - Rajeev K. Varshney
- Centre for Crop & Food Innovation, State Agricultural Biotechnology CentreFood Futures Institute, Murdoch UniversityMurdochWestern AustraliaAustralia
| | - Weijian Zhuang
- Center for Legume Plant Genetics and System Biology, College of AgronomyFujian Agriculture and Forestry UniversityFuzhouFujianChina
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3
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Lewinski M, Brüggemann M, Köster T, Reichel M, Bergelt T, Meyer K, König J, Zarnack K, Staiger D. Mapping protein-RNA binding in plants with individual-nucleotide-resolution UV cross-linking and immunoprecipitation (plant iCLIP2). Nat Protoc 2024; 19:1183-1234. [PMID: 38278964 DOI: 10.1038/s41596-023-00935-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2023] [Accepted: 10/20/2023] [Indexed: 01/28/2024]
Abstract
Despite crucial roles of RNA-binding proteins (RBPs) in plant physiology and development, methods for determining their transcriptome-wide binding landscape are less developed than those used in other model organisms. Cross-linking and immunoprecipitation (CLIP) methods (based on UV-mediated generation of covalent bonds between RNAs and cognate RBPs in vivo, purification of the cross-linked complexes and identification of the co-purified RNAs by high-throughput sequencing) have been applied mainly in mammalian cells growing in monolayers or in translucent tissue. We have developed plant iCLIP2, an efficient protocol for performing individual-nucleotide-resolution CLIP (iCLIP) in plants, tailored to overcome the experimental hurdles posed by plant tissue. We optimized the UV dosage to efficiently cross-link RNA and proteins in plants and expressed epitope-tagged RBPs under the control of their native promoters in loss-of-function mutants. We select epitopes for which nanobodies are available, allowing stringent conditions for immunopurification of the RNA-protein complexes to be established. To overcome the inherently high RNase content of plant cells, RNase inhibitors are added and the limited RNA fragmentation step is modified. We combine the optimized isolation of RBP-bound RNAs with iCLIP2, a streamlined protocol that greatly enhances the efficiency of library preparation for high-throughput sequencing. Plant researchers with experience in molecular biology and handling of RNA can complete this iCLIP2 protocol in ~5 d. Finally, we describe a bioinformatics workflow to determine targets of Arabidopsis RBPs from iCLIP data, covering all steps from downloading sequencing reads to identifying cross-linking events ( https://github.com/malewins/Plant-iCLIPseq ), and present the R/Bioconductor package BindingSiteFinder to extract reproducible binding sites ( https://bioconductor.org/packages/release/bioc/html/BindingSiteFinder.html ).
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Affiliation(s)
- Martin Lewinski
- RNA Biology and Molecular Physiology, Faculty of Biology, Bielefeld University, Bielefeld, Germany
| | - Mirko Brüggemann
- Buchmann Institute for Molecular Life Sciences (BMLS) & Institute of Molecular Biosciences, Goethe University Frankfurt, Frankfurt, Germany
| | - Tino Köster
- RNA Biology and Molecular Physiology, Faculty of Biology, Bielefeld University, Bielefeld, Germany
| | - Marlene Reichel
- RNA Biology and Molecular Physiology, Faculty of Biology, Bielefeld University, Bielefeld, Germany
| | - Thorsten Bergelt
- RNA Biology and Molecular Physiology, Faculty of Biology, Bielefeld University, Bielefeld, Germany
| | - Katja Meyer
- RNA Biology and Molecular Physiology, Faculty of Biology, Bielefeld University, Bielefeld, Germany
| | - Julian König
- Institute of Molecular Biology (IMB), Mainz, Germany
| | - Kathi Zarnack
- Buchmann Institute for Molecular Life Sciences (BMLS) & Institute of Molecular Biosciences, Goethe University Frankfurt, Frankfurt, Germany
| | - Dorothee Staiger
- RNA Biology and Molecular Physiology, Faculty of Biology, Bielefeld University, Bielefeld, Germany.
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Ohm H, Åstrand J, Ceplitis A, Bengtsson D, Hammenhag C, Chawade A, Grimberg Å. Novel SNP markers for flowering and seed quality traits in faba bean ( Vicia faba L.): characterization and GWAS of a diversity panel. FRONTIERS IN PLANT SCIENCE 2024; 15:1348014. [PMID: 38510437 PMCID: PMC10950902 DOI: 10.3389/fpls.2024.1348014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/01/2023] [Accepted: 02/21/2024] [Indexed: 03/22/2024]
Abstract
Faba bean (Vicia faba L.) is a legume crop grown in diverse climates worldwide. It has a high potential for increased cultivation to meet the need for more plant-based proteins in human diets, a prerequisite for a more sustainable food production system. Characterization of diversity panels of crops can identify variation in and genetic markers for target traits of interest for plant breeding. In this work, we collected a diversity panel of 220 accessions of faba bean from around the world consisting of gene bank material and commercially available cultivars. The aims of this study were to quantify the phenotypic diversity in target traits to analyze the impact of breeding on these traits, and to identify genetic markers associated with traits through a genome-wide association study (GWAS). Characterization under field conditions at Nordic latitude across two years revealed a large genotypic variation and high broad-sense heritability for eleven agronomic and seed quality traits. Pairwise correlations showed that seed yield was positively correlated to plant height, number of seeds per plant, and days to maturity. Further, susceptibility to bean weevil damage was significantly higher for early flowering accessions and accessions with larger seeds. In this study, no yield penalty was found for higher seed protein content, but protein content was negatively correlated to starch content. Our results showed that while breeding advances in faba bean germplasm have resulted in increased yields and number of seeds per plant, they have also led to a selection pressure towards delayed onset of flowering and maturity. DArTseq genotyping identified 6,606 single nucleotide polymorphisms (SNPs) by alignment to the faba bean reference genome. These SNPs were used in a GWAS, revealing 51 novel SNP markers significantly associated with ten of the assessed traits. Three markers for days to flowering were found in predicted genes encoding proteins for which homologs in other plant species regulate flowering. Altogether, this work enriches the growing pool of phenotypic and genotypic data on faba bean as a valuable resource for developing efficient breeding strategies to expand crop cultivation.
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Affiliation(s)
- Hannah Ohm
- Department of Plant Breeding, Swedish University of Agricultural Sciences (SLU), Lomma, Sweden
| | - Johanna Åstrand
- Department of Plant Breeding, Swedish University of Agricultural Sciences (SLU), Lomma, Sweden
- Lantmännen Agriculture, Plant Breeding, Svalöv, Sweden
| | - Alf Ceplitis
- Lantmännen Agriculture, Plant Breeding, Svalöv, Sweden
| | | | - Cecilia Hammenhag
- Department of Plant Breeding, Swedish University of Agricultural Sciences (SLU), Lomma, Sweden
| | - Aakash Chawade
- Department of Plant Breeding, Swedish University of Agricultural Sciences (SLU), Lomma, Sweden
| | - Åsa Grimberg
- Department of Plant Breeding, Swedish University of Agricultural Sciences (SLU), Lomma, Sweden
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5
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Loeser J, Bauer J, Janßen K, Rockenbach K, Wachter A. A transient in planta editing assay identifies specific binding of the splicing regulator PTB as a prerequisite for cassette exon inclusion. PLANT MOLECULAR BIOLOGY 2024; 114:22. [PMID: 38443687 PMCID: PMC10914923 DOI: 10.1007/s11103-024-01414-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/18/2023] [Accepted: 12/31/2023] [Indexed: 03/07/2024]
Abstract
The dynamic interaction of RNA-binding proteins (RBPs) with their target RNAs contributes to the diversity of ribonucleoprotein (RNP) complexes that are involved in a myriad of biological processes. Identifying the RNP components at high resolution and defining their interactions are key to understanding their regulation and function. Expressing fusions between an RBP of interest and an RNA editing enzyme can result in nucleobase changes in target RNAs, representing a recent addition to experimental approaches for profiling RBP/RNA interactions. Here, we have used the MS2 protein/RNA interaction to test four RNA editing proteins for their suitability to detect target RNAs of RBPs in planta. We have established a transient test system for fast and simple quantification of editing events and identified the hyperactive version of the catalytic domain of an adenosine deaminase (hADARcd) as the most suitable editing enzyme. Examining fusions between homologs of polypyrimidine tract binding proteins (PTBs) from Arabidopsis thaliana and hADARcd allowed determining target RNAs with high sensitivity and specificity. Moreover, almost complete editing of a splicing intermediate provided insight into the order of splicing reactions and PTB dependency of this particular splicing event. Addition of sequences for nuclear localisation of the fusion protein increased the editing efficiency, highlighting this approach's potential to identify RBP targets in a compartment-specific manner. Our studies have established the editing-based analysis of interactions between RBPs and their RNA targets in a fast and straightforward assay, offering a new system to study the intricate composition and functions of plant RNPs in vivo.
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Affiliation(s)
- Jorinde Loeser
- Institute for Molecular Physiology (imP), University of Mainz, Hanns-Dieter-Hüsch-Weg 17, 55128, Mainz, Germany
| | - Julia Bauer
- Institute for Molecular Physiology (imP), University of Mainz, Hanns-Dieter-Hüsch-Weg 17, 55128, Mainz, Germany
| | - Kim Janßen
- Institute for Molecular Physiology (imP), University of Mainz, Hanns-Dieter-Hüsch-Weg 17, 55128, Mainz, Germany
| | - Kevin Rockenbach
- Institute for Molecular Physiology (imP), University of Mainz, Hanns-Dieter-Hüsch-Weg 17, 55128, Mainz, Germany
| | - Andreas Wachter
- Institute for Molecular Physiology (imP), University of Mainz, Hanns-Dieter-Hüsch-Weg 17, 55128, Mainz, Germany.
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6
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Liu S, Luo S, Yang D, Huang J, Jiang X, Yu S, Fu J, Zhou D, Chen X, He H, Fu H. Alternative polyadenylation profiles of susceptible and resistant rice (Oryza sativa L.) in response to bacterial leaf blight using RNA-seq. BMC PLANT BIOLOGY 2024; 24:145. [PMID: 38413866 PMCID: PMC10900630 DOI: 10.1186/s12870-024-04839-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/08/2023] [Accepted: 02/20/2024] [Indexed: 02/29/2024]
Abstract
BACKGROUND Alternative polyadenylation (APA) is an important pattern of post-transcriptional regulation of genes widely existing in eukaryotes, involving plant physiological and pathological processes. However, there is a dearth of studies investigating the role of APA profile in rice leaf blight. RESULTS In this study, we compared the APA profile of leaf blight-susceptible varieties (CT 9737-613P-M) and resistant varieties (NSIC RC154) following bacterial blight infection. Through gene enrichment analysis, we found that the genes of two varieties typically exhibited distal poly(A) (PA) sites that play different roles in two kinds of rice, indicating differential APA regulatory mechanisms. In this process, many disease-resistance genes displayed multiple transcripts via APA. Moreover, we also found five polyadenylation factors of similar expression patterns of rice, highlighting the critical roles of these five factors in rice response to leaf blight about PA locus diversity. CONCLUSION Notably, the present study provides the first dynamic changes of APA in rice in early response to biotic stresses and proposes a possible functional conjecture of APA in plant immune response, which lays the theoretical foundation for in-depth determination of the role of APA events in plant stress response and other life processes.
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Affiliation(s)
- Shaochun Liu
- Key Laboratory of Crop Physiology, Ecology, and Genetic Breeding, Ministry of Education, Jiangxi Agricultural University, Nanchang, 330045, China
| | - Shuqi Luo
- Key Laboratory of Crop Physiology, Ecology, and Genetic Breeding, Ministry of Education, Jiangxi Agricultural University, Nanchang, 330045, China
| | - Dewei Yang
- Institute of Rice, Fujian Academy of Agricultural Sciences, Fuzhou, China
| | - Junying Huang
- Key Laboratory of Crop Physiology, Ecology, and Genetic Breeding, Ministry of Education, Jiangxi Agricultural University, Nanchang, 330045, China
| | - Xinlei Jiang
- Key Laboratory of Crop Physiology, Ecology, and Genetic Breeding, Ministry of Education, Jiangxi Agricultural University, Nanchang, 330045, China
| | - Shangwei Yu
- Key Laboratory of Crop Physiology, Ecology, and Genetic Breeding, Ministry of Education, Jiangxi Agricultural University, Nanchang, 330045, China
| | - Junru Fu
- Key Laboratory of Crop Physiology, Ecology, and Genetic Breeding, Ministry of Education, Jiangxi Agricultural University, Nanchang, 330045, China
| | - Dahu Zhou
- Key Laboratory of Crop Physiology, Ecology, and Genetic Breeding, Ministry of Education, Jiangxi Agricultural University, Nanchang, 330045, China
| | - Xiaorong Chen
- Key Laboratory of Crop Physiology, Ecology, and Genetic Breeding, Ministry of Education, Jiangxi Agricultural University, Nanchang, 330045, China
| | - Haohua He
- Key Laboratory of Crop Physiology, Ecology, and Genetic Breeding, Ministry of Education, Jiangxi Agricultural University, Nanchang, 330045, China.
| | - Haihui Fu
- Key Laboratory of Crop Physiology, Ecology, and Genetic Breeding, Ministry of Education, Jiangxi Agricultural University, Nanchang, 330045, China.
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7
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Xia X, Hao L, Sun Y, Lv Y, Wang Y, Wu H, Jiang Z, Li X, Yan Y, Chen X, Li B, Li H, Li M, Sun Y, Ren W, Xue Y, You Q, Zhu L, Liao Q, Xie S, Zhang Y, Zhao C, Zhu H, Liang C, Qiu J, Song Z, Deng Y, Pan Y, Zou Y, Zhang Y, Yang Y. Unravelling chilling-stress resistance mechanisms in endangered Mangrove plant Lumnitzera littorea (Jack) Voigt. MARINE ENVIRONMENTAL RESEARCH 2023; 192:106210. [PMID: 37788964 DOI: 10.1016/j.marenvres.2023.106210] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/17/2023] [Revised: 09/03/2023] [Accepted: 09/25/2023] [Indexed: 10/05/2023]
Abstract
Lumnitzera littorea (Jack) Voigt is one of the most endangered mangrove species in China. Previous studies have showed the impact of chilling stress on L. littorea and the repsonses at physiological and biochemical levels, but few attentions have been paid at molecular level. In this study, we conducted genome-wide investigation of transcriptional and post-transcriptional dynamics in L. littorea in response to chilling stress (8 °C day/5 °C night). In the seedlings of L. littorea, chilling sensing and signal transducing, photosystem II regeneration and peroxidase-mediated reactive oxygen species (ROS) scavenging were substantially enhanced to combat the adverse impact induced by chilling exposure. We further revealed that alternative polyadenylation (APA) events participated in chilling stress-responsive processes, including energy metabolism and steroid biosynthesis. Furthermore, APA-mediated miRNA regulations downregulated the expression of the genes involved in fatty acid biosynthesis and elongation, and protein phosphorylation, reflecting the important role of post-transcriptional regulation in modulating chilling tolerance in L. littorea. Our findings present a molecular view to the adaptive characteristics of L. littorea and shed light on the conservation genomic approaches of endangered mangrove species.
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Affiliation(s)
- Xinhui Xia
- State Key Laboratory of Biocontrol, School of Ecology, Sun Yat-sen University, Shenzhen, 518107, China
| | - Lulu Hao
- National and Local Joint Engineering Research Center of Ecological Treatment Technology for Urban Water Pollution, College of Life and Environmental Science, Wenzhou University, Wenzhou, 325035, China; Mangrove Institute, Lingnan Normal University, Zhanjiang, 524048, China
| | - Yifei Sun
- State Key Laboratory of Biocontrol, School of Ecology, Sun Yat-sen University, Shenzhen, 518107, China
| | - Yiqing Lv
- State Key Laboratory of Biocontrol, School of Ecology, Sun Yat-sen University, Shenzhen, 518107, China
| | - Yihong Wang
- State Key Laboratory of Biocontrol, School of Ecology, Sun Yat-sen University, Shenzhen, 518107, China
| | - Haiyu Wu
- State Key Laboratory of Biocontrol, School of Ecology, Sun Yat-sen University, Shenzhen, 518107, China
| | - Zongjin Jiang
- State Key Laboratory of Biocontrol, School of Ecology, Sun Yat-sen University, Shenzhen, 518107, China
| | - Xinru Li
- State Key Laboratory of Biocontrol, School of Ecology, Sun Yat-sen University, Shenzhen, 518107, China
| | - Yuhan Yan
- State Key Laboratory of Biocontrol, School of Ecology, Sun Yat-sen University, Shenzhen, 518107, China
| | - Xiaojian Chen
- State Key Laboratory of Biocontrol, School of Ecology, Sun Yat-sen University, Shenzhen, 518107, China
| | - Binghou Li
- State Key Laboratory of Biocontrol, School of Ecology, Sun Yat-sen University, Shenzhen, 518107, China
| | - Hao Li
- State Key Laboratory of Biocontrol, School of Ecology, Sun Yat-sen University, Shenzhen, 518107, China
| | - Minhui Li
- State Key Laboratory of Biocontrol, School of Ecology, Sun Yat-sen University, Shenzhen, 518107, China
| | - Yuanyuan Sun
- State Key Laboratory of Biocontrol, School of Ecology, Sun Yat-sen University, Shenzhen, 518107, China
| | - Wenxu Ren
- State Key Laboratory of Biocontrol, School of Ecology, Sun Yat-sen University, Shenzhen, 518107, China
| | - Yalin Xue
- State Key Laboratory of Biocontrol, School of Ecology, Sun Yat-sen University, Shenzhen, 518107, China
| | - Qing You
- State Key Laboratory of Biocontrol, School of Ecology, Sun Yat-sen University, Shenzhen, 518107, China
| | - Lei Zhu
- State Key Laboratory of Biocontrol, School of Ecology, Sun Yat-sen University, Shenzhen, 518107, China
| | - Qiuchang Liao
- State Key Laboratory of Biocontrol, School of Ecology, Sun Yat-sen University, Shenzhen, 518107, China
| | - Shiyun Xie
- State Key Laboratory of Biocontrol, School of Ecology, Sun Yat-sen University, Shenzhen, 518107, China
| | - Yunsen Zhang
- State Key Laboratory of Biocontrol, School of Ecology, Sun Yat-sen University, Shenzhen, 518107, China
| | - Chunyu Zhao
- State Key Laboratory of Biocontrol, School of Ecology, Sun Yat-sen University, Shenzhen, 518107, China
| | - Haowen Zhu
- State Key Laboratory of Biocontrol, School of Ecology, Sun Yat-sen University, Shenzhen, 518107, China
| | - Chengrui Liang
- State Key Laboratory of Biocontrol, School of Ecology, Sun Yat-sen University, Shenzhen, 518107, China
| | - Jin Qiu
- State Key Laboratory of Biocontrol, School of Ecology, Sun Yat-sen University, Shenzhen, 518107, China
| | - Zilong Song
- State Key Laboratory of Biocontrol, School of Ecology, Sun Yat-sen University, Shenzhen, 518107, China
| | - Yeyu Deng
- State Key Laboratory of Biocontrol, School of Ecology, Sun Yat-sen University, Shenzhen, 518107, China
| | - Ying Pan
- State Key Laboratory of Biocontrol, School of Ecology, Sun Yat-sen University, Shenzhen, 518107, China
| | - Yuan Zou
- State Key Laboratory of Biocontrol, School of Ecology, Sun Yat-sen University, Shenzhen, 518107, China
| | - Ying Zhang
- Mangrove Institute, Lingnan Normal University, Zhanjiang, 524048, China.
| | - Yuchen Yang
- State Key Laboratory of Biocontrol, School of Ecology, Sun Yat-sen University, Shenzhen, 518107, China.
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8
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Cheng K, Zhang C, Lu Y, Li J, Tang H, Ma L, Zhu H. The Glycine-Rich RNA-Binding Protein Is a Vital Post-Transcriptional Regulator in Crops. PLANTS (BASEL, SWITZERLAND) 2023; 12:3504. [PMID: 37836244 PMCID: PMC10575402 DOI: 10.3390/plants12193504] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/29/2023] [Revised: 10/02/2023] [Accepted: 10/05/2023] [Indexed: 10/15/2023]
Abstract
Glycine-rich RNA binding proteins (GR-RBPs), a branch of RNA binding proteins (RBPs), play integral roles in regulating various aspects of RNA metabolism regulation, such as RNA processing, transport, localization, translation, and stability, and ultimately regulate gene expression and cell fate. However, our current understanding of GR-RBPs has predominantly been centered on Arabidopsis thaliana, a model plant for investigating plant growth and development. Nonetheless, an increasing body of literature has emerged in recent years, shedding light on the presence and functions of GRPs in diverse crop species. In this review, we not only delineate the distinctive structural domains of plant GR-RBPs but also elucidate several contemporary mechanisms of GR-RBPs in the post-transcriptional regulation of RNA. These mechanisms encompass intricate processes, including RNA alternative splicing, polyadenylation, miRNA biogenesis, phase separation, and RNA translation. Furthermore, we offer an exhaustive synthesis of the diverse roles that GR-RBPs fulfill within crop plants. Our overarching objective is to provide researchers and practitioners in the field of agricultural genetics with valuable insights that may inform and guide the application of plant genetic engineering for enhanced crop development and sustainable agriculture.
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Affiliation(s)
- Ke Cheng
- The College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083, China; (K.C.); (Y.L.); (J.L.); (H.T.); (L.M.)
| | - Chunjiao Zhang
- Supervision, Inspection & Testing Center of Agricultural Products Quality, Ministry of Agriculture and Rural Affairs, Beijing 100083, China;
| | - Yao Lu
- The College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083, China; (K.C.); (Y.L.); (J.L.); (H.T.); (L.M.)
| | - Jinyan Li
- The College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083, China; (K.C.); (Y.L.); (J.L.); (H.T.); (L.M.)
| | - Hui Tang
- The College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083, China; (K.C.); (Y.L.); (J.L.); (H.T.); (L.M.)
| | - Liqun Ma
- The College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083, China; (K.C.); (Y.L.); (J.L.); (H.T.); (L.M.)
| | - Hongliang Zhu
- The College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083, China; (K.C.); (Y.L.); (J.L.); (H.T.); (L.M.)
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9
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Zhou S, Zhao F, Zhu D, Zhang Q, Dai Z, Wu Z. Coupling of co-transcriptional splicing and 3' end Pol II pausing during termination in Arabidopsis. Genome Biol 2023; 24:206. [PMID: 37697420 PMCID: PMC10496290 DOI: 10.1186/s13059-023-03050-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2022] [Accepted: 09/04/2023] [Indexed: 09/13/2023] Open
Abstract
BACKGROUND In Arabidopsis, RNA Polymerase II (Pol II) often pauses within a few hundred base pairs downstream of the polyadenylation site, reflecting efficient transcriptional termination, but how such pausing is regulated remains largely elusive. RESULT Here, we analyze Pol II dynamics at 3' ends by combining comprehensive experiments with mathematical modelling. We generate high-resolution serine 2 phosphorylated (Ser2P) Pol II positioning data specifically enriched at 3' ends and define a 3' end pause index (3'PI). The position but not the extent of the 3' end pause correlates with the termination window size. The 3'PI is not decreased but even mildly increased in the termination deficient mutant xrn3, indicating 3' end pause is a regulatory step early during the termination and before XRN3-mediated RNA decay that releases Pol II. Unexpectedly, 3'PI is closely associated with gene exon numbers and co-transcriptional splicing efficiency. Multiple exons genes often display stronger 3' end pauses and more efficient on-chromatin splicing than genes with fewer exons. Chemical inhibition of splicing strongly reduces the 3'PI and disrupts its correlation with exon numbers but does not globally impact 3' end readthrough levels. These results are further confirmed by fitting Pol II positioning data with a mathematical model, which enables the estimation of parameters that define Pol II dynamics. CONCLUSION Our work highlights that the number of exons via co-transcriptional splicing is a major determinant of Pol II pausing levels at the 3' end of genes in plants.
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Affiliation(s)
- Sixian Zhou
- Harbin Institute of Technology, Harbin, 150001, China
- Key Laboratory of Molecular Design for Plant Cell Factory of Guangdong Higher Education Institutes, Institute of Plant and Food Science, Department of Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, 518055, China
| | - Fengli Zhao
- Key Laboratory of Molecular Design for Plant Cell Factory of Guangdong Higher Education Institutes, Institute of Plant and Food Science, Department of Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, 518055, China
| | - Danling Zhu
- Key Laboratory of Molecular Design for Plant Cell Factory of Guangdong Higher Education Institutes, Institute of Plant and Food Science, Department of Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, 518055, China
| | - Qiqi Zhang
- Key Laboratory of Molecular Design for Plant Cell Factory of Guangdong Higher Education Institutes, Institute of Plant and Food Science, Department of Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, 518055, China
| | - Ziwei Dai
- Department of Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, 518055, China.
| | - Zhe Wu
- Key Laboratory of Molecular Design for Plant Cell Factory of Guangdong Higher Education Institutes, Institute of Plant and Food Science, Department of Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, 518055, China.
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10
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Zhang Y, Xu Y, Skaggs TH, Ferreira JFS, Chen X, Sandhu D. Plant phase extraction: A method for enhanced discovery of the RNA-binding proteome and its dynamics in plants. THE PLANT CELL 2023; 35:2750-2772. [PMID: 37144845 PMCID: PMC10396368 DOI: 10.1093/plcell/koad124] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Revised: 04/11/2023] [Accepted: 04/13/2023] [Indexed: 05/06/2023]
Abstract
RNA-binding proteins (RBPs) play critical roles in posttranscriptional gene regulation. Current methods of systematically profiling RBPs in plants have been predominantly limited to proteins interacting with polyadenylated (poly(A)) RNAs. We developed a method called plant phase extraction (PPE), which yielded a highly comprehensive RNA-binding proteome (RBPome), uncovering 2,517 RBPs from Arabidopsis (Arabidopsis thaliana) leaf and root samples with a highly diverse array of RNA-binding domains. We identified traditional RBPs that participate in various aspects of RNA metabolism and a plethora of nonclassical proteins moonlighting as RBPs. We uncovered constitutive and tissue-specific RBPs essential for normal development and, more importantly, revealed RBPs crucial for salinity stress responses from a RBP-RNA dynamics perspective. Remarkably, 40% of the RBPs are non-poly(A) RBPs that were not previously annotated as RBPs, signifying the advantage of PPE in unbiasedly retrieving RBPs. We propose that intrinsically disordered regions contribute to their nonclassical binding and provide evidence that enzymatic domains from metabolic enzymes have additional roles in RNA binding. Taken together, our findings demonstrate that PPE is an impactful approach for identifying RBPs from complex plant tissues and pave the way for investigating RBP functions under different physiological and stress conditions at the posttranscriptional level.
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Affiliation(s)
- Yong Zhang
- U.S. Salinity Lab (USDA-ARS), Riverside, CA 92507, USA
- Department of Environmental Sciences, University of California, Riverside, CA 92521, USA
| | - Ye Xu
- Department of Botany and Plant Sciences, Institute of Integrative Genome Biology, University of California, Riverside, CA 92521, USA
| | - Todd H Skaggs
- U.S. Salinity Lab (USDA-ARS), Riverside, CA 92507, USA
| | | | - Xuemei Chen
- Department of Botany and Plant Sciences, Institute of Integrative Genome Biology, University of California, Riverside, CA 92521, USA
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11
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Wang Y, Wang H, Wang H, Zhou R, Wu J, Zhang Z, Jin Y, Li T, Kohnen MV, Liu X, Wei W, Chen K, Gao Y, Ding J, Zhang H, Liu B, Lin C, Gu L. Multi-omics of Circular RNAs and Their Responses to Hormones in Moso Bamboo (Phyllostachys edulis). GENOMICS, PROTEOMICS & BIOINFORMATICS 2023; 21:866-885. [PMID: 36805531 PMCID: PMC10787125 DOI: 10.1016/j.gpb.2023.01.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/10/2021] [Revised: 01/04/2023] [Accepted: 01/31/2023] [Indexed: 02/18/2023]
Abstract
Circular RNAs (circRNAs) are endogenous non-coding RNAs with covalently closed structures, which have important functions in plants. However, their biogenesis, degradation, and function upon treatment with gibberellins (GAs) and auxins (1-naphthaleneacetic acid, NAA) remain unknown. Here, we systematically identified and characterized the expression patterns, evolutionary conservation, genomic features, and internal structures of circRNAs using RNase R-treated libraries from moso bamboo (Phyllostachys edulis) seedlings. Moreover, we investigated the biogenesis of circRNAs dependent on both cis- and trans-regulation. We explored the function of circRNAs, including their roles in regulating microRNA (miRNA)-related genes and modulating the alternative splicing of their linear counterparts. Importantly, we developed a customized degradome sequencing approach to detect miRNA-mediated cleavage of circRNAs. Finally, we presented a comprehensive view of the participation of circRNAs in the regulation of hormone metabolism upon treatment of bamboo seedlings with GA and NAA. Collectively, our study provides insights into the biogenesis, function, and miRNA-mediated degradation of circRNAs in moso bamboo.
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Affiliation(s)
- Yongsheng Wang
- Basic Forestry and Proteomics Research Center, College of Forestry, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Huihui Wang
- Basic Forestry and Proteomics Research Center, College of Forestry, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Huiyuan Wang
- Basic Forestry and Proteomics Research Center, College of Forestry, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Ruifan Zhou
- Basic Forestry and Proteomics Research Center, College of Forestry, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Ji Wu
- Basic Forestry and Proteomics Research Center, College of Forestry, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Zekun Zhang
- Basic Forestry and Proteomics Research Center, College of Forestry, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Yandong Jin
- Basic Forestry and Proteomics Research Center, College of Forestry, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Tao Li
- Basic Forestry and Proteomics Research Center, College of Forestry, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Markus V Kohnen
- Basic Forestry and Proteomics Research Center, College of Forestry, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Xuqing Liu
- Basic Forestry and Proteomics Research Center, College of Forestry, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Wentao Wei
- Basic Forestry and Proteomics Research Center, College of Forestry, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Kai Chen
- Basic Forestry and Proteomics Research Center, College of Forestry, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Yubang Gao
- Basic Forestry and Proteomics Research Center, College of Forestry, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Jiazhi Ding
- Basic Forestry and Proteomics Research Center, College of Forestry, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Hangxiao Zhang
- Basic Forestry and Proteomics Research Center, College of Forestry, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Bo Liu
- College of Forestry, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Chentao Lin
- Department of Molecular, Cell and Developmental Biology, University of California at Los Angeles, Los Angeles, CA 90095, USA
| | - Lianfeng Gu
- Basic Forestry and Proteomics Research Center, College of Forestry, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Fujian Agriculture and Forestry University, Fuzhou 350002, China.
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12
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Mateos JL, Staiger D. Toward a systems view on RNA-binding proteins and associated RNAs in plants: Guilt by association. THE PLANT CELL 2023; 35:1708-1726. [PMID: 36461946 PMCID: PMC10226577 DOI: 10.1093/plcell/koac345] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/19/2022] [Revised: 11/08/2022] [Accepted: 11/17/2022] [Indexed: 05/30/2023]
Abstract
RNA-binding proteins (RBPs) have a broad impact on most biochemical, physiological, and developmental processes in a plant's life. RBPs engage in an on-off relationship with their RNA partners, accompanying virtually every stage in RNA processing and function. While the function of a plethora of RBPs in plant development and stress responses has been described, we are lacking a systems-level understanding of components in RNA-based regulation. Novel techniques have substantially enlarged the compendium of proteins with experimental evidence for binding to RNAs in the cell, the RNA-binding proteome. Furthermore, ribonomics methods have been adapted for use in plants to profile the in vivo binding repertoire of RBPs genome-wide. Here, we discuss how recent technological achievements have provided novel insights into the mode of action of plant RBPs at a genome-wide scale. Furthermore, we touch upon two emerging topics, the connection of RBPs to phase separation in the cell and to extracellular RNAs. Finally, we define open questions to be addressed to move toward an integrated understanding of RBP function.
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Affiliation(s)
- Julieta L Mateos
- Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Instituto de Fisiología, Biología Molecular y Neurociencias (IFIBYNE-CONICET-UBA), Buenos Aires, Argentina
- RNA Biology and Molecular Physiology, Faculty of Biology, Bielefeld University, 33615 Bielefeld, Germany
| | - Dorothee Staiger
- RNA Biology and Molecular Physiology, Faculty of Biology, Bielefeld University, 33615 Bielefeld, Germany
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13
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Lin J, Li QQ. Coupling epigenetics and RNA polyadenylation: missing links. TRENDS IN PLANT SCIENCE 2023; 28:223-234. [PMID: 36175275 DOI: 10.1016/j.tplants.2022.08.023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/18/2022] [Revised: 08/30/2022] [Accepted: 08/31/2022] [Indexed: 06/16/2023]
Abstract
Precise regulation of gene expression is crucial for plant survival. As a cotranscriptional regulatory mechanism, pre-mRNA polyadenylation is essential for fine-tuning gene expression. Polyadenylation can be alternatively projected at various sites of a transcript, which contributes to transcriptome diversity. Epigenetic modification is another mechanism of transcriptional control. Recent studies have uncovered crosstalk between cotranscriptional polyadenylation processes and both epigenomic and epitranscriptomic markers. Genetic analyses have demonstrated that DNA methylation, histone modifications, and epitranscriptomic modification are involved in regulating polyadenylation in plants. Here we summarize current understanding of the links between epigenetics and polyadenylation and their novel biological efficacy for plant development and environmental responses. Unresolved issues and future directions are discussed to shed light on the field.
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Affiliation(s)
- Juncheng Lin
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, College of the Environment and Ecology, Xiamen University, Xiamen, Fujian 361102, China; FAFU-UCR Joint Center, Horticulture Biology and Metabolomics Center, Haixia Institute of Science and Technology, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, China
| | - Qingshun Quinn Li
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, College of the Environment and Ecology, Xiamen University, Xiamen, Fujian 361102, China; Biomedical Science Division, College of Dental Medicine, Western University of Health Sciences, Pomona, CA 91766, USA.
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14
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Xiao J, Jin S, Wang X, Huang J, Zou H. CELF1 Selectively Regulates Alternative Splicing of DNA Repair Genes Associated With Cataract in Human Lens Cell Line. Biochem Genet 2022:10.1007/s10528-022-10324-2. [PMID: 36585568 DOI: 10.1007/s10528-022-10324-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2022] [Accepted: 12/16/2022] [Indexed: 12/31/2022]
Abstract
Cataract is a global eye disease caused by the opacification of lens, while its underlying molecular pathogenesis is not clear, making it difficult for prevention. CELF1, an RNA binding protein, mediates Alternative Splicing (AS) of genes involved in diverse diseases and regulates development or defects of lens. Utilizing transcriptome-wide approaches, we analyzed and compared AS patterns between human lens epithelial cells (SRA01/04) with CELF1 overexpression (CELF1-OE) and control cells. Extensive changes in AS patterns upon CELF1-OE were identified in SRA01/04 cells. We finally identified 840 CELF1-regulated AS events (RASEs) and found that CELF1-OE preferred to repress exon skipping events in SRA01/04 cells. CELF1-regulated AS genes were enriched in the regulation of DNA repair, cellular response to DNA damage stimulus, and apoptosis pathways (including HMGA2, CSNK1E, and YAP1). These biological functions and pathways have been reported to be associated with lens development or other eye diseases. To further explore the mechanisms of CELF1 in regulating AS genes, we downloaded and re-analyzed a set of CELF1-RNA interactome data. We found that 194 genes were bound and regulated by CELF1 at the AS level. 10 genes involved in DNA repair-related pathways were also bound by CELF1. Motif analysis for CELF1-bound peaks and splicing sites of RASEs showed that CELF1 regulates AS by binding to the AGGU[AG]AG motif in SRA01/04 cells. CELF1 could mediate AS of DNA repair-related genes through directly binding to their transcripts with distinct motif bias. The functional mechanism of CELF1 may ultimately participate in cataract formation and lens development.
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Affiliation(s)
- Jun Xiao
- Department of Ophthalmology, The Second Hospital of Jilin University, Changchun, China
| | - Siyan Jin
- Department of Ophthalmology, The Second Hospital of Jilin University, Changchun, China
| | - Xue Wang
- Department of Ophthalmology, The Second Hospital of Jilin University, Changchun, China
| | - Ju Huang
- Department of Ophthalmology, The Second Hospital of Jilin University, Changchun, China
| | - He Zou
- Department of Ophthalmology, The Second Hospital of Jilin University, Changchun, China.
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15
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Liu T, Zhang X, Zhang H, Cheng Z, Liu J, Zhou C, Luo S, Luo W, Li S, Xing X, Chang Y, Shi C, Ren Y, Zhu S, Lei C, Guo X, Wang J, Zhao Z, Wang H, Zhai H, Lin Q, Wan J. Dwarf and High Tillering1 represses rice tillering through mediating the splicing of D14 pre-mRNA. THE PLANT CELL 2022; 34:3301-3318. [PMID: 35670739 PMCID: PMC9421477 DOI: 10.1093/plcell/koac169] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/16/2021] [Accepted: 05/11/2022] [Indexed: 06/09/2023]
Abstract
Strigolactones (SLs) constitute a class of plant hormones that regulate many aspects of plant development, including repressing tillering in rice (Oryza sativa). However, how SL pathways are regulated is still poorly understood. Here, we describe a rice mutant dwarf and high tillering1 (dht1), which exhibits pleiotropic phenotypes (such as dwarfism and increased tiller numbers) similar to those of mutants defective in SL signaling. We show that DHT1 encodes a monocotyledon-specific hnRNP-like protein that acts as a previously unrecognized intron splicing factor for many precursor mRNAs (pre-mRNAs), including for the SL receptor gene D14. We find that the dht1 (DHT1I232F) mutant protein is impaired in its stability and RNA binding activity, causing defective splicing of D14 pre-mRNA and reduced D14 expression, and consequently leading to the SL signaling-defective phenotypes. Overall, our findings deepen our understanding of the functional diversification of hnRNP-like proteins and establish a connection between posttranscriptional splicing and SL signaling in the regulation of plant development.
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Affiliation(s)
| | | | | | | | - Jun Liu
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Chunlei Zhou
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, Jiangsu Plant Gene Engineering Research Center, Nanjing Agricultural University, Nanjing 210095, China
| | - Sheng Luo
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Weifeng Luo
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Shuai Li
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Xinxin Xing
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Yanqi Chang
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Cuilan Shi
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Yulong Ren
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Shanshan Zhu
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Cailin Lei
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Xiuping Guo
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Jie Wang
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Zhichao Zhao
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Haiyang Wang
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Huqu Zhai
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Qibing Lin
- Author for correspondence: (J.W.), (Q.L.)
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16
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Coulter M, Entizne JC, Guo W, Bayer M, Wonneberger R, Milne L, Schreiber M, Haaning A, Muehlbauer GJ, McCallum N, Fuller J, Simpson C, Stein N, Brown JWS, Waugh R, Zhang R. BaRTv2: a highly resolved barley reference transcriptome for accurate transcript-specific RNA-seq quantification. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2022; 111:1183-1202. [PMID: 35704392 PMCID: PMC9546494 DOI: 10.1111/tpj.15871] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/18/2021] [Revised: 05/02/2022] [Accepted: 06/09/2022] [Indexed: 06/15/2023]
Abstract
Accurate characterisation of splice junctions (SJs) as well as transcription start and end sites in reference transcriptomes allows precise quantification of transcripts from RNA-seq data, and enables detailed investigations of transcriptional and post-transcriptional regulation. Using novel computational methods and a combination of PacBio Iso-seq and Illumina short-read sequences from 20 diverse tissues and conditions, we generated a comprehensive and highly resolved barley reference transcript dataset from the European 2-row spring barley cultivar Barke (BaRTv2.18). Stringent and thorough filtering was carried out to maintain the quality and accuracy of the SJs and transcript start and end sites. BaRTv2.18 shows increased transcript diversity and completeness compared with an earlier version, BaRTv1.0. The accuracy of transcript level quantification, SJs and transcript start and end sites have been validated extensively using parallel technologies and analysis, including high-resolution reverse transcriptase-polymerase chain reaction and 5'-RACE. BaRTv2.18 contains 39 434 genes and 148 260 transcripts, representing the most comprehensive and resolved reference transcriptome in barley to date. It provides an important and high-quality resource for advanced transcriptomic analyses, including both transcriptional and post-transcriptional regulation, with exceptional resolution and precision.
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Affiliation(s)
- Max Coulter
- Division of Plant SciencesUniversity of Dundee, James Hutton InstituteInvergowrieDundeeDD2 5DAScotlandUK
| | - Juan Carlos Entizne
- Division of Plant SciencesUniversity of Dundee, James Hutton InstituteInvergowrieDundeeDD2 5DAScotlandUK
| | - Wenbin Guo
- Information and Computational SciencesJames Hutton InstituteInvergowrieDundeeDD2 5DAScotlandUK
| | - Micha Bayer
- Information and Computational SciencesJames Hutton InstituteInvergowrieDundeeDD2 5DAScotlandUK
| | - Ronja Wonneberger
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK)Corrensstrasse 3D‐06466Stadt SeelandGermany
| | - Linda Milne
- Information and Computational SciencesJames Hutton InstituteInvergowrieDundeeDD2 5DAScotlandUK
| | - Miriam Schreiber
- Division of Plant SciencesUniversity of Dundee, James Hutton InstituteInvergowrieDundeeDD2 5DAScotlandUK
| | - Allison Haaning
- Department of Agronomy and Plant GeneticsUniversity of Minnesota1991 Upper Buford Circle, 542 Borlaug HallSt PaulMinnesota55108USA
| | - Gary J. Muehlbauer
- Department of Agronomy and Plant GeneticsUniversity of Minnesota1991 Upper Buford Circle, 542 Borlaug HallSt PaulMinnesota55108USA
| | - Nicola McCallum
- Cell and Molecular SciencesJames Hutton InstituteInvergowrieDundeeDD2 5DAScotlandUK
| | - John Fuller
- Cell and Molecular SciencesJames Hutton InstituteInvergowrieDundeeDD2 5DAScotlandUK
| | - Craig Simpson
- Cell and Molecular SciencesJames Hutton InstituteInvergowrieDundeeDD2 5DAScotlandUK
| | - Nils Stein
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK)Corrensstrasse 3D‐06466Stadt SeelandGermany
- Center for Integrated Breeding Research (CiBreed)Georg‐August‐UniversityGöttingenGermany
| | - John W. S. Brown
- Division of Plant SciencesUniversity of Dundee, James Hutton InstituteInvergowrieDundeeDD2 5DAScotlandUK
- Cell and Molecular SciencesJames Hutton InstituteInvergowrieDundeeDD2 5DAScotlandUK
| | - Robbie Waugh
- Division of Plant SciencesUniversity of Dundee, James Hutton InstituteInvergowrieDundeeDD2 5DAScotlandUK
- Cell and Molecular SciencesJames Hutton InstituteInvergowrieDundeeDD2 5DAScotlandUK
- School of Agriculture and Wine & Waite Research InstituteUniversity of AdelaideWaite CampusGlen OsmondSouth Australia5064Australia
| | - Runxuan Zhang
- Information and Computational SciencesJames Hutton InstituteInvergowrieDundeeDD2 5DAScotlandUK
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17
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Ribonomics Approaches to Identify RBPome in Plants and Other Eukaryotes: Current Progress and Future Prospects. Int J Mol Sci 2022; 23:ijms23115923. [PMID: 35682602 PMCID: PMC9180120 DOI: 10.3390/ijms23115923] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2022] [Revised: 05/16/2022] [Accepted: 05/20/2022] [Indexed: 02/01/2023] Open
Abstract
RNA-binding proteins (RBPs) form complex interactions with RNA to regulate the cell’s activities including cell development and disease resistance. RNA-binding proteome (RBPome) aims to profile and characterize the RNAs and proteins that interact with each other to carry out biological functions. Generally, RNA-centric and protein-centric ribonomic approaches have been successfully developed to profile RBPome in different organisms including plants and animals. Further, more and more novel methods that were firstly devised and applied in mammalians have shown great potential to unravel RBPome in plants such as RNA-interactome capture (RIC) and orthogonal organic phase separation (OOPS). Despise the development of various robust and state-of-the-art ribonomics techniques, genome-wide RBP identifications and characterizations in plants are relatively fewer than those in other eukaryotes, indicating that ribonomics techniques have great opportunities in unraveling and characterizing the RNA–protein interactions in plant species. Here, we review all the available approaches for analyzing RBPs in living organisms. Additionally, we summarize the transcriptome-wide approaches to characterize both the coding and non-coding RBPs in plants and the promising use of RBPome for booming agriculture.
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18
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Yu Z, Hong L, Li QQ. Signatures of mRNA Alternative Polyadenylation in Arabidopsis Leaf Development. Front Genet 2022; 13:863253. [PMID: 35559042 PMCID: PMC9086830 DOI: 10.3389/fgene.2022.863253] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2022] [Accepted: 03/15/2022] [Indexed: 11/26/2022] Open
Abstract
Alternative polyadenylation (APA) of pre-mRNA is an important co-transcriptional mechanism that modulates gene expression, leading to transcriptomic and functional diversities. The role of APA in Arabidopsis leaf development, however, remains elusive. We applied a poly(A)-tag sequencing (PAT-seq) technique to characterize APA-mediated regulation events in cotyledon and in five stages of true leaf development. Over 60% APA was identified in genes expressed in leaves, consistent with the results in previous publications. However, a reduced APA level was detected in younger leaves, reaching 44% in the 18th true leaf. Importantly, we also found that >70% of the poly(A) site usages were altered in the second true leaf relative to the cotyledon. Compared with the cotyledon, more genes in the second true leaf tended to use the distal site of 3′UTR, but this was not found in pairwise comparison among other true leaves. In addition, a significant APA gene was found to be decreased in a pairwise comparison among true leaves, including differentially expressed genes. The APA genes identified herein were associated with specific biological processes, including metabolic and cellular processes and response to stimuli and hormones. These results provide a new insight into the regulation of Arabidopsis leaf development through APA.
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Affiliation(s)
- Zhibo Yu
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystem, College of the Environment and Ecology, Xiamen University, Xiamen, China
| | - Liwei Hong
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystem, College of the Environment and Ecology, Xiamen University, Xiamen, China
| | - Qingshun Q Li
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystem, College of the Environment and Ecology, Xiamen University, Xiamen, China.,Graduate College of Biomedical Sciences, Western University of Health Sciences, Pomona, CA, United States
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19
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Abstract
Plants form stress granules made of RNA binding proteins and RNA in response to various stresses. In this issue of Developmental Cell, Zhu et al. identify two RNA-binding proteins, RBGD2/4, that phase, separate, and localize stress granules to promote heat stress tolerance.
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20
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Zhu S, Gu J, Yao J, Li Y, Zhang Z, Xia W, Wang Z, Gui X, Li L, Li D, Zhang H, Liu C. Liquid-liquid phase separation of RBGD2/4 is required for heat stress resistance in Arabidopsis. Dev Cell 2022; 57:583-597.e6. [DOI: 10.1016/j.devcel.2022.02.005] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2020] [Revised: 08/24/2021] [Accepted: 02/02/2022] [Indexed: 12/28/2022]
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21
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Xie J, Zhang X, Zheng J, Hong X, Tong X, Liu X, Xue Y, Wang X, Zhang Y, Liu S. Two novel RNA-binding proteins identification through computational prediction and experimental validation. Genomics 2021; 114:149-160. [PMID: 34921931 DOI: 10.1016/j.ygeno.2021.12.003] [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: 01/14/2021] [Revised: 08/05/2021] [Accepted: 12/13/2021] [Indexed: 11/16/2022]
Abstract
Since RBPs play important roles in the cell, it's particularly important to find new RBPs. We performed iRIP-seq and CLIP-seq to verify two proteins, CLIP1 and DMD, predicted by RBPPred whether are RBPs or not. The experimental results confirm that these two proteins have RNA-binding activity. We identified significantly enriched binding motifs UGGGGAGG, CUUCCG and CCCGU for CLIP1 (iRIP-seq), DMD (iRIP-seq) and DMD (CLIP-seq), respectively. The computational KEGG and GO analysis show that the CLIP1 and DMD share some biological processes and functions. Besides, we found that the SNPs between DMD and its RNA partners may be associated with Becker muscular dystrophy, Duchenne muscular dystrophy, Dilated cardiomyopathy 3B and Cardiovascular phenotype. Among the thirteen cancers data, CLIP1 and another 300 oncogenes always co-occur, and 123 of these 300 genes interact with CLIP1. These cancers may be associated with the mutations occurred in both CLIP1 and the genes it interacts with.
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Affiliation(s)
- Juan Xie
- School of Physics, Huazhong University of Science and Technology, Wuhan, Hubei 430074, China
| | - Xiaoli Zhang
- School of Physics, Huazhong University of Science and Technology, Wuhan, Hubei 430074, China
| | - Jinfang Zheng
- School of Physics, Huazhong University of Science and Technology, Wuhan, Hubei 430074, China
| | - Xu Hong
- School of Physics, Huazhong University of Science and Technology, Wuhan, Hubei 430074, China
| | - Xiaoxue Tong
- School of Physics, Huazhong University of Science and Technology, Wuhan, Hubei 430074, China
| | - Xudong Liu
- School of Physics, Huazhong University of Science and Technology, Wuhan, Hubei 430074, China
| | - Yaqiang Xue
- Laboratory for Genome Regulation and Human Health, ABLife Inc., Wuhan, Hubei 430075, China
| | - Xuelian Wang
- ABLife BioBigData Institute, Wuhan, Hubei 430075, China
| | - Yi Zhang
- ABLife BioBigData Institute, Wuhan, Hubei 430075, China
| | - Shiyong Liu
- School of Physics, Huazhong University of Science and Technology, Wuhan, Hubei 430074, China.
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22
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Zimmer G, Miller MJ, Steketee CJ, Jackson SA, de Tunes LVM, Li Z. Genetic control and allele variation among soybean maturity groups 000 through IX. THE PLANT GENOME 2021; 14:e20146. [PMID: 34514734 DOI: 10.1002/tpg2.20146] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/19/2021] [Accepted: 07/06/2021] [Indexed: 06/13/2023]
Abstract
Soybean [Glycinemax (L.) Merr.] maturity determines the growing region of a given soybean variety and is a primary factor in yield and other agronomic traits. The objectives of this research were to identify the quantitative trait loci (QTL) associated with maturity groups (MGs) and determine the genetic control of soybean maturity in each MG. Using data from 16,879 soybean accessions, genome-wide association (GWA) analyses were conducted for each paired MG and across MGs 000 through IX. Genome-wide association analyses were also performed using 184 genotypes (MGs V-IX) with days to flowering (DTF) and maturity (DTM) collected in the field. A total of 58 QTL were identified to be significantly associated with MGs in individual GWAs, which included 12 reported maturity loci and two stem termination genes. Genome-wide associations across MGs 000-IX detected a total of 103 QTL and confirmed 54 QTL identified in the individual GWAs. Of significant loci identified, qMG-5.2 had effects on the highest number (9) of MGs, followed by E2, E3, Dt2, qMG-15.5, E1, qMG-13.1, qMG-7.1, and qMG-16.1, which affected five to seven MGs. A high number of genetic loci (8-25) that affected MGs 0-V were observed. Stem termination genes Dt1 and Dt2 mainly had significant allele variation in MGs II-V. Genome-wide associations for DTF, DTM, and reproductive period (RP) in the diversity panel confirmed 15 QTL, of which seven were observed in MGs V-IX. The results generated can help soybean breeders manipulate the maturity loci for genetic improvement of soybean yield.
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Affiliation(s)
- Gustavo Zimmer
- Institute of Plant Breeding, Genetics, and Genomics, and Department of Crop and Soil Sciences, University of Georgia, Athens, GA, 30602, USA
- Department of Crop Production, Federal University of Pelotas, Capão do Leão, RS, 96160-000, Brazil
| | - Mark J Miller
- Institute of Plant Breeding, Genetics, and Genomics, and Department of Crop and Soil Sciences, University of Georgia, Athens, GA, 30602, USA
| | - Clinton J Steketee
- Institute of Plant Breeding, Genetics, and Genomics, and Department of Crop and Soil Sciences, University of Georgia, Athens, GA, 30602, USA
| | - Scott A Jackson
- Institute of Plant Breeding, Genetics, and Genomics, and Department of Crop and Soil Sciences, University of Georgia, Athens, GA, 30602, USA
| | | | - Zenglu Li
- Institute of Plant Breeding, Genetics, and Genomics, and Department of Crop and Soil Sciences, University of Georgia, Athens, GA, 30602, USA
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23
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Li X, Chen L, Yao L, Zou J, Hao J, Wu W. Calcium-dependent protein kinase CPK32 mediates calcium signaling in regulating Arabidopsis flowering time. Natl Sci Rev 2021; 9:nwab180. [PMID: 35079411 PMCID: PMC8783668 DOI: 10.1093/nsr/nwab180] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2021] [Revised: 08/29/2021] [Accepted: 09/14/2021] [Indexed: 11/22/2022] Open
Abstract
Appropriate flowering time is critical for the reproductive success of plant species. Emerging evidence indicates that calcium may play an important role in the regulation of flowering time. However, the underlying molecular mechanisms remain unclear. In this study, we demonstrate that calcium-dependent protein kinase 32 (CPK32) regulates flowering time by affecting the alternative polyadenylation of FLOWERING CONTROL LOCUS A (FCA) and altering the transcription of FLOWERING LOCUS C (FLC), a central repressor of flowering time. The knockdown of CPK32 results in an obvious late flowering phenotype and dramatically enhanced FLC transcription. CPK32 interacts with FCA, and phosphorylates the serine592 of FCA in a Ca2+-dependent manner. Moreover, the ratio of abundance of the FCA transcripts (FCA-D and FCA-P) changes significantly in the cpk32 mutant, which subsequently affects FLC expression and consequently regulates floral transition. The present evidence demonstrates that CPK32 modulates flowering time by regulating FCA alternative polyadenylation and consequent FLC expression.
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Affiliation(s)
- Xidong Li
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing 100193, China
| | - Limei Chen
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing 100193, China
- Center for Crop Functional Genomics and Molecular Breeding, China Agricultural University, Beijing 100193, China
| | - Li Yao
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing 100193, China
- Syngenta Biotechnology China Co., Ltd., Beijing 102206, China
| | - Junjie Zou
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing 100193, China
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Jie Hao
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing 100193, China
| | - Weihua Wu
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing 100193, China
- Center for Crop Functional Genomics and Molecular Breeding, China Agricultural University, Beijing 100193, China
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24
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Zhou G, Niu R, Zhou Y, Luo M, Peng Y, Wang H, Wang Z, Xu G. Proximity editing to identify RNAs in phase-separated RNA binding protein condensates. Cell Discov 2021; 7:72. [PMID: 34426573 PMCID: PMC8382829 DOI: 10.1038/s41421-021-00288-9] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2020] [Accepted: 06/03/2021] [Indexed: 11/09/2022] Open
Affiliation(s)
- Guilong Zhou
- State Key Laboratory of Hybrid Rice, Institute for Advanced Studies (IAS), Wuhan University, 430072, Wuhan, Hubei, China
| | - Ruixia Niu
- State Key Laboratory of Hybrid Rice, Institute for Advanced Studies (IAS), Wuhan University, 430072, Wuhan, Hubei, China
| | - Yulu Zhou
- State Key Laboratory of Hybrid Rice, Institute for Advanced Studies (IAS), Wuhan University, 430072, Wuhan, Hubei, China
| | - Ming Luo
- State Key Laboratory of Hybrid Rice, Institute for Advanced Studies (IAS), Wuhan University, 430072, Wuhan, Hubei, China
| | - Yao Peng
- State Key Laboratory of Hybrid Rice, Institute for Advanced Studies (IAS), Wuhan University, 430072, Wuhan, Hubei, China
| | - Hui Wang
- State Key Laboratory of Hybrid Rice, Institute for Advanced Studies (IAS), Wuhan University, 430072, Wuhan, Hubei, China
| | - Zhao Wang
- State Key Laboratory of Hybrid Rice, Institute for Advanced Studies (IAS), Wuhan University, 430072, Wuhan, Hubei, China
| | - Guoyong Xu
- State Key Laboratory of Hybrid Rice, Institute for Advanced Studies (IAS), Wuhan University, 430072, Wuhan, Hubei, China.
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25
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Decoding co-/post-transcriptional complexities of plant transcriptomes and epitranscriptome using next-generation sequencing technologies. Biochem Soc Trans 2021; 48:2399-2414. [PMID: 33196096 DOI: 10.1042/bst20190492] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2020] [Revised: 10/06/2020] [Accepted: 10/22/2020] [Indexed: 12/12/2022]
Abstract
Next-generation sequencing (NGS) technologies - Illumina RNA-seq, Pacific Biosciences isoform sequencing (PacBio Iso-seq), and Oxford Nanopore direct RNA sequencing (DRS) - have revealed the complexity of plant transcriptomes and their regulation at the co-/post-transcriptional level. Global analysis of mature mRNAs, transcripts from nuclear run-on assays, and nascent chromatin-bound mRNAs using short as well as full-length and single-molecule DRS reads have uncovered potential roles of different forms of RNA polymerase II during the transcription process, and the extent of co-transcriptional pre-mRNA splicing and polyadenylation. These tools have also allowed mapping of transcriptome-wide start sites in cap-containing RNAs, poly(A) site choice, poly(A) tail length, and RNA base modifications. The emerging theme from recent studies is that reprogramming of gene expression in response to developmental cues and stresses at the co-/post-transcriptional level likely plays a crucial role in eliciting appropriate responses for optimal growth and plant survival under adverse conditions. Although the mechanisms by which developmental cues and different stresses regulate co-/post-transcriptional splicing are largely unknown, a few recent studies indicate that the external cues target spliceosomal and splicing regulatory proteins to modulate alternative splicing. In this review, we provide an overview of recent discoveries on the dynamics and complexities of plant transcriptomes, mechanistic insights into splicing regulation, and discuss critical gaps in co-/post-transcriptional research that need to be addressed using diverse genomic and biochemical approaches.
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26
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Parker MT, Knop K, Zacharaki V, Sherwood AV, Tomé D, Yu X, Martin PGP, Beynon J, Michaels SD, Barton GJ, Simpson GG. Widespread premature transcription termination of Arabidopsis thaliana NLR genes by the spen protein FPA. eLife 2021; 10:e65537. [PMID: 33904405 PMCID: PMC8116057 DOI: 10.7554/elife.65537] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2020] [Accepted: 04/26/2021] [Indexed: 12/18/2022] Open
Abstract
Genes involved in disease resistance are some of the fastest evolving and most diverse components of genomes. Large numbers of nucleotide-binding, leucine-rich repeat (NLR) genes are found in plant genomes and are required for disease resistance. However, NLRs can trigger autoimmunity, disrupt beneficial microbiota or reduce fitness. It is therefore crucial to understand how NLRs are controlled. Here, we show that the RNA-binding protein FPA mediates widespread premature cleavage and polyadenylation of NLR transcripts, thereby controlling their functional expression and impacting immunity. Using long-read Nanopore direct RNA sequencing, we resolved the complexity of NLR transcript processing and gene annotation. Our results uncover a co-transcriptional layer of NLR control with implications for understanding the regulatory and evolutionary dynamics of NLRs in the immune responses of plants.
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Affiliation(s)
- Matthew T Parker
- School of Life Sciences, University of DundeeDundeeUnited Kingdom
| | - Katarzyna Knop
- School of Life Sciences, University of DundeeDundeeUnited Kingdom
| | | | - Anna V Sherwood
- School of Life Sciences, University of DundeeDundeeUnited Kingdom
| | - Daniel Tomé
- School of Life Sciences, University of WarwickCoventryUnited Kingdom
| | - Xuhong Yu
- Department of Biology, Indiana UniversityBloomingtonUnited States
| | - Pascal GP Martin
- Department of Biology, Indiana UniversityBloomingtonUnited States
| | - Jim Beynon
- School of Life Sciences, University of WarwickCoventryUnited Kingdom
| | - Scott D Michaels
- Department of Biology, Indiana UniversityBloomingtonUnited States
| | | | - Gordon G Simpson
- School of Life Sciences, University of DundeeDundeeUnited Kingdom
- The James Hutton InstituteInvergowrieUnited Kingdom
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27
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Song P, Yang J, Wang C, Lu Q, Shi L, Tayier S, Jia G. Arabidopsis N 6-methyladenosine reader CPSF30-L recognizes FUE signals to control polyadenylation site choice in liquid-like nuclear bodies. MOLECULAR PLANT 2021; 14:571-587. [PMID: 33515768 DOI: 10.1016/j.molp.2021.01.014] [Citation(s) in RCA: 91] [Impact Index Per Article: 30.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/30/2020] [Revised: 09/10/2020] [Accepted: 12/11/2020] [Indexed: 05/16/2023]
Abstract
The biological functions of the epitranscriptomic modification N6-methyladenosine (m6A) in plants are not fully understood. CPSF30-L is a predominant isoform of the polyadenylation factor CPSF30 and consists of CPSF30-S and an m6A-binding YTH domain. Little is known about the biological roles of CPSF30-L and the molecular mechanism underlying its m6A-binding function in alternative polyadenylation. Here, we characterized CPSF30-L as an Arabidopsis m6A reader whose m6A-binding function is required for the floral transition and abscisic acid (ABA) response. We found that the m6A-binding activity of CPSF30-L enhances the formation of liquid-like nuclear bodies, where CPSF30-L mainly recognizes m6A-modified far-upstream elements to control polyadenylation site choice. Deficiency of CPSF30-L lengthens the 3' untranslated region of three phenotypes-related transcripts, thereby accelerating their mRNA degradation and leading to late flowering and ABA hypersensitivity. Collectively, this study uncovers a new molecular mechanism for m6A-driven phase separation and polyadenylation in plants.
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Affiliation(s)
- Peizhe Song
- Synthetic and Functional Biomolecules Center, Beijing National Laboratory for Molecular Sciences, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Junbo Yang
- Synthetic and Functional Biomolecules Center, Beijing National Laboratory for Molecular Sciences, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Chunling Wang
- Synthetic and Functional Biomolecules Center, Beijing National Laboratory for Molecular Sciences, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Qiang Lu
- Synthetic and Functional Biomolecules Center, Beijing National Laboratory for Molecular Sciences, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Linqing Shi
- Medical Isotopes Research Center and, Department of Radiation Medicine, School of Basic Medical Sciences, Peking University Health Science Center, Beijing 100191, China
| | - Subiding Tayier
- Synthetic and Functional Biomolecules Center, Beijing National Laboratory for Molecular Sciences, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Guifang Jia
- Synthetic and Functional Biomolecules Center, Beijing National Laboratory for Molecular Sciences, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China.
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28
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Hou Y, Sun J, Wu B, Gao Y, Nie H, Nie Z, Quan S, Wang Y, Cao X, Li S. CPSF30-L-mediated recognition of mRNA m 6A modification controls alternative polyadenylation of nitrate signaling-related gene transcripts in Arabidopsis. MOLECULAR PLANT 2021; 14:688-699. [PMID: 33515769 DOI: 10.1016/j.molp.2021.01.013] [Citation(s) in RCA: 74] [Impact Index Per Article: 24.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/05/2020] [Revised: 12/10/2020] [Accepted: 01/21/2021] [Indexed: 05/16/2023]
Abstract
N6-methyladenosine (m6A), a ubiquitous internal modification of eukaryotic mRNAs, plays a vital role in almost every aspect of mRNA metabolism. However, there is little evidence documenting the role of m6A in regulating alternative polyadenylation (APA) in plants. APA is controlled by a large protein-RNA complex with many components, including CLEAVAGE AND POLYADENYLATION SPECIFICITY FACTOR30 (CPSF30). In Arabidopsis, CPSF30 has two isoforms and the longer isoform (CPSF30-L) contains a YT512-B Homology (YTH) domain, which is unique to plants. In this study, we showed that CPSF30-L YTH domain binds to m6A in vitro. In the cpsf30-2 mutant, the transcripts of many genes including several important nitrate signaling-related genes had shifts in polyadenylation sites that were correlated with m6A peaks, indicating that these gene transcripts carrying m6A tend to be regulated by APA. Wild-type CPSF30-L could rescue the defects in APA and nitrate metabolism in cpsf30-2, but m6A-binding-defective mutants of CPSF30-L could not. Taken together, our results demonstrated that m6A modification regulates APA in Arabidopsis and revealed that the m6A reader CPSF30-L affects nitrate signaling by controlling APA, shedding new light on the roles of the m6A modification during RNA 3'-end processing in nitrate metabolism.
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Affiliation(s)
- Yifeng Hou
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Jing Sun
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Baixing Wu
- Department of Biology, Southern University of Science and Technology, Shenzhen, Guangdong 518055, China
| | - Yangyang Gao
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Tai'an, Shandong 271018, China
| | - Hongbo Nie
- Department of Biology, Southern University of Science and Technology, Shenzhen, Guangdong 518055, China
| | - Zhentian Nie
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Tai'an, Shandong 271018, China
| | - Shuxuan Quan
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Tai'an, Shandong 271018, China
| | - Yong Wang
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Tai'an, Shandong 271018, China.
| | - Xiaofeng Cao
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China; Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Beijing 100101, China.
| | - Sisi Li
- Department of Biology, Southern University of Science and Technology, Shenzhen, Guangdong 518055, China.
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29
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Zhang Z, Wang H, Wang Y, Xi F, Wang H, Kohnen MV, Gao P, Wei W, Chen K, Liu X, Gao Y, Han X, Hu K, Zhang H, Zhu Q, Zheng Y, Liu B, Ahmad A, Hsu YH, Jacobsen SE, Gu L. Whole-genome characterization of chronological age-associated changes in methylome and circular RNAs in moso bamboo (Phyllostachys edulis) from vegetative to floral growth. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2021; 106:435-453. [PMID: 33506534 DOI: 10.1111/tpj.15174] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/29/2020] [Revised: 12/30/2020] [Accepted: 01/05/2021] [Indexed: 06/12/2023]
Abstract
In mammals, DNA methylation is associated with aging. However, age-related DNA methylation changes during phase transitions largely remain unstudied in plants. Moso bamboo (Phyllostachys edulis) requires a very long time to transition from the vegetative to the floral phase. To comprehensively investigate the association of DNA methylation with aging, we present here single-base-resolution DNA methylation profiles using both high-throughput bisulfite sequencing and single-molecule nanopore-based DNA sequencing, covering the long period of vegetative growth and transition to flowering in moso bamboo. We discovered that CHH methylation gradually accumulates from vegetative to reproductive growth in a time-dependent fashion. Differentially methylated regions, correlating with chronological aging, occurred preferentially at both transcription start sites and transcription termination sites. Genes with CG methylation changes showed an enrichment of Gene Ontology (GO) categories in 'vegetative to reproductive phase transition of meristem'. Combining methylation data with mRNA sequencing revealed that DNA methylation in promoters, introns and exons may have different roles in regulating gene expression. Finally, circular RNA (circRNA) sequencing revealed that the flanking introns of circRNAs are hypermethylated and enriched in long terminal repeat (LTR) retrotransposons. Together, the observations in this study provide insights into the dynamic DNA methylation and circRNA landscapes, correlating with chronological age, which paves the way to study further the impact of epigenetic factors on flowering in moso bamboo.
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Affiliation(s)
- Zeyu Zhang
- Basic Forestry and Proteomics Research Center, College of Forestry, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Huihui Wang
- Basic Forestry and Proteomics Research Center, College of Forestry, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Yongsheng Wang
- Basic Forestry and Proteomics Research Center, College of life science, Fuzhou, 350002, China
| | - Feihu Xi
- Basic Forestry and Proteomics Research Center, College of life science, Fuzhou, 350002, China
| | - Huiyuan Wang
- Basic Forestry and Proteomics Research Center, College of Forestry, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Markus V Kohnen
- Basic Forestry and Proteomics Research Center, College of Forestry, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Pengfei Gao
- Basic Forestry and Proteomics Research Center, College of Forestry, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Wentao Wei
- Basic Forestry and Proteomics Research Center, College of Forestry, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Kai Chen
- Basic Forestry and Proteomics Research Center, College of life science, Fuzhou, 350002, China
| | - Xuqing Liu
- Basic Forestry and Proteomics Research Center, College of Forestry, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Yubang Gao
- Basic Forestry and Proteomics Research Center, College of life science, Fuzhou, 350002, China
| | - Ximei Han
- Basic Forestry and Proteomics Research Center, College of Forestry, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Kaiqiang Hu
- Basic Forestry and Proteomics Research Center, College of Forestry, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Hangxiao Zhang
- Basic Forestry and Proteomics Research Center, College of Forestry, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Qiang Zhu
- Basic Forestry and Proteomics Research Center, College of Forestry, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Yushan Zheng
- College of Forestry, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Bo Liu
- College of Forestry, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Ayaz Ahmad
- Department of Biotechnology, Abdul Wali Khan University Mardan, Mardan, Pakistan
| | - Yau-Heiu Hsu
- Graduate Institute of Biotechnology, National Chung Hsing University, Taichung, Taiwan
| | - Steven E Jacobsen
- Department of Molecular, Cell & Developmental Biology, Howard Hughes Medical Institute, University of California, Los Angeles, CA, 90095, USA
| | - Lianfeng Gu
- Basic Forestry and Proteomics Research Center, College of Forestry, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
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30
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Burjoski V, Reddy ASN. The Landscape of RNA-Protein Interactions in Plants: Approaches and Current Status. Int J Mol Sci 2021; 22:2845. [PMID: 33799602 PMCID: PMC7999938 DOI: 10.3390/ijms22062845] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2021] [Revised: 02/25/2021] [Accepted: 03/10/2021] [Indexed: 12/28/2022] Open
Abstract
RNAs transmit information from DNA to encode proteins that perform all cellular processes and regulate gene expression in multiple ways. From the time of synthesis to degradation, RNA molecules are associated with proteins called RNA-binding proteins (RBPs). The RBPs play diverse roles in many aspects of gene expression including pre-mRNA processing and post-transcriptional and translational regulation. In the last decade, the application of modern techniques to identify RNA-protein interactions with individual proteins, RNAs, and the whole transcriptome has led to the discovery of a hidden landscape of these interactions in plants. Global approaches such as RNA interactome capture (RIC) to identify proteins that bind protein-coding transcripts have led to the identification of close to 2000 putative RBPs in plants. Interestingly, many of these were found to be metabolic enzymes with no known canonical RNA-binding domains. Here, we review the methods used to analyze RNA-protein interactions in plants thus far and highlight the understanding of plant RNA-protein interactions these techniques have provided us. We also review some recent protein-centric, RNA-centric, and global approaches developed with non-plant systems and discuss their potential application to plants. We also provide an overview of results from classical studies of RNA-protein interaction in plants and discuss the significance of the increasingly evident ubiquity of RNA-protein interactions for the study of gene regulation and RNA biology in plants.
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Affiliation(s)
| | - Anireddy S. N. Reddy
- Department of Biology and Program in Cell and Molecular Biology, Colorado State University, Fort Collins, CO 80523, USA;
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31
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Hafner M, Katsantoni M, Köster T, Marks J, Mukherjee J, Staiger D, Ule J, Zavolan M. CLIP and complementary methods. ACTA ACUST UNITED AC 2021. [DOI: 10.1038/s43586-021-00018-1] [Citation(s) in RCA: 50] [Impact Index Per Article: 16.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
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32
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Processing of coding and non-coding RNAs in plant development and environmental responses. Essays Biochem 2020; 64:931-945. [DOI: 10.1042/ebc20200029] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2020] [Revised: 10/21/2020] [Accepted: 10/23/2020] [Indexed: 12/14/2022]
Abstract
Abstract
Precursor RNAs undergo extensive processing to become mature RNAs. RNA transcripts are subjected to 5′ capping, 3′-end processing, splicing, and modification; they also form dynamic secondary structures during co-transcriptional and post-transcriptional processing. Like coding RNAs, non-coding RNAs (ncRNAs) undergo extensive processing. For example, secondary small interfering RNA (siRNA) transcripts undergo RNA processing, followed by further cleavage to become mature siRNAs. Transcriptome studies have revealed roles for co-transcriptional and post-transcriptional RNA processing in the regulation of gene expression and the coordination of plant development and plant–environment interactions. In this review, we present the latest progress on RNA processing in gene expression and discuss phased siRNAs (phasiRNAs), a kind of germ cell-specific secondary small RNA (sRNA), focusing on their functions in plant development and environmental responses.
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33
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Hwang JY, Jung S, Kook TL, Rouchka EC, Bok J, Park JW. rMAPS2: an update of the RNA map analysis and plotting server for alternative splicing regulation. Nucleic Acids Res 2020; 48:W300-W306. [PMID: 32286627 PMCID: PMC7319468 DOI: 10.1093/nar/gkaa237] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2020] [Revised: 03/26/2020] [Accepted: 04/01/2020] [Indexed: 11/17/2022] Open
Abstract
The rMAPS2 (RNA Map Analysis and Plotting Server 2) web server, freely available at http://rmaps.cecsresearch.org/, has provided the high-throughput sequencing data research community with curated tools for the identification of RNA binding protein sites. rMAPS2 analyzes differential alternative splicing or CLIP peak data obtained from high-throughput sequencing data analysis tools like MISO, rMATS, Piranha, PIPE-CLIP and PARalyzer, and then, graphically displays enriched RNA-binding protein target sites. The initial release of rMAPS focused only on the most common alternative splicing event, skipped exon or exon skipping. However, there was a high demand for the analysis of other major types of alternative splicing events, especially for retained intron events since this is the most common type of alternative splicing in plants, such as Arabidopsis thaliana. Here, we expanded the implementation of rMAPS2 to facilitate analyses for all five major types of alternative splicing events: skipped exon, mutually exclusive exons, alternative 5′ splice site, alternative 3′ splice site and retained intron. In addition, by employing multi-threading, rMAPS2 has vastly improved the user experience with significant reductions in running time, ∼3.5 min for the analysis of all five major alternative splicing types at once.
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Affiliation(s)
- Jae Y Hwang
- Department of Computer Science and Engineering, University of Louisville, Louisville, KY 40292, USA
| | - Sungbo Jung
- Department of Computer Science and Engineering, University of Louisville, Louisville, KY 40292, USA
| | - Tae L Kook
- Department of Computer Science and Engineering, University of Louisville, Louisville, KY 40292, USA
| | - Eric C Rouchka
- Department of Computer Science and Engineering, University of Louisville, Louisville, KY 40292, USA.,KBRIN Bioinformatics Core, University of Louisville, Louisville, KY 40292, USA
| | - Jinwoong Bok
- Department of Anatomy, Yonsei University College of Medicine, Seoul 03722, Republic of Korea.,Department of Otorhinolaryngology, Yonsei University College of Medicine, Seoul 03722, Republic of Korea.,BK21 PLUS project for Medical Science, Yonsei University College of Medicine, Seoul 03722, Republic of Korea
| | - Juw W Park
- Department of Computer Science and Engineering, University of Louisville, Louisville, KY 40292, USA.,KBRIN Bioinformatics Core, University of Louisville, Louisville, KY 40292, USA
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34
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Plant Individual Nucleotide Resolution Cross-Linking and Immunoprecipitation to Characterize RNA-Protein Complexes. Methods Mol Biol 2020. [PMID: 32710414 DOI: 10.1007/978-1-0716-0712-1_15] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2024]
Abstract
In recent years, it has become increasingly recognized that regulation at the RNA level pervasively shapes the transcriptome in eukaryotic cells. This has fostered an interest in the mode of action of RNA-binding proteins that, via interaction with specific RNA sequence motifs, modulate gene expression. Understanding such posttranscriptional networks controlled by an RNA-binding protein requires a comprehensive identification of its in vivo targets. In metazoans and yeast, methods have been devised to stabilize RNA-protein interactions by UV cross-linking before isolating RNA-protein complexes using antibodies, followed by identification of associated RNAs by next-generation sequencing. These methods are collectively referred to as CLIP-Seq (cross-linking immunoprecipitation-high-throughput sequencing). Here, we present a version of the individual nucleotide resolution cross-linking and immunoprecipitation procedure that is suitable for use in the model plant Arabidopsis thaliana.
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35
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Reichel M, Köster T, Staiger D. Marking RNA: m6A writers, readers, and functions in Arabidopsis. J Mol Cell Biol 2020; 11:899-910. [PMID: 31336387 PMCID: PMC6884701 DOI: 10.1093/jmcb/mjz085] [Citation(s) in RCA: 65] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2019] [Revised: 06/24/2019] [Accepted: 07/02/2019] [Indexed: 12/18/2022] Open
Abstract
N6-methyladenosine (m6A) emerges as an important modification in eukaryotic mRNAs. m6A has first been reported in 1974, and its functional significance in mammalian gene regulation and importance for proper development have been well established. An arsenal of writer, eraser, and reader proteins accomplish deposition, removal, and interpretation of the m6A mark, resulting in dynamic function. This led to the concept of an epitranscriptome, the compendium of RNA species with chemical modification of the nucleobases in the cell, in analogy to the epigenome. While m6A has long been known to also exist in plant mRNAs, proteins involved in m6A metabolism have only recently been detected by mutant analysis, homology search, and mRNA interactome capture in the reference plant Arabidopsis thaliana. Dysregulation of the m6A modification causes severe developmental abnormalities of leaves and roots and altered timing of reproductive development. Furthermore, m6A modification affects viral infection. Here, we discuss recent progress in identifying m6A sites transcriptome-wide, in identifying the molecular players involved in writing, removing, and reading the mark, and in assigning functions to this RNA modification in A. thaliana. We highlight similarities and differences to m6A modification in mammals and provide an outlook on important questions that remain to be addressed.
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Affiliation(s)
- Marlene Reichel
- RNA Biology and Molecular Physiology, Faculty of Biology, Bielefeld University, 33615 Bielefeld, Germany
| | - Tino Köster
- RNA Biology and Molecular Physiology, Faculty of Biology, Bielefeld University, 33615 Bielefeld, Germany
| | - Dorothee Staiger
- RNA Biology and Molecular Physiology, Faculty of Biology, Bielefeld University, 33615 Bielefeld, Germany
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Chakrabarti M, de Lorenzo L, Abdel-Ghany SE, Reddy ASN, Hunt AG. Wide-ranging transcriptome remodelling mediated by alternative polyadenylation in response to abiotic stresses in Sorghum. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2020; 102:916-930. [PMID: 31909843 DOI: 10.1111/tpj.14671] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/26/2019] [Revised: 12/14/2019] [Accepted: 01/02/2020] [Indexed: 05/28/2023]
Abstract
Alternative polyadenylation (APA) regulates diverse developmental and physiological processes through its effects on gene expression, mRNA stability, translatability, and transport. Sorghum is a major cereal crop in the world and, despite its importance, not much is known about the role of post-transcriptional regulation in mediating responses to abiotic stresses in Sorghum. A genome-wide APA analysis unveiled widespread occurrence of APA in Sorghum in response to drought, heat, and salt stress. Abiotic stress treatments incited changes in poly(A) site choice in a large number of genes. Interestingly, abiotic stresses led to the re-directing of transcriptional output into non-productive pathways defined by the class of poly(A) site utilized. This result revealed APA to be part of a larger global response of Sorghum to abiotic stresses that involves the re-direction of transcriptional output into non-productive transcriptional and translational pathways. Large numbers of stress-inducible poly(A) sites could not be linked with known, annotated genes, suggestive of the existence of numerous unidentified genes whose expression is strongly regulated by abiotic stresses. Furthermore, we uncovered a novel stress-specific cis-element in intronic poly(A) sites used in drought- and heat-stressed plants that might play an important role in non-canonical poly(A) site choice in response to abiotic stresses.
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Affiliation(s)
- Manohar Chakrabarti
- Department of Plant and Soil Sciences, University of Kentucky, Lexington, KY, 40546, USA
| | - Laura de Lorenzo
- Department of Plant and Soil Sciences, University of Kentucky, Lexington, KY, 40546, USA
| | - Salah E Abdel-Ghany
- Department of Biology, and Program in Cell and Molecular Biology, Colorado State University, Fort Collins, CO, 80523, USA
| | - Anireddy S N Reddy
- Department of Biology, and Program in Cell and Molecular Biology, Colorado State University, Fort Collins, CO, 80523, USA
| | - Arthur G Hunt
- Department of Plant and Soil Sciences, University of Kentucky, Lexington, KY, 40546, USA
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37
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Yang GQ, Huang JC, Yuan JJ, Zhang Q, Gong CX, Chen Q, Xie Q, Xie LX, Chen R, Qiu ZM, Zhou K, Xu R, Jiang GH, Xiong XY, Yang QW. Prdx1 Reduces Intracerebral Hemorrhage-Induced Brain Injury via Targeting Inflammation- and Apoptosis-Related mRNA Stability. Front Neurosci 2020; 14:181. [PMID: 32210752 PMCID: PMC7076121 DOI: 10.3389/fnins.2020.00181] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2019] [Accepted: 02/19/2020] [Indexed: 12/19/2022] Open
Abstract
RNA-binding proteins (RBPs) have been shown to be involved in posttranscriptional regulation, which plays an important role in the pathophysiology of intracerebral hemorrhage (ICH). Peroxiredoxin 1 (Prdx1), an RBP, plays an important role in regulating inflammation and apoptosis. On the basis that inflammation and apoptosis may contribute to ICH-induced brain injury, in this study, we used ICH models coupled with in vitro experiments, to investigate the role and mechanism of Prdx1 in regulating inflammation and apoptosis by acting as an RBP after ICH. We first found that Prdx1 was significantly up-regulated in response to ICH-induced brain injury and was mainly expressed in astrocytes and microglia in ICH rat brains. After overexpressing Prdx1 by injecting adeno-associated virus (AAV) into the striatum of rats at 3 weeks, we constructed ICH models and found that Prdx1 overexpression markedly reduced inflammation and apoptosis after ICH. Furthermore, RNA immunoprecipitation combined with high-throughput sequencing (RIP-seq) in vitro revealed that Prdx1 affects the stability of inflammation- and apoptosis-related mRNA, resulting in the inhibition of inflammation and apoptosis. Finally, overexpression of Prdx1 significantly alleviated the symptoms and mortality of rats subjected to ICH. Our results show that Prdx1 reduces ICH-induced brain injury by targeting inflammation- and apoptosis-related mRNA stability. Prdx1 may be an improved therapeutic target for alleviating the brain injury caused by ICH.
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Affiliation(s)
- Guo-Qiang Yang
- Department of Neurology, Xinqiao Hospital, Army Medical University, Chongqing, China
| | - Jia-Cheng Huang
- Department of Neurology, Xinqiao Hospital, Army Medical University, Chongqing, China
| | - Jun-Jie Yuan
- Department of Neurology, Xinqiao Hospital, Army Medical University, Chongqing, China
| | - Qin Zhang
- Department of Neurology, Xinqiao Hospital, Army Medical University, Chongqing, China
| | - Chang-Xiong Gong
- Department of Neurology, Xinqiao Hospital, Army Medical University, Chongqing, China
| | - Qiong Chen
- Department of Neurology, Xinqiao Hospital, Army Medical University, Chongqing, China
| | - Qi Xie
- Department of Neurology, Xinqiao Hospital, Army Medical University, Chongqing, China
| | - Le-Xing Xie
- Department of Neurology, Xinqiao Hospital, Army Medical University, Chongqing, China
| | - Ru Chen
- Department of Neurology, Xinqiao Hospital, Army Medical University, Chongqing, China
| | - Zhong-Ming Qiu
- Department of Neurology, Xinqiao Hospital, Army Medical University, Chongqing, China
| | - Kai Zhou
- Department of Neurology, Xinqiao Hospital, Army Medical University, Chongqing, China
| | - Rui Xu
- Department of Neurology, Xinqiao Hospital, Army Medical University, Chongqing, China
| | - Guo-Hui Jiang
- Department of Neurology, Xinqiao Hospital, Army Medical University, Chongqing, China
| | - Xiao-Yi Xiong
- Department of Neurology, Xinqiao Hospital, Army Medical University, Chongqing, China
| | - Qing-Wu Yang
- Department of Neurology, Xinqiao Hospital, Army Medical University, Chongqing, China
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38
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Zhu D, Mao F, Tian Y, Lin X, Gu L, Gu H, Qu LJ, Wu Y, Wu Z. The Features and Regulation of Co-transcriptional Splicing in Arabidopsis. MOLECULAR PLANT 2020; 13:278-294. [PMID: 31760161 DOI: 10.1016/j.molp.2019.11.004] [Citation(s) in RCA: 46] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/18/2019] [Revised: 09/29/2019] [Accepted: 11/15/2019] [Indexed: 05/20/2023]
Abstract
Precursor mRNA (pre-mRNA) splicing is essential for gene expression in most eukaryotic organisms. Previous studies from mammals, Drosophila, and yeast show that the majority of splicing events occurs co-transcriptionally. In plants, however, the features of co-transcriptional splicing (CTS) and its regulation still remain largely unknown. Here, we used chromatin-bound RNA sequencing to study CTS in Arabidopsis thaliana. We found that CTS is widespread in Arabidopsis seedlings, with a large proportion of alternative splicing events determined co-transcriptionally. CTS efficiency correlated with gene expression level, the chromatin landscape and, most surprisingly, the number of introns and exons of individual genes, but is independent of gene length. In combination with enhanced crosslinking and immunoprecipitation sequencing analysis, we further showed that the hnRNP-like proteins RZ-1B and RZ-1C promote efficient CTS globally through direct binding, frequently to exonic sequences. Notably, this general effect of RZ-1B/1C on splicing promotion is mainly observed at the chromatin level, not at the mRNA level. RZ-1C promotes CTS of multiple-exon genes in association with its binding to regions both proximal and distal to the regulated introns. We propose that RZ-1C promotes efficient CTS of genes with multiple exons through cooperative interactions with many exons, introns, and splicing factors. Our work thus reveals important features of CTS in plants and provides methodologies for the investigation of CTS and RNA-binding proteins in plants.
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Affiliation(s)
- Danling Zhu
- SUSTech-PKU Institute of Plant and Food Science, Department of Biology, Southern University of Science and Technology, Shenzhen 518055, China
| | - Fei Mao
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, Bioinformatics Center, Nanjing Agriculture University, Nanjing, Jiangsu 210095, China
| | - Yuanchun Tian
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, Bioinformatics Center, Nanjing Agriculture University, Nanjing, Jiangsu 210095, China
| | - Xiaoya Lin
- State Key Laboratory of Protein and Plant Gene Research, Peking-Tsinghua Center for Life Sciences, College of Life Sciences, Peking University, Beijing 100871, China
| | - Lianfeng Gu
- Basic Forestry and Proteomics Research Center, College of Forestry, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Hongya Gu
- State Key Laboratory of Protein and Plant Gene Research, Peking-Tsinghua Center for Life Sciences, College of Life Sciences, Peking University, Beijing 100871, China
| | - Li-Jia Qu
- State Key Laboratory of Protein and Plant Gene Research, Peking-Tsinghua Center for Life Sciences, College of Life Sciences, Peking University, Beijing 100871, China
| | - Yufeng Wu
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, Bioinformatics Center, Nanjing Agriculture University, Nanjing, Jiangsu 210095, China.
| | - Zhe Wu
- SUSTech-PKU Institute of Plant and Food Science, Department of Biology, Southern University of Science and Technology, Shenzhen 518055, China.
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39
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Wu Z, Fang X, Zhu D, Dean C. Autonomous Pathway: FLOWERING LOCUS C Repression through an Antisense-Mediated Chromatin-Silencing Mechanism. PLANT PHYSIOLOGY 2020; 182:27-37. [PMID: 31740502 PMCID: PMC6945862 DOI: 10.1104/pp.19.01009] [Citation(s) in RCA: 68] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/16/2019] [Accepted: 10/28/2019] [Indexed: 05/19/2023]
Abstract
The timing of flowering is vital for plant reproductive success and is therefore tightly regulated by endogenous and exogenous cues. In summer annual Arabidopsis (Arabidopsis thaliana) accessions, like Columbia-0, rapid flowering is promoted by repression of the floral repressor FLOWERING LOCUS C (FLC). This is through the activity of the autonomous pathway, a group of proteins with diverse functions including RNA 3'-end processing factors, spliceosome components, a transcription elongation factor, and chromatin modifiers. These factors function at the FLC locus linking alternative processing of an antisense long noncoding RNA, called COOLAIR, with delivery of a repressive chromatin environment that affects the transcriptional output. The transcriptional output feeds back to influence the chromatin environment, reinforcing and stabilizing that state. This review summarizes our current knowledge of the autonomous pathway and compares it with similar cotranscriptional mechanisms in other organisms.
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Affiliation(s)
- Zhe Wu
- SUSTech-PKU Institute of Plant and Food Science, Department of Biology, Southern University of Science and Technology, Shenzhen 518055, China
- Cell and Developmental Biology, John Innes Centre, Norwich NR4 7UH, United Kingdom
| | - Xiaofeng Fang
- Cell and Developmental Biology, John Innes Centre, Norwich NR4 7UH, United Kingdom
| | - Danling Zhu
- SUSTech-PKU Institute of Plant and Food Science, Department of Biology, Southern University of Science and Technology, Shenzhen 518055, China
- Cell and Developmental Biology, John Innes Centre, Norwich NR4 7UH, United Kingdom
| | - Caroline Dean
- Cell and Developmental Biology, John Innes Centre, Norwich NR4 7UH, United Kingdom
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40
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Muhammad II, Kong SL, Akmar Abdullah SN, Munusamy U. RNA-seq and ChIP-seq as Complementary Approaches for Comprehension of Plant Transcriptional Regulatory Mechanism. Int J Mol Sci 2019; 21:E167. [PMID: 31881735 PMCID: PMC6981605 DOI: 10.3390/ijms21010167] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2019] [Revised: 12/19/2019] [Accepted: 12/23/2019] [Indexed: 02/07/2023] Open
Abstract
The availability of data produced from various sequencing platforms offer the possibility to answer complex questions in plant research. However, drawbacks can arise when there are gaps in the information generated, and complementary platforms are essential to obtain more comprehensive data sets relating to specific biological process, such as responses to environmental perturbations in plant systems. The investigation of transcriptional regulation raises different challenges, particularly in associating differentially expressed transcription factors with their downstream responsive genes. In this paper, we discuss the integration of transcriptional factor studies through RNA sequencing (RNA-seq) and Chromatin Immunoprecipitation sequencing (ChIP-seq). We show how the data from ChIP-seq can strengthen information generated from RNA-seq in elucidating gene regulatory mechanisms. In particular, we discuss how integration of ChIP-seq and RNA-seq data can help to unravel transcriptional regulatory networks. This review discusses recent advances in methods for studying transcriptional regulation using these two methods. It also provides guidelines for making choices in selecting specific protocols in RNA-seq pipelines for genome-wide analysis to achieve more detailed characterization of specific transcription regulatory pathways via ChIP-seq.
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Affiliation(s)
- Isiaka Ibrahim Muhammad
- Laboratory of Plantation Science and Technology, Institute of Plantation Studies, Universiti Putra Malaysia, Selangor 43400, Malaysia; (I.I.M.); (S.L.K.); (U.M.)
| | - Sze Ling Kong
- Laboratory of Plantation Science and Technology, Institute of Plantation Studies, Universiti Putra Malaysia, Selangor 43400, Malaysia; (I.I.M.); (S.L.K.); (U.M.)
| | - Siti Nor Akmar Abdullah
- Laboratory of Plantation Science and Technology, Institute of Plantation Studies, Universiti Putra Malaysia, Selangor 43400, Malaysia; (I.I.M.); (S.L.K.); (U.M.)
- Department of Agriculture Technology, Faculty of Agriculture, Universiti Putra Malaysia, Selangor 43400, Malaysia
| | - Umaiyal Munusamy
- Laboratory of Plantation Science and Technology, Institute of Plantation Studies, Universiti Putra Malaysia, Selangor 43400, Malaysia; (I.I.M.); (S.L.K.); (U.M.)
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41
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Multi-strategic RNA-seq analysis reveals a high-resolution transcriptional landscape in cotton. Nat Commun 2019; 10:4714. [PMID: 31624240 PMCID: PMC6797763 DOI: 10.1038/s41467-019-12575-x] [Citation(s) in RCA: 43] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2019] [Accepted: 09/18/2019] [Indexed: 11/09/2022] Open
Abstract
Cotton is an important natural fiber crop, however, its comprehensive and high-resolution gene map is lacking. Here we integrate four complementary high-throughput techniques, including Pacbio long read Iso-seq, strand-specific RNA-seq, CAGE-seq, and PolyA-seq, to systematically explore the transcription landscape across 16 tissues or different organ types in Gossypium arboreum. We devise a computational pipeline, named IGIA, to reconstruct accurate gene structures from the integrated data. Our results reveal a dynamic and diverse transcriptional map in cotton: tissue-specific gene expression, alternative usage of TSSs and polyadenylation sites, hotspot of alternative splicing, and transcriptional read-through. These regulated events affect many genes in various aspects such as gain or loss of functional RNA motifs and protein domains, fine-tuning of DNA binding activity, and co-regulation for genes in the same complex or pathway. The methods and findings provide valuable resources for further functional genomic studies such as understanding natural SNP variations for plant community.
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42
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Cho H, Cho HS, Hwang I. Emerging roles of RNA-binding proteins in plant development. CURRENT OPINION IN PLANT BIOLOGY 2019; 51:51-57. [PMID: 31071564 DOI: 10.1016/j.pbi.2019.03.016] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/15/2019] [Revised: 03/27/2019] [Accepted: 03/30/2019] [Indexed: 05/22/2023]
Abstract
RNA-binding proteins (RBPs) influence the fate of target RNAs via direct interactions. During transcription, RBPs and interacting partners are recruited to and modify transcripts, after which they may also participate in critical steps to generate functional RNA. RBP-RNA interactions govern post-transcriptional processing of RNA, consequently regulating gene expression in a spatio-temporal manner. In plants, an increasing number of proteins have been classified as RBPs, many of which have been shown to function as key players in diverse developmental processes. However, a comprehensive understanding of how RBPs function, which RNAs are targeted, and where RBP-RNA interactions occur within plant cells is lacking. Here, we discuss recent findings in the field and newly defined roles for RBPs in plant growth and development. We also describe the mechanistic effects of RBPs on target RNA metabolism and translation.
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Affiliation(s)
- Hyunwoo Cho
- Department of Industrial Plant Science and Technology, College of Agricultural, Life and Environmental Sciences, Chungbuk National University, Cheongju 2864, Republic of Korea
| | - Hyun Seob Cho
- Department of Life Sciences, POSTECH Biotech Center, Pohang University of Science and Technology, Pohang 37673, Republic of Korea
| | - Ildoo Hwang
- Department of Life Sciences, POSTECH Biotech Center, Pohang University of Science and Technology, Pohang 37673, Republic of Korea.
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43
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Yu Z, Lin J, Li QQ. Transcriptome Analyses of FY Mutants Reveal Its Role in mRNA Alternative Polyadenylation. THE PLANT CELL 2019; 31:2332-2352. [PMID: 31427469 PMCID: PMC6790095 DOI: 10.1105/tpc.18.00545] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/26/2019] [Revised: 07/15/2019] [Accepted: 08/19/2019] [Indexed: 05/10/2023]
Abstract
A crucial step for mRNA polyadenylation is poly(A) signal recognition by trans-acting factors. The mammalian cleavage and polyadenylation specificity factor (CPSF) complex components CPSF30 and WD repeat-containing protein33 (WDR33) recognize the canonical AAUAAA for polyadenylation. In Arabidopsis (Arabidopsis thaliana), the flowering time regulator FY is the homolog of WDR33. However, its role in mRNA polyadenylation is poorly understood. Using poly(A) tag sequencing, we found that >50% of alternative polyadenylation (APA) events are altered in fy single mutants or double mutants with oxt6 (a null mutant of AtCPSF30), but mutation of the FY WD40-repeat has a stronger effect than deletion of the plant-unique Pro-Pro-Leu-Pro-Pro (PPLPP) domain. fy mutations disrupt AAUAAA or AAUAAA-like poly(A) signal recognition. Notably, A-rich signal usage is suppressed in the WD40-repeat mutation but promoted in PPLPP-domain deficiency. However, fy mutations do not aggravate the altered signal usage in oxt6 Furthermore, the WD40-repeat mutation shows a preference for 3' untranslated region shortening, but the PPLPP-domain deficiency shows a preference for lengthening. Interestingly, the WD40-repeat mutant exhibits shortened primary roots and late flowering with alteration of APA of related genes. Importantly, the long transcripts of two APA genes affected in fy are related to abiotic stress responses. These results reveal a conserved and specific role of FY in mRNA polyadenylation.
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Affiliation(s)
- Zhibo Yu
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, College of the Environment and Ecology, Xiamen University, Xiamen, Fujian, China 361102
| | - Juncheng Lin
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, College of the Environment and Ecology, Xiamen University, Xiamen, Fujian, China 361102
- Graduate College of Biomedical Sciences, Western University of Health Sciences, Pomona, California 91766
| | - Qingshun Quinn Li
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, College of the Environment and Ecology, Xiamen University, Xiamen, Fujian, China 361102
- Graduate College of Biomedical Sciences, Western University of Health Sciences, Pomona, California 91766
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Gao Y, Xi F, zhang H, Liu X, Wang H, zhao L, Reddy AS, Gu L. Single-molecule Real-time (SMRT) Isoform Sequencing (Iso-Seq) in Plants: The Status of the Bioinformatics Tools to Unravel the Transcriptome Complexity. Curr Bioinform 2019. [DOI: 10.2174/1574893614666190204151746] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Background:
The advent of the Single-Molecule Real-time (SMRT) Isoform Sequencing
(Iso-Seq) has paved the way to obtain longer full-length transcripts. This method was found to
be much superior in identifying full-length splice variants and other post-transcriptional events as
compared to the Next Generation Sequencing (NGS)-based short read sequencing (RNA-Seq).
Several different bioinformatics tools to analyze the Iso-Seq data have been developed and some
of them are still being refined to address different aspects of transcriptome complexity. However, a
comprehensive summary of the available tools and their utility is still lacking.
Objective:
Here, we summarized the existing Iso-Seq analysis tools and presented an integrated
bioinformatics pipeline for Iso-Seq analysis, which overcomes the limitations of NGS and generates
long contiguous Full-Length Non-Chimeric (FLNC) reads for the analysis of posttranscriptional
events.
Results:
In this review, we summarized recent applications of Iso-Seq in plants, which include improved
genome annotations, identification of novel genes and lncRNAs, identification of fulllength
splice isoforms, detection of novel Alternative Splicing (AS) and Alternative Polyadenylation
(APA) events. In addition, we also discussed the bioinformatics pipeline for comprehensive
Iso-Seq data analysis, including how to reduce the error rate in the reads and how to identify and
quantify post-transcriptional events. Furthermore, the visualization approach of Iso-Seq was discussed
as well. Finally, we discussed methods to combine Iso-Seq data with RNA-Seq for transcriptome
quantification.
Conclusion:
Overall, this review demonstrates that the Iso-Seq is pivotal for analyzing transcriptome
complexity and this new method offers unprecedented opportunities to comprehensively understand
transcripts diversity.
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Affiliation(s)
- Yubang Gao
- Basic Forestry and Proteomics Research Center, College of Forestry, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, College of Life Science, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Feihu Xi
- Basic Forestry and Proteomics Research Center, College of Forestry, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, College of Life Science, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Hangxiao zhang
- Basic Forestry and Proteomics Research Center, College of Forestry, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, College of Life Science, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Xuqing Liu
- Basic Forestry and Proteomics Research Center, College of Forestry, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, College of Life Science, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Huiyuan Wang
- Basic Forestry and Proteomics Research Center, College of Forestry, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, College of Life Science, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Liangzhen zhao
- Basic Forestry and Proteomics Research Center, College of Forestry, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, College of Life Science, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Anireddy S.N. Reddy
- Department of Biology, Program in Molecular Plant Biology, Program in Cell and Molecular Biology, Colorado State University, Fort Collins, Colorado 80523, United States
| | - Lianfeng Gu
- Basic Forestry and Proteomics Research Center, College of Forestry, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, College of Life Science, Fujian Agriculture and Forestry University, Fuzhou 350002, China
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Köster T, Reichel M, Staiger D. CLIP and RNA interactome studies to unravel genome-wide RNA-protein interactions in vivo in Arabidopsis thaliana. Methods 2019; 178:63-71. [PMID: 31494244 DOI: 10.1016/j.ymeth.2019.09.005] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2019] [Revised: 05/14/2019] [Accepted: 09/01/2019] [Indexed: 12/11/2022] Open
Abstract
Post-transcriptional regulation makes an important contribution to adjusting the transcriptome to environmental changes in plants. RNA-binding proteins are key players that interact specifically with mRNAs to co-ordinate their fate. While the regulatory interactions between proteins and RNA are well understood in animals, until recently little information was available on the global binding landscape of RNA-binding proteins in higher plants. This is not least due to technical challenges in plants. In turn, while numerous RNA-binding proteins have been identified through mutant analysis and homology-based searches in plants, only recently a full compendium of proteins with RNA-binding activity has been experimentally determined for the reference plant Arabidopsis thaliana. State-of-the-art techniques to determine RNA-protein interactions genome-wide in animals are based on the covalent fixation of RNA and protein in vivo by UV light. This has only recently been successfully applied to plants. Here, we present practical considerations on the application of UV irradiation based methods to comprehensively determine in vivo RNA-protein interactions in Arabidopsis thaliana, focussing on individual nucleotide resolution crosslinking immunoprecipitation (iCLIP) and mRNA interactome capture.
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Affiliation(s)
- Tino Köster
- RNA Biology and Molecular Physiology, Faculty of Biology, Bielefeld University, 33615 Bielefeld, Germany
| | - Marlene Reichel
- RNA Biology and Molecular Physiology, Faculty of Biology, Bielefeld University, 33615 Bielefeld, Germany
| | - Dorothee Staiger
- RNA Biology and Molecular Physiology, Faculty of Biology, Bielefeld University, 33615 Bielefeld, Germany.
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Zhao T, Huan Q, Sun J, Liu C, Hou X, Yu X, Silverman IM, Zhang Y, Gregory BD, Liu CM, Qian W, Cao X. Impact of poly(A)-tail G-content on Arabidopsis PAB binding and their role in enhancing translational efficiency. Genome Biol 2019; 20:189. [PMID: 31481099 PMCID: PMC6724284 DOI: 10.1186/s13059-019-1799-8] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2018] [Accepted: 08/22/2019] [Indexed: 01/01/2023] Open
Abstract
BACKGROUND Polyadenylation plays a key role in producing mature mRNAs in eukaryotes. It is widely believed that the poly(A)-binding proteins (PABs) uniformly bind to poly(A)-tailed mRNAs, regulating their stability and translational efficiency. RESULTS We observe that the homozygous triple mutant of broadly expressed Arabidopsis thaliana PABs, AtPAB2, AtPAB4, and AtPAB8, is embryonic lethal. To understand the molecular basis, we characterize the RNA-binding landscape of these PABs. The AtPAB-binding efficiency varies over one order of magnitude among genes. To identify the sequences accounting for the variation, we perform poly(A)-seq that directly sequences the full-length poly(A) tails. More than 10% of poly(A) tails contain at least one guanosine (G); among them, the G-content varies from 0.8 to 28%. These guanosines frequently divide poly(A) tails into interspersed A-tracts and therefore cause the variation in the AtPAB-binding efficiency among genes. Ribo-seq and genome-wide RNA stability assays show that AtPAB-binding efficiency of a gene is positively correlated with translational efficiency rather than mRNA stability. Consistently, genes with stronger AtPAB binding exhibit a greater reduction in translational efficiency when AtPAB is depleted. CONCLUSIONS Our study provides a new mechanism that translational efficiency of a gene can be regulated through the G-content-dependent PAB binding, paving the way for a better understanding of poly(A) tail-associated regulation of gene expression.
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Affiliation(s)
- Taolan Zhao
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
- Key Laboratory of Genetic Network Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Qing Huan
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
- Key Laboratory of Genetic Network Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Jing Sun
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Chunyan Liu
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Xiuli Hou
- University of Chinese Academy of Sciences, Beijing, 100049, China
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
| | - Xiang Yu
- Department of Biology, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Ian M Silverman
- Department of Biology, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Yi Zhang
- Laboratory for Genome Regulation and Human Health and Center for Genome Analysis, ABLife Inc, Wuhan, 430075, Hubei, China
| | - Brian D Gregory
- Department of Biology, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Chun-Ming Liu
- University of Chinese Academy of Sciences, Beijing, 100049, China
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
| | - Wenfeng Qian
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China.
- Key Laboratory of Genetic Network Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China.
- University of Chinese Academy of Sciences, Beijing, 100049, China.
| | - Xiaofeng Cao
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China.
- University of Chinese Academy of Sciences, Beijing, 100049, China.
- CAS Center for Excellence in Molecular Plant Sciences, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China.
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Prall W, Sharma B, Gregory BD. Transcription Is Just the Beginning of Gene Expression Regulation: The Functional Significance of RNA-Binding Proteins to Post-transcriptional Processes in Plants. PLANT & CELL PHYSIOLOGY 2019; 60:1939-1952. [PMID: 31155676 DOI: 10.1093/pcp/pcz067] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/23/2019] [Accepted: 04/03/2019] [Indexed: 06/09/2023]
Abstract
Plants have developed sophisticated mechanisms to compensate and respond to ever-changing environmental conditions. Research focus in this area has recently shifted towards understanding the post-transcriptional mechanisms that contribute to RNA transcript maturation, abundance and function as key regulatory steps in allowing plants to properly react and adapt to these never-ending shifts in their environments. At the center of these regulatory mechanisms are RNA-binding proteins (RBPs), the functional mediators of all post-transcriptional processes. In plants, RBPs are becoming increasingly appreciated as the critical modulators of core cellular processes during development and in response to environmental stimuli. With the majority of research on RBPs and their functions historically in prokaryotic and mammalian systems, it has more recently been unveiled that plants have expanded families of conserved and novel RBPs compared with their eukaryotic counterparts. To better understand the scope of RBPs in plants, we present past and current literature detailing specific roles of RBPs during stress response, development and other fundamental transition periods. In this review, we highlight examples of complex regulation coordinated by RBPs with a focus on the diverse mechanisms of plant RBPs and the unique processes they regulate. Additionally, we discuss the importance for additional research into understanding global interactions of RBPs on a systems and network-scale, with genome mining and annotation providing valuable insight for potential uses in improving crop plants in order to maintain high-level production in this era of global climate change.
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Affiliation(s)
- Wil Prall
- Department of Biology, University of Pennsylvania, Philadelphia, PA, USA
| | - Bishwas Sharma
- Department of Biology, University of Pennsylvania, Philadelphia, PA, USA
| | - Brian D Gregory
- Department of Biology, University of Pennsylvania, Philadelphia, PA, USA
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48
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Yang R, Li P, Mei H, Wang D, Sun J, Yang C, Hao L, Cao S, Chu C, Hu S, Song X, Cao X. Fine-Tuning of MiR528 Accumulation Modulates Flowering Time in Rice. MOLECULAR PLANT 2019; 12:1103-1113. [PMID: 31059825 DOI: 10.1016/j.molp.2019.04.009] [Citation(s) in RCA: 50] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/28/2019] [Revised: 03/28/2019] [Accepted: 04/25/2019] [Indexed: 05/18/2023]
Abstract
In plants, microRNA (miRNA) functions in the post-transcriptional repression of target mRNAs have been well explored. However, the mechanisms regulating the accumulation of miRNAs remain poorly understood. Here, we report that distinct mechanisms regulate accumulation of a monocot-specific miRNA, rice (Oryza sativa) miR528. At the transcriptional level, miR528 accumulated to higher levels in older plants than in young seedlings and exhibited aging-modulated gradual accumulation and diurnal rhythms in leaves; at the post-transcriptional level, aging also modulated miR528 levels by enhancing pri-miR528 alternative splicing. We found that miR528 promotes rice flowering under long-day conditions by targeting RED AND FAR-RED INSENSITIVE 2 (OsRFI2). Moreover, natural variations in the MIR528 promoter region caused differences in miR528 expression among rice varieties, which are correlated with their different binding affinities with the transcription factor OsSPL9 that activates the expression of miR528. Taken together, our findings reveal rice plants have evolved sophisticated modes fine-tuning miR528 levels and provide insight into the mechanisms that regulate MIRNA expression in plants.
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Affiliation(s)
- Rongxin Yang
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research (Beijing), Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China; Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China
| | - Pingchuan Li
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research (Beijing), Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Hailiang Mei
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research (Beijing), Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Dong Wang
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research (Beijing), Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China; Key Laboratory of Molecular Biology and Gene Engineering in Jiangxi Province, College of Life Science, Nanchang University, Nanchang, Jiangxi 330031, China
| | - Jing Sun
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research (Beijing), Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Chao Yang
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research (Beijing), Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Lili Hao
- Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China
| | - Shouyun Cao
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research (Beijing), Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Chengcai Chu
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research (Beijing), Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Songnian Hu
- Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China
| | - Xianwei Song
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research (Beijing), Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China.
| | - Xiaofeng Cao
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research (Beijing), Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China; Center for Excellence in Molecular Plant Sciences, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China.
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49
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Morton M, AlTamimi N, Butt H, Reddy ASN, Mahfouz M. Serine/Arginine-rich protein family of splicing regulators: New approaches to study splice isoform functions. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2019; 283:127-134. [PMID: 31128682 DOI: 10.1016/j.plantsci.2019.02.017] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/10/2018] [Revised: 02/19/2019] [Accepted: 02/23/2019] [Indexed: 05/06/2023]
Abstract
Serine/arginine-rich (SR) proteins are conserved RNA-binding proteins that play major roles in RNA metabolism. They function as molecular adaptors, facilitate spliceosome assembly and modulate constitutive and alternative splicing of pre-mRNAs. Pre-mRNAs encoding SR proteins and many other proteins involved in stress responses are extensively alternatively spliced in response to diverse stresses. Hence, it is proposed that stress-induced changes in splice isoforms contribute to the adaptation of plants to stress responses. However, functions of most SR genes and their splice isoforms in stress responses are not known. Lack of easy and robust tools hindered the progress in this area. Emerging technologies such as CRISPR/Cas9 will facilitate studies of SR function by enabling the generation of single and multiple knock-out mutants of SR subfamily members. Moreover, CRISPR/Cas13 allows targeted manipulation of splice isoforms from SR and other genes in a constitutive or tissue-specific manner to evaluate functions of individual splice variants. Identification of the in vivo targets of SR proteins and their splice variants using the recently developed TRIBE (Targets of RNA-binding proteins Identified By Editing) and other methods will help unravel their mode of action and splicing regulatory elements under various conditions. These new approaches are expected to provide significant new insights into the roles of SRs and splice isoforms in plants adaptation to diverse stresses.
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Affiliation(s)
- Mitchell Morton
- Division of Biological Sciences, 4700 King Abdullah University of Science and Technology, Thuwal 23955-6900, Saudi Arabia
| | - Nadia AlTamimi
- Division of Biological Sciences, 4700 King Abdullah University of Science and Technology, Thuwal 23955-6900, Saudi Arabia
| | - Haroon Butt
- Laboratory for Genome Engineering, Division of Biological Sciences, 4700 King Abdullah University of Science and Technology, Thuwal 23955-6900, Saudi Arabia
| | - Anireddy S N Reddy
- Department of Biology, Program in Cell and Molecular Biology, Colorado State University, Fort Collins, CO, USA
| | - Magdy Mahfouz
- Division of Biological Sciences, 4700 King Abdullah University of Science and Technology, Thuwal 23955-6900, Saudi Arabia; Laboratory for Genome Engineering, Division of Biological Sciences, 4700 King Abdullah University of Science and Technology, Thuwal 23955-6900, Saudi Arabia.
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50
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Lenka SK, Singh AK, Muthusamy SK, Smita S, Chinnusamy V, Bansal KC. Heterologous expression of rice RNA-binding glycine-rich (RBG) gene OsRBGD3 in transgenic Arabidopsis thaliana confers cold stress tolerance. FUNCTIONAL PLANT BIOLOGY : FPB 2019; 46:482-491. [PMID: 30940336 DOI: 10.1071/fp18241] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/14/2018] [Accepted: 01/23/2019] [Indexed: 06/09/2023]
Abstract
Imparting cold stress tolerance to crops is a major challenge in subtropical agriculture. New genes conferring cold tolerance needs to be identified and characterised for sustainable crop production in low-temperature stress affected areas. Here we report functional characterisation of OsRBGD3, classified previously as a class D glycine-rich RNA recognition motif (RRM) containing proteins from a drought-tolerant Indica rice cultivar N22. The gene was isolated by screening yeast one-hybrid library using the minimal promoter region of the OsMYB38 that is necessary for cold stress-responsive expression. OsRBGD3 exhibited cold, drought and salt stress inductive expression in a drought tolerant N22 rice cultivar as compared with susceptible variety IR64. OsRBGD3 was found to be localised to both nuclear and cytoplasmic subcellular destinations. Constitutive overexpression of the OsRBGD3 in transgenic Arabidopsis conferred tolerance to cold stress. ABA sensitivity was also observed in transgenic lines suggesting the regulatory role of this gene in the ABA signalling pathway. OsRBGD3 overexpression also attributed to significant root development and early flowering in transgenics. Hence, OsRBGD3 could be an important target for developing cold tolerant early flowering rice and other crops' genotypes for increasing production in low temperature affected areas.
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Affiliation(s)
- Sangram K Lenka
- ICAR-National Research Centre on Plant Biotechnology, Indian Agricultural Research Institute, New Delhi, 110012, India; and TERI-Deakin NanoBiotechnology Centre, The Energy and Resources Institute, New Delhi, 110003, India
| | - Amit K Singh
- ICAR-National Research Centre on Plant Biotechnology, Indian Agricultural Research Institute, New Delhi, 110012, India
| | - Senthilkumar K Muthusamy
- ICAR-National Research Centre on Plant Biotechnology, Indian Agricultural Research Institute, New Delhi, 110012, India; and ICAR-Central Tuber Crops Research Institute, Thiruvananthapuram, 695017, India
| | - Shuchi Smita
- ICAR-National Research Centre on Plant Biotechnology, Indian Agricultural Research Institute, New Delhi, 110012, India; and Department of Immunology, School of Medicine, University of Pittsburgh, PA 15261, USA
| | - Viswanathan Chinnusamy
- ICAR-Indian Agricultural Research Institute, Division of Plant Physiology, New Delhi, 110012, India
| | - Kailash C Bansal
- ICAR-National Research Centre on Plant Biotechnology, Indian Agricultural Research Institute, New Delhi, 110012, India; and TERI-Deakin NanoBiotechnology Centre, The Energy and Resources Institute, New Delhi, 110003, India; and Corresponding author.
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