1
|
Gorjifard S, Jores T, Tonnies J, Mueth NA, Bubb K, Wrightsman T, Buckler ES, Fields S, Cuperus JT, Queitsch C. Arabidopsis and maize terminator strength is determined by GC content, polyadenylation motifs and cleavage probability. Nat Commun 2024; 15:5868. [PMID: 38997252 PMCID: PMC11245536 DOI: 10.1038/s41467-024-50174-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2023] [Accepted: 07/03/2024] [Indexed: 07/14/2024] Open
Abstract
The 3' end of a gene, often called a terminator, modulates mRNA stability, localization, translation, and polyadenylation. Here, we adapted Plant STARR-seq, a massively parallel reporter assay, to measure the activity of over 50,000 terminators from the plants Arabidopsis thaliana and Zea mays. We characterize thousands of plant terminators, including many that outperform bacterial terminators commonly used in plants. Terminator activity is species-specific, differing in tobacco leaf and maize protoplast assays. While recapitulating known biology, our results reveal the relative contributions of polyadenylation motifs to terminator strength. We built a computational model to predict terminator strength and used it to conduct in silico evolution that generated optimized synthetic terminators. Additionally, we discover alternative polyadenylation sites across tens of thousands of terminators; however, the strongest terminators tend to have a dominant cleavage site. Our results establish features of plant terminator function and identify strong naturally occurring and synthetic terminators.
Collapse
Affiliation(s)
- Sayeh Gorjifard
- Department of Genome Sciences, University of Washington, Seattle, WA, 98195, USA
| | - Tobias Jores
- Department of Genome Sciences, University of Washington, Seattle, WA, 98195, USA
| | - Jackson Tonnies
- Department of Genome Sciences, University of Washington, Seattle, WA, 98195, USA
- Graduate Program in Biology, University of Washington, Seattle, WA, 98195, USA
| | - Nicholas A Mueth
- Department of Genome Sciences, University of Washington, Seattle, WA, 98195, USA
| | - Kerry Bubb
- Department of Genome Sciences, University of Washington, Seattle, WA, 98195, USA
| | - Travis Wrightsman
- Section of Plant Breeding and Genetics, Cornell University, Ithaca, NY, 14853, USA
| | - Edward S Buckler
- Section of Plant Breeding and Genetics, Cornell University, Ithaca, NY, 14853, USA
- Agricultural Research Service, United States Department of Agriculture, Ithaca, NY, 14853, USA
- Institute for Genomic Diversity, Cornell University, Ithaca, NY, 14853, USA
| | - Stanley Fields
- Department of Genome Sciences, University of Washington, Seattle, WA, 98195, USA
- Department of Medicine, University of Washington, Seattle, WA, 98195, USA
| | - Josh T Cuperus
- Department of Genome Sciences, University of Washington, Seattle, WA, 98195, USA
| | - Christine Queitsch
- Department of Genome Sciences, University of Washington, Seattle, WA, 98195, USA.
| |
Collapse
|
2
|
Alternative Splicing in the Regulatory Circuit of Plant Temperature Response. Int J Mol Sci 2023; 24:ijms24043878. [PMID: 36835290 PMCID: PMC9962249 DOI: 10.3390/ijms24043878] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2023] [Revised: 02/08/2023] [Accepted: 02/10/2023] [Indexed: 02/17/2023] Open
Abstract
As sessile organisms, plants have evolved complex mechanisms to rapidly respond to ever-changing ambient temperatures. Temperature response in plants is modulated by a multilayer regulatory network, including transcriptional and post-transcriptional regulations. Alternative splicing (AS) is an essential post-transcriptional regulatory mechanism. Extensive studies have confirmed its key role in plant temperature response, from adjustment to diurnal and seasonal temperature changes to response to extreme temperatures, which has been well documented by previous reviews. As a key node in the temperature response regulatory network, AS can be modulated by various upstream regulations, such as chromatin modification, transcription rate, RNA binding proteins, RNA structure and RNA modifications. Meanwhile, a number of downstream mechanisms are affected by AS, such as nonsense-mediated mRNA decay (NMD) pathway, translation efficiency and production of different protein variants. In this review, we focus on the links between splicing regulation and other mechanisms in plant temperature response. Recent advances regarding how AS is regulated and the following consequences in gene functional modulation in plant temperature response will be discussed. Substantial evidence suggests that a multilayer regulatory network integrating AS in plant temperature response has been unveiled.
Collapse
|
3
|
Dharmateja P, Yadav R, Kumar M, Babu P, Jain N, Mandal PK, Pandey R, Shrivastava M, Gaikwad KB, Bainsla NK, Tomar V, Sugumar S, Saifi N, Ranjan R. Genome-wide association studies reveal putative QTLs for physiological traits under contrasting phosphorous conditions in wheat (Triticum aestivum L.). Front Genet 2022; 13:984720. [DOI: 10.3389/fgene.2022.984720] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2022] [Accepted: 10/17/2022] [Indexed: 11/13/2022] Open
Abstract
A Genome-wide association (GWAS) study was conducted for phosphorous (P)-use responsive physiological traits in bread wheat at the seedling stage under contrasting P regimes. A panel of 158 diverse advanced breeding lines and released varieties, and a set of 10,800 filtered single nucleotide polymorphism (SNP) markers were used to study marker-trait associations over the eight shoot traits. Principle component analysis separated the two environments (P regimes) because of the differential response of the traits indicating the essentiality of the separate breeding programmes for each environment. Significant variations for genotypic, environmental, and genotype × environment (GEI) effects were observed for all the traits in the combined analysis of variance with moderately high broad sense heritability traits (0.50–0.73). With the different algorithms of association mapping viz., BLINK, FarmCPU, and MLM, 38 unique QTLs under non-limiting P (NLP) and 45 QTLs for limiting P (LP) conditions for various shoot traits were identified. Some of these QTLs were captured by all three algorithms. Interestingly, a Q.iari.dt.sdw.1 on chromosome 1D was found to explain the significant variations in three important physiological traits under non-limiting phosphorus (NLP) conditions. We identified the putative candidate genes for QTLs namely Q.iari.dt.chl.1, Q.iari.dt.sdw.16, Q.iari.dt.sdw.9 and Q.iari.dt.tpc.1 which are potentially involved in the mechanism regulating phosphorus use efficiency through improved P absorption due to improved root architectural traits and better mobilization such as sulfotransferase involved in postembryonic root development, WALLS ARE THIN1 (WAT1), a plant-specific protein that facilitates auxin export; lectin receptor-like kinase essentially involved in plant development, stress response during germination and lateral root development and F-box component of the SKP-Cullin-F box E3 ubiquitin ligase complex and strigolactone signal perception. Expression profiling of putative genes located in identified genomic regions against the wheat expression atlas revealed their significance based on the expression of these genes for stress response and growth development processes in wheat. Our results thus provide an important insight into understanding the genetic basis for improving PUE under phosphorus stress conditions and can shape the future breeding programme by developing and integrating molecular markers for these difficult-to-score important traits.
Collapse
|
4
|
Chen Q, Tian F, Cheng T, Jiang J, Zhu G, Gao Z, Lin H, Hu J, Qian Q, Fang X, Chen F. Translational repression of FZP mediated by CU-rich element/OsPTB interactions modulates panicle development in rice. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2022; 110:1319-1331. [PMID: 35293072 DOI: 10.1111/tpj.15737] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/16/2021] [Revised: 03/03/2022] [Accepted: 03/07/2022] [Indexed: 06/14/2023]
Abstract
Panicle development is an important determinant of the grain number in rice. A thorough characterization of the molecular mechanism underlying panicle development will lead to improved breeding of high-yielding rice varieties. Frizzy Panicle (FZP), a critical gene for panicle development, is regulated by OsBZR1 and OsARFs at the transcriptional stage. However, the translational modulation of FZP has not been reported. We reveal that the CU-rich elements (CUREs) in the 3' UTR of the FZP mRNA are crucial for efficient FZP translation. The knockout of CUREs in the FZP 3' UTR or the over-expression of the FZP 3' UTR fragment containing CUREs resulted in an increase in FZP mRNA translation efficiency. Moreover, the number of secondary branches (NSB) and the grain number per panicle (GNP) decreased in the transformed rice plants. The CUREs in the 3' UTR of FZP mRNA were verified as the targets of the polypyrimidine tract-binding proteins OsPTB1 and OsPTB2 in rice. Both OsPTB1 and OsPTB2 were highly expressed in young panicles. The knockout of OsPTB1/2 resulted in an increase in the FZP translational efficiency and a decrease in the NSB and GNP. Furthermore, the over-expression of OsPTB1/2 decreased the translation of the reporter gene fused to FZP 3' UTR in vivo and in vitro. These results suggest that OsPTB1/2 can mediate FZP translational repression by interacting with CUREs in the 3' UTR of FZP mRNA, leading to changes in the NSB and GNP. Accordingly, in addition to transcriptional regulation, FZP expression is also fine-tuned at the translational stage during rice panicle development.
Collapse
Affiliation(s)
- Qiong Chen
- State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, The Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing, 100101, China
- Hainan Yazhou Bay Seed Laboratory, Sanya, 572025, China
| | - Fa'an Tian
- State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, The Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing, 100101, China
| | - Tingting Cheng
- State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, The Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing, 100101, China
| | - Jun'e Jiang
- State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, The Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing, 100101, China
| | - Guanlin Zhu
- State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, The Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing, 100101, China
| | - Zhenyu Gao
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, 310006, China
| | - Haiyan Lin
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, 310006, China
| | - Jiang Hu
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, 310006, China
| | - Qian Qian
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, 310006, China
| | - Xiaohua Fang
- Genetic Resource R&D Center, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Chang Zhou, 213001, China
| | - Fan Chen
- State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, The Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing, 100101, China
- Hainan Yazhou Bay Seed Laboratory, Sanya, 572025, China
| |
Collapse
|
5
|
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.
Collapse
Affiliation(s)
| | - Anireddy S. N. Reddy
- Department of Biology and Program in Cell and Molecular Biology, Colorado State University, Fort Collins, CO 80523, USA;
| |
Collapse
|
6
|
Liu Z, Liu Q, Yang X, Zhang Y, Norris M, Chen X, Cheema J, Zhang H, Ding Y. In vivo nuclear RNA structurome reveals RNA-structure regulation of mRNA processing in plants. Genome Biol 2021; 22:11. [PMID: 33397430 PMCID: PMC7784297 DOI: 10.1186/s13059-020-02236-4] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2020] [Accepted: 12/11/2020] [Indexed: 01/02/2023] Open
Abstract
BACKGROUND mRNA processing is critical for gene expression. A challenge in regulating mRNA processing is how to recognize the actual mRNA processing sites, such as splice and polyadenylation sites, when the sequence content is insufficient for this purpose. Previous studies suggested that RNA structure affects mRNA processing. However, the regulatory role of RNA structure in mRNA processing remains unclear. RESULTS Here, we perform in vivo selective 2'-hydroxyl acylation analyzed by primer extension (SHAPE) chemical profiling on Arabidopsis and generate the in vivo nuclear RNA structure landscape. We find that nuclear mRNAs fold differently from cytosolic mRNAs across translation start and stop sites. Notably, we discover a two-nucleotide single-stranded RNA structure feature upstream of 5' splice sites that is strongly associated with splicing and the selection of alternative 5' splice sites. The regulatory role of this RNA structure feature is further confirmed by experimental validation. Moreover, we find the single-strandedness of branch sites is also associated with 3' splice site recognition. We also identify an RNA structure feature comprising two close-by single-stranded regions that is specifically associated with both polyadenylation and alternative polyadenylation events. CONCLUSIONS We successfully identify pre-mRNA structure features associated with splicing and polyadenylation at whole-genome scale and validate an RNA structure feature which can regulate splicing. Our study unveils a new RNA structure regulatory mechanism for mRNA processing.
Collapse
Affiliation(s)
- Zhenshan Liu
- Department of Cell and Developmental Biology, John Innes Centre, Norwich Research Park, Norwich, NR4 7UH UK
| | - Qi Liu
- Department of Cell and Developmental Biology, John Innes Centre, Norwich Research Park, Norwich, NR4 7UH UK
| | - Xiaofei Yang
- Department of Cell and Developmental Biology, John Innes Centre, Norwich Research Park, Norwich, NR4 7UH UK
| | - Yueying Zhang
- Department of Cell and Developmental Biology, John Innes Centre, Norwich Research Park, Norwich, NR4 7UH UK
| | - Matthew Norris
- Department of Cell and Developmental Biology, John Innes Centre, Norwich Research Park, Norwich, NR4 7UH UK
| | - Xiaoxi Chen
- Department of Cell and Developmental Biology, John Innes Centre, Norwich Research Park, Norwich, NR4 7UH UK
| | - Jitender Cheema
- Department of Cell and Developmental Biology, John Innes Centre, Norwich Research Park, Norwich, NR4 7UH UK
| | - Huakun Zhang
- Key Laboratory of Molecular Epigenetics of the Ministry of Education, Northeast Normal University, Changchun, 130024 China
| | - Yiliang Ding
- Department of Cell and Developmental Biology, John Innes Centre, Norwich Research Park, Norwich, NR4 7UH UK
| |
Collapse
|
7
|
Kumar A, Sharma S, Chunduri V, Kaur A, Kaur S, Malhotra N, Kumar A, Kapoor P, Kumari A, Kaur J, Sonah H, Garg M. Genome-wide Identification and Characterization of Heat Shock Protein Family Reveals Role in Development and Stress Conditions in Triticum aestivum L. Sci Rep 2020; 10:7858. [PMID: 32398647 PMCID: PMC7217896 DOI: 10.1038/s41598-020-64746-2] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2019] [Accepted: 04/01/2020] [Indexed: 12/02/2022] Open
Abstract
Heat shock proteins (HSPs) have a significant role in protein folding and are considered as prominent candidates for development of heat-tolerant crops. Understanding of wheat HSPs has great importance since wheat is severely affected by heat stress, particularly during the grain filling stage. In the present study, efforts were made to identify HSPs in wheat and to understand their role during plant development and under different stress conditions. HSPs in wheat genome were first identified by using Position-Specific Scoring Matrix (PSSMs) of known HSP domains and then also confirmed by sequence homology with already known HSPs. Collectively, 753 TaHSPs including 169 TaSHSP, 273 TaHSP40, 95 TaHSP60, 114 TaHSP70, 18 TaHSP90 and 84 TaHSP100 were identified in the wheat genome. Compared with other grass species, number of HSPs in wheat was relatively high probably due to the higher ploidy level. Large number of tandem duplication was identified in TaHSPs, especially TaSHSPs. The TaHSP genes showed random distribution on chromosomes, however, there were more TaHSPs in B and D sub-genomes as compared to the A sub-genome. Extensive computational analysis was performed using the available genomic resources to understand gene structure, gene expression and phylogentic relationship of TaHSPs. Interestingly, apart from high expression under heat stress, high expression of TaSHSP was also observed during seed development. The study provided a list of candidate HSP genes for improving thermo tolerance during developmental stages and also for understanding the seed development process in bread wheat.
Collapse
Affiliation(s)
- Ashish Kumar
- South Asian University, Chankyapuri, New Delhi, 110021, India
| | - Saloni Sharma
- Agri-Biotechnology Division, National Agri-Food Biotechnology Institute (NABI), S.A.S. Nagar (Mohali), Punjab, India
| | - Venkatesh Chunduri
- Agri-Biotechnology Division, National Agri-Food Biotechnology Institute (NABI), S.A.S. Nagar (Mohali), Punjab, India
| | - Amandeep Kaur
- Agri-Biotechnology Division, National Agri-Food Biotechnology Institute (NABI), S.A.S. Nagar (Mohali), Punjab, India
| | - Satinder Kaur
- Punjab Agricultural University, Ludhiana, 141004, India
| | - Nikhil Malhotra
- Agri-Biotechnology Division, National Agri-Food Biotechnology Institute (NABI), S.A.S. Nagar (Mohali), Punjab, India
| | - Aman Kumar
- Agri-Biotechnology Division, National Agri-Food Biotechnology Institute (NABI), S.A.S. Nagar (Mohali), Punjab, India
| | - Payal Kapoor
- Agri-Biotechnology Division, National Agri-Food Biotechnology Institute (NABI), S.A.S. Nagar (Mohali), Punjab, India
| | - Anita Kumari
- Agri-Biotechnology Division, National Agri-Food Biotechnology Institute (NABI), S.A.S. Nagar (Mohali), Punjab, India
| | | | - Humira Sonah
- Agri-Biotechnology Division, National Agri-Food Biotechnology Institute (NABI), S.A.S. Nagar (Mohali), Punjab, India.
| | - Monika Garg
- Agri-Biotechnology Division, National Agri-Food Biotechnology Institute (NABI), S.A.S. Nagar (Mohali), Punjab, India.
| |
Collapse
|
8
|
Yang Y, Li Y, Sancar A, Oztas O. The circadian clock shapes the Arabidopsis transcriptome by regulating alternative splicing and alternative polyadenylation. J Biol Chem 2020; 295:7608-7619. [PMID: 32303634 DOI: 10.1074/jbc.ra120.013513] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2020] [Revised: 04/10/2020] [Indexed: 01/24/2023] Open
Abstract
The circadian clock in plants temporally coordinates biological processes throughout the day, synchronizing gene expression with diurnal environmental changes. Circadian oscillator proteins are known to regulate the expression of clock-controlled plant genes by controlling their transcription. Here, using a high-throughput RNA-Seq approach, we examined genome-wide circadian and diurnal control of the Arabidopsis transcriptome, finding that the oscillation patterns of different transcripts of multitranscript genes can exhibit substantial differences and demonstrating that the circadian clock affects posttranscriptional regulation. In parallel, we found that two major posttranscriptional mechanisms, alternative splicing (AS; especially intron retention) and alternative polyadenylation (APA), display circadian rhythmicity resulting from oscillation in the genes involved in AS and APA. Moreover, AS-related genes exhibited rhythmic AS and APA regulation, adding another layer of complexity to circadian regulation of gene expression. We conclude that the Arabidopsis circadian clock not only controls transcription of genes but also affects their posttranscriptional regulation by influencing alternative splicing and alternative polyadenylation.
Collapse
Affiliation(s)
- Yuchen Yang
- Department of Genetics, University of North Carolina, Chapel Hill, North Carolina
| | - Yun Li
- Department of Genetics, University of North Carolina, Chapel Hill, North Carolina.,Department of Biostatistics, University of North Carolina, Chapel Hill, North Carolina.,Department of Computer Science, University of North Carolina, Chapel Hill, North Carolina
| | - Aziz Sancar
- Department of Biochemistry and Biophysics, University of North Carolina, Chapel Hill, North Carolina
| | - Onur Oztas
- Department of Biochemistry and Biophysics, University of North Carolina, Chapel Hill, North Carolina
| |
Collapse
|
9
|
Traubenik S, Reynoso MA, Hobecker K, Lancia M, Hummel M, Rosen B, Town C, Bailey-Serres J, Blanco F, Zanetti ME. Reprogramming of Root Cells during Nitrogen-Fixing Symbiosis Involves Dynamic Polysome Association of Coding and Noncoding RNAs. THE PLANT CELL 2020; 32:352-373. [PMID: 31748328 PMCID: PMC7008484 DOI: 10.1105/tpc.19.00647] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/21/2019] [Revised: 10/11/2019] [Accepted: 11/20/2019] [Indexed: 05/04/2023]
Abstract
Translational control is a widespread mechanism that allows the cell to rapidly modulate gene expression in order to provide flexibility and adaptability to eukaryotic organisms. We applied translating ribosome affinity purification combined with RNA sequencing to characterize translational regulation of mRNAs at early stages of the nitrogen-fixing symbiosis established between Medicago truncatula and Sinorhizobium meliloti Our analysis revealed a poor correlation between transcriptional and translational changes and identified hundreds of regulated protein-coding and long noncoding RNAs (lncRNAs), some of which are regulated in specific cell types. We demonstrated that a short variant of the lncRNA Trans-acting small interference RNA3 (TAS3) increased its association to the translational machinery in response to rhizobia. Functional analysis revealed that this short variant of TAS3 might act as a target mimic that captures microRNA390, contributing to reduce trans acting small interference Auxin Response Factor production and modulating nodule formation and rhizobial infection. The analysis of alternative transcript variants identified a translationally upregulated mRNA encoding subunit 3 of the SUPERKILLER complex (SKI3), which participates in mRNA decay. Knockdown of SKI3 decreased nodule initiation and development, as well as the survival of bacteria within nodules. Our results highlight the importance of translational control and mRNA decay pathways for the successful establishment of the nitrogen-fixing symbiosis.
Collapse
Affiliation(s)
- Soledad Traubenik
- Instituto de Biotecnología y Biología Molecular, Facultad de Ciencias Exactas, Universidad Nacional de La Plata, Centro Científico y Tecnológico-La Plata, Consejo Nacional de Investigaciones Científicas y Técnicas, 1900-La Plata, Argentina
| | - Mauricio Alberto Reynoso
- Instituto de Biotecnología y Biología Molecular, Facultad de Ciencias Exactas, Universidad Nacional de La Plata, Centro Científico y Tecnológico-La Plata, Consejo Nacional de Investigaciones Científicas y Técnicas, 1900-La Plata, Argentina
| | - Karen Hobecker
- Instituto de Biotecnología y Biología Molecular, Facultad de Ciencias Exactas, Universidad Nacional de La Plata, Centro Científico y Tecnológico-La Plata, Consejo Nacional de Investigaciones Científicas y Técnicas, 1900-La Plata, Argentina
| | - Marcos Lancia
- Instituto de Biotecnología y Biología Molecular, Facultad de Ciencias Exactas, Universidad Nacional de La Plata, Centro Científico y Tecnológico-La Plata, Consejo Nacional de Investigaciones Científicas y Técnicas, 1900-La Plata, Argentina
| | - Maureen Hummel
- Department of Botany and Plant Sciences, Center for Plant Cell Biology, University of California, Riverside, California 92521
| | | | | | - Julia Bailey-Serres
- Department of Botany and Plant Sciences, Center for Plant Cell Biology, University of California, Riverside, California 92521
| | - Flavio Blanco
- Instituto de Biotecnología y Biología Molecular, Facultad de Ciencias Exactas, Universidad Nacional de La Plata, Centro Científico y Tecnológico-La Plata, Consejo Nacional de Investigaciones Científicas y Técnicas, 1900-La Plata, Argentina
| | - María Eugenia Zanetti
- Instituto de Biotecnología y Biología Molecular, Facultad de Ciencias Exactas, Universidad Nacional de La Plata, Centro Científico y Tecnológico-La Plata, Consejo Nacional de Investigaciones Científicas y Técnicas, 1900-La Plata, Argentina
| |
Collapse
|
10
|
Wang PH, Kumar S, Zeng J, McEwan R, Wright TR, Gupta M. Transcription Terminator-Mediated Enhancement in Transgene Expression in Maize: Preponderance of the AUGAAU Motif Overlapping With Poly(A) Signals. FRONTIERS IN PLANT SCIENCE 2020; 11:570778. [PMID: 33178242 PMCID: PMC7591816 DOI: 10.3389/fpls.2020.570778] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/09/2020] [Accepted: 09/11/2020] [Indexed: 05/08/2023]
Abstract
The selection of transcription terminators (TTs) for pairing with high expressing constitutive promoters in chimeric constructs is crucial to deliver optimal transgene expression in plants. In this study, the use of the native combinations of four polyubiquitin gene promoters and corresponding TTs resulted in up to >3-fold increase in transgene expression in maize. Of the eight polyubiquitin promoter and TT regulatory elements utilized, seven were novel and identified from the polyubiquitin genes of Brachypodium distachyon, Setaria italica, and Zea mays. Furthermore, gene expression driven by the Cassava mosaic virus promoter was studied by pairing the promoter with distinct TTs derived from the high expressing genes of Arabidopsis. Of the three TTs studied, the polyubiquitin10 gene TT produced the highest transgene expression in maize. Polyadenylation patterns and mRNA abundance from eight distinct TTs were analyzed using 3'-RACE and next-generation sequencing. The results exhibited one to three unique polyadenylation sites in the TTs. The poly(A) site patterns for the StPinII TT were consistent when the same TT was deployed in chimeric constructs irrespective of the reporter gene and promoter used. Distal to the poly(A) sites, putative polyadenylation signals were identified in the near-upstream regions of the TTs based on previously reported mutagenesis and bioinformatics studies in rice and Arabidopsis. The putative polyadenylation signals were 9 to 11 nucleotides in length. Six of the eight TTs contained the putative polyadenylation signals that were overlaps of either canonical AAUAAA or AAUAAA-like polyadenylation signals and AUGAAU, a top-ranking-hexamer of rice and Arabidopsis gene near-upstream regions. Three of the polyubiquitin gene TTs contained the identical 9-nucleotide overlap, AUGAAUAAG, underscoring the functional significance of such overlaps in mRNA 3' end processing. In addition to identifying new combinations of regulatory elements for high constitutive trait gene expression in maize, this study demonstrated the importance of TTs for optimizing gene expression in plants. Learning from this study could be applied to other dicotyledonous and monocotyledonous plant species for transgene expression. Research on TTs is not limited to transgene expression but could be extended to the introduction of appropriate mutations into TTs via genome editing, paving the way for expression modulation of endogenous genes.
Collapse
Affiliation(s)
- Po-Hao Wang
- Applied Science & Technology, Corteva Agriscience, Johnston, IA, United States
| | - Sandeep Kumar
- Applied Science & Technology, Corteva Agriscience, Johnston, IA, United States
- *Correspondence: Sandeep Kumar,
| | - Jia Zeng
- Data Science & Informatics, Corteva Agriscience, Indianapolis, IN, United States
| | - Robert McEwan
- Applied Science & Technology, Corteva Agriscience, Johnston, IA, United States
| | - Terry R. Wright
- Trait Discovery, Corteva Agriscience, Indianapolis, IN, United States
| | - Manju Gupta
- Trait Product Development, Dow Agrosciences, Indianapolis, IN, United States
| |
Collapse
|
11
|
Bernardes WS, Menossi M. Plant 3' Regulatory Regions From mRNA-Encoding Genes and Their Uses to Modulate Expression. FRONTIERS IN PLANT SCIENCE 2020; 11:1252. [PMID: 32922424 PMCID: PMC7457121 DOI: 10.3389/fpls.2020.01252] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/25/2020] [Accepted: 07/29/2020] [Indexed: 05/08/2023]
Abstract
Molecular biotechnology has made it possible to explore the potential of plants for different purposes. The 3' regulatory regions have a great diversity of cis-regulatory elements directly involved in polyadenylation, stability, transport and mRNA translation, essential to achieve the desired levels of gene expression. A complex interaction between the cleavage and polyadenylation molecular complex and cis-elements determine the polyadenylation site, which may result in the choice of non-canonical sites, resulting in alternative polyadenylation events, involved in the regulation of more than 80% of the genes expressed in plants. In addition, after transcription, a wide array of RNA-binding proteins interacts with cis-acting elements located mainly in the 3' untranslated region, determining the fate of mRNAs in eukaryotic cells. Although a small number of 3' regulatory regions have been identified and validated so far, many studies have shown that plant 3' regulatory regions have a higher potential to regulate gene expression in plants compared to widely used 3' regulatory regions, such as NOS and OCS from Agrobacterium tumefaciens and 35S from cauliflower mosaic virus. In this review, we discuss the role of 3' regulatory regions in gene expression, and the superior potential that plant 3' regulatory regions have compared to NOS, OCS and 35S 3' regulatory regions.
Collapse
|
12
|
Capturing the Alternative Cleavage and Polyadenylation Sites of 14 NAC Genes in Populus Using a Combination of 3'-RACE and High-Throughput Sequencing. Molecules 2018. [PMID: 29518015 PMCID: PMC6017670 DOI: 10.3390/molecules23030608] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Detection of complex splice sites (SSs) and polyadenylation sites (PASs) of eukaryotic genes is essential for the elucidation of gene regulatory mechanisms. Transcriptome-wide studies using high-throughput sequencing (HTS) have revealed prevalent alternative splicing (AS) and alternative polyadenylation (APA) in plants. However, small-scale and high-depth HTS aimed at detecting genes or gene families are very few and limited. We explored a convenient and flexible method for profiling SSs and PASs, which combines rapid amplification of 3′-cDNA ends (3′-RACE) and HTS. Fourteen NAC (NAM, ATAF1/2, CUC2) transcription factor genes of Populus trichocarpa were analyzed by 3′-RACE-seq. Based on experimental reproducibility, boundary sequence analysis and reverse transcription PCR (RT-PCR) verification, only canonical SSs were considered to be authentic. Based on stringent criteria, candidate PASs without any internal priming features were chosen as authentic PASs and assumed to be PAS-rich markers. Thirty-four novel canonical SSs, six intronic/internal exons and thirty 3′-UTR PAS-rich markers were revealed by 3′-RACE-seq. Using 3′-RACE and real-time PCR, we confirmed that three APA transcripts ending in/around PAS-rich markers were differentially regulated in response to plant hormones. Our results indicate that 3′-RACE-seq is a robust and cost-effective method to discover SSs and label active regions subjected to APA for genes or gene families. The method is suitable for small-scale AS and APA research in the initial stage.
Collapse
|
13
|
Guo C, Spinelli M, Liu M, Li QQ, Liang C. A Genome-wide Study of "Non-3UTR" Polyadenylation Sites in Arabidopsis thaliana. Sci Rep 2016; 6:28060. [PMID: 27301740 PMCID: PMC4908657 DOI: 10.1038/srep28060] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2016] [Accepted: 05/20/2016] [Indexed: 11/18/2022] Open
Abstract
Alternative polyadenylation has been recognized as a key contributor of gene expression regulation by generating different transcript isoforms with altered 3′ ends. Although polyadenylation is well known for marking the end of a 3′ UTR, an increasing number of studies have reported previously less-addressed polyadenylation events located in other parts of genes in many eukaryotic organisms. These other locations include 5′ UTRs, introns and coding sequences (termed herein as non-3UTR), as well as antisense and intergenic polyadenlation. Focusing on the non-3UTR polyadenylation sites (n3PASs), we detected and characterized more than 11000 n3PAS clusters in the Arabidopsis genome using poly(A)-tag sequencing data (PAT-Seq). Further analyses suggested that the occurrence of these n3PASs were positively correlated with certain characteristics of their respective host genes, including the presence of spliced, diminutive or diverse beginning of 5′ UTRs, number of introns and whether introns have extreme lengths. The interaction of the host genes with surrounding genetic elements, like a convergently overlapped gene and associated transposable element, may contribute to the generation of a n3PAS as well. Collectively, these results provide a better understanding of n3PASs, and offer some new insights of the underlying mechanisms for non-3UTR polyadenylation and its regulation in plants.
Collapse
Affiliation(s)
- Cheng Guo
- Department of Biology, Miami University, Oxford, OH 45056, USA
| | | | - Man Liu
- Department of Biology, Miami University, Oxford, OH 45056, USA
| | - Qingshun Q Li
- Key Laboratory of the Ministry of Education for Costal and Wetland Ecosystems, College of the Environment and Ecology, Xiamen University, Xiamen, Fujian 361102, China.,Graduate College of Biomedical Sciences, Western University of Health Sciences, Pomona, CA 91766, USA
| | - Chun Liang
- Department of Biology, Miami University, Oxford, OH 45056, USA
| |
Collapse
|
14
|
Misra RC, Garg A, Roy S, Chanotiya CS, Vasudev PG, Ghosh S. Involvement of an ent-copalyl diphosphate synthase in tissue-specific accumulation of specialized diterpenes in Andrographis paniculata. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2015; 240:50-64. [PMID: 26475187 DOI: 10.1016/j.plantsci.2015.08.016] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/07/2015] [Revised: 08/13/2015] [Accepted: 08/22/2015] [Indexed: 05/24/2023]
Abstract
Ent-labdane-related diterpene (ent-LRD) specialized (i.e. secondary) metabolites of the medicinal plant kalmegh (Andrographis paniculata) have long been known for several pharmacological activities. However, our understanding of the ent-LRD biosynthetic pathway has remained largely incomplete. Since ent-LRDs accumulate in leaves, we carried out a comparative transcriptional analysis using leaf and root tissues, and identified 389 differentially expressed transcripts, including 223 transcripts that were preferentially expressed in leaf tissue. Analysis of the transcripts revealed various specialized metabolic pathways, including transcripts of the ent-LRD biosynthetic pathway. Two class II diterpene synthases (ApCPS1 and ApCPS2) along with one (ApCPS1') and two (ApCPS2' and ApCPS2″) transcriptional variants that were the outcomes of alternative splicing of the precursor mRNA and alternative transcriptional termination, respectively, were identified. ApCPS1 and ApCPS2 encode for 832- and 817-amino acids proteins, respectively, and are phylogenetically related to the dicotyledons ent-copalyl diphosphate synthases (ent-CPSs). The spatio-temporal patterns of ent-LRD metabolites accumulation and gene expression suggested a likely role for ApCPS1 in general (i.e. primary) metabolism, perhaps by providing precursor for the biosynthesis of phytohormone gibberellin (GA). However, ApCPS2 is potentially involved in tissue-specific accumulation of ent-LRD specialized metabolites. Bacterially expressed recombinant ApCPS2 catalyzed the conversion of (E,E,E)-geranylgeranyl diphosphate (GGPP), the general precursor of diterpenes to ent-copalyl diphosphate (ent-CPP), the precursor of ent-LRDs. Taken together, these results advance our understanding of the tissue-specific accumulation of specialized ent-LRDs of medicinal importance.
Collapse
Affiliation(s)
- Rajesh Chandra Misra
- Biotechnology Division, Council of Scientific and Industrial Research-Central Institute of Medicinal and Aromatic Plants, Lucknow, 226015, India
| | - Anchal Garg
- Biotechnology Division, Council of Scientific and Industrial Research-Central Institute of Medicinal and Aromatic Plants, Lucknow, 226015, India
| | - Sudeep Roy
- Biotechnology Division, Council of Scientific and Industrial Research-Central Institute of Medicinal and Aromatic Plants, Lucknow, 226015, India
| | - Chandan Singh Chanotiya
- Chemical Sciences Division, Council of Scientific and Industrial Research-Central Institute of Medicinal and Aromatic Plants, Lucknow, 226015, India
| | - Prema G Vasudev
- Metabolic and Structural Biology Division, Council of Scientific and Industrial Research-Central Institute of Medicinal and Aromatic Plants, Lucknow 226015, India
| | - Sumit Ghosh
- Biotechnology Division, Council of Scientific and Industrial Research-Central Institute of Medicinal and Aromatic Plants, Lucknow, 226015, India.
| |
Collapse
|
15
|
Browning KS, Bailey-Serres J. Mechanism of cytoplasmic mRNA translation. THE ARABIDOPSIS BOOK 2015; 13:e0176. [PMID: 26019692 PMCID: PMC4441251 DOI: 10.1199/tab.0176] [Citation(s) in RCA: 144] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
Protein synthesis is a fundamental process in gene expression that depends upon the abundance and accessibility of the mRNA transcript as well as the activity of many protein and RNA-protein complexes. Here we focus on the intricate mechanics of mRNA translation in the cytoplasm of higher plants. This chapter includes an inventory of the plant translational apparatus and a detailed review of the translational processes of initiation, elongation, and termination. The majority of mechanistic studies of cytoplasmic translation have been carried out in yeast and mammalian systems. The factors and mechanisms of translation are for the most part conserved across eukaryotes; however, some distinctions are known to exist in plants. A comprehensive understanding of the complex translational apparatus and its regulation in plants is warranted, as the modulation of protein production is critical to development, environmental plasticity and biomass yield in diverse ecosystems and agricultural settings.
Collapse
Affiliation(s)
- Karen S. Browning
- Department of Molecular Biosciences and Institute for Cell and Molecular Biology, University of Texas at Austin, Austin TX 78712-0165
- Both authors contributed equally to this work
| | - Julia Bailey-Serres
- Department of Botany and Plant Sciences and Center for Plant Cell Biology, University of California, Riverside, CA, 92521 USA
- Both authors contributed equally to this work
| |
Collapse
|
16
|
Wu X, Gaffney B, Hunt AG, Li QQ. Genome-wide determination of poly(A) sites in Medicago truncatula: evolutionary conservation of alternative poly(A) site choice. BMC Genomics 2014; 15:615. [PMID: 25048171 PMCID: PMC4117952 DOI: 10.1186/1471-2164-15-615] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2014] [Accepted: 07/15/2014] [Indexed: 11/16/2022] Open
Abstract
Background Alternative polyadenylation (APA) plays an important role in the post-transcriptional regulation of gene expression. Little is known about how APA sites may evolve in homologous genes in different plant species. To this end, comparative studies of APA sites in different organisms are needed. In this study, a collection of poly(A) sites in Medicago truncatula, a model system for legume plants, has been generated and compared with APA sites in Arabidopsis thaliana. Results The poly(A) tags from a deep-sequencing protocol were mapped to the annotated M. truncatula genome, and the identified poly(A) sites used to update the annotations of 14,203 genes. The results show that 64% of M. truncatula genes possess more than one poly(A) site, comparable to the percentages reported for Arabidopsis and rice. In addition, the poly(A) signals associated with M. truncatula genes were similar to those seen in Arabidopsis and other plants. The 3′-UTR lengths are correlated in pairs of orthologous genes between M. truncatula and Arabidopsis. Very little conservation of intronic poly(A) sites was found between Arabidopsis and M. truncatula, which suggests that such sites are likely to be species-specific in plants. In contrast, there is a greater conservation of CDS-localized poly(A) sites in these two species. A sizeable number of M. truncatula antisense poly(A) sites were found. A high percentage of the associated target genes possess Arabidopsis orthologs that are also associated with antisense sites. This is suggestive of important roles for antisense regulation of these target genes. Conclusions Our results reveal some distinct patterns of sense and antisense poly(A) sites in Arabidopsis and M. truncatula. In so doing, this study lends insight into general evolutionary trends of alternative polyadenylation in plants. Electronic supplementary material The online version of this article (doi:10.1186/1471-2164-15-615) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
| | | | - Arthur G Hunt
- Department of Plant and Soil Sciences, University of Kentucky, Lexington, KY, USA.
| | | |
Collapse
|
17
|
Reddy AS, Marquez Y, Kalyna M, Barta A. Complexity of the alternative splicing landscape in plants. THE PLANT CELL 2013; 25:3657-83. [PMID: 24179125 PMCID: PMC3877793 DOI: 10.1105/tpc.113.117523] [Citation(s) in RCA: 516] [Impact Index Per Article: 46.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/17/2013] [Revised: 09/27/2013] [Accepted: 10/08/2013] [Indexed: 05/18/2023]
Abstract
Alternative splicing (AS) of precursor mRNAs (pre-mRNAs) from multiexon genes allows organisms to increase their coding potential and regulate gene expression through multiple mechanisms. Recent transcriptome-wide analysis of AS using RNA sequencing has revealed that AS is highly pervasive in plants. Pre-mRNAs from over 60% of intron-containing genes undergo AS to produce a vast repertoire of mRNA isoforms. The functions of most splice variants are unknown. However, emerging evidence indicates that splice variants increase the functional diversity of proteins. Furthermore, AS is coupled to transcript stability and translation through nonsense-mediated decay and microRNA-mediated gene regulation. Widespread changes in AS in response to developmental cues and stresses suggest a role for regulated splicing in plant development and stress responses. Here, we review recent progress in uncovering the extent and complexity of the AS landscape in plants, its regulation, and the roles of AS in gene regulation. The prevalence of AS in plants has raised many new questions that require additional studies. New tools based on recent technological advances are allowing genome-wide analysis of RNA elements in transcripts and of chromatin modifications that regulate AS. Application of these tools in plants will provide significant new insights into AS regulation and crosstalk between AS and other layers of gene regulation.
Collapse
Affiliation(s)
- 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
- Address correspondence to
| | - Yamile Marquez
- Max F. Perutz Laboratories, Medical University of Vienna, Vienna A-1030, Austria
| | - Maria Kalyna
- Max F. Perutz Laboratories, Medical University of Vienna, Vienna A-1030, Austria
| | - Andrea Barta
- Max F. Perutz Laboratories, Medical University of Vienna, Vienna A-1030, Austria
| |
Collapse
|
18
|
Plant polyadenylation factors: conservation and variety in the polyadenylation complex in plants. BMC Genomics 2012; 13:641. [PMID: 23167306 PMCID: PMC3538716 DOI: 10.1186/1471-2164-13-641] [Citation(s) in RCA: 58] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2012] [Accepted: 11/07/2012] [Indexed: 01/10/2023] Open
Abstract
Background Polyadenylation, an essential step in eukaryotic gene expression, requires both cis-elements and a plethora of trans-acting polyadenylation factors. The polyadenylation factors are largely conserved across mammals and fungi. The conservation seems also extended to plants based on the analyses of Arabidopsis polyadenylation factors. To extend this observation, we systemically identified the orthologs of yeast and human polyadenylation factors from 10 plant species chosen based on both the availability of their genome sequences and their positions in the evolutionary tree, which render them representatives of different plant lineages. Results The evolutionary trajectories revealed several interesting features of plant polyadenylation factors. First, the number of genes encoding plant polyadenylation factors was clearly increased from “lower” to “higher” plants. Second, the gene expansion in higher plants was biased to some polyadenylation factors, particularly those involved in RNA binding. Finally, while there are clear commonalities, the differences in the polyadenylation apparatus were obvious across different species, suggesting an ongoing process of evolutionary change. These features lead to a model in which the plant polyadenylation complex consists of a conserved core, which is rather rigid in terms of evolutionary conservation, and a panoply of peripheral subunits, which are less conserved and associated with the core in various combinations, forming a collection of somewhat distinct complex assemblies. Conclusions The multiple forms of plant polyadenylation complex, together with the diversified polyA signals may explain the intensive alternative polyadenylation (APA) and its regulatory role in biological functions of higher plants.
Collapse
|
19
|
Rühl C, Stauffer E, Kahles A, Wagner G, Drechsel G, Rätsch G, Wachter A. Polypyrimidine tract binding protein homologs from Arabidopsis are key regulators of alternative splicing with implications in fundamental developmental processes. THE PLANT CELL 2012; 24:4360-75. [PMID: 23192226 PMCID: PMC3531839 DOI: 10.1105/tpc.112.103622] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/01/2012] [Revised: 10/09/2012] [Accepted: 10/24/2012] [Indexed: 05/18/2023]
Abstract
Alternative splicing (AS) generates transcript variants by variable exon/intron definition and massively expands transcriptome diversity. Changes in AS patterns have been found to be linked to manifold biological processes, yet fundamental aspects, such as the regulation of AS and its functional implications, largely remain to be addressed. In this work, widespread AS regulation by Arabidopsis thaliana Polypyrimidine tract binding protein homologs (PTBs) was revealed. In total, 452 AS events derived from 307 distinct genes were found to be responsive to the levels of the splicing factors PTB1 and PTB2, which predominantly triggered splicing of regulated introns, inclusion of cassette exons, and usage of upstream 5' splice sites. By contrast, no major AS regulatory function of the distantly related PTB3 was found. Dependent on their position within the mRNA, PTB-regulated events can both modify the untranslated regions and give rise to alternative protein products. We find that PTB-mediated AS events are connected to diverse biological processes, and the functional implications of selected instances were further elucidated. Specifically, PTB misexpression changes AS of PHYTOCHROME INTERACTING FACTOR6, coinciding with altered rates of abscisic acid-dependent seed germination. Furthermore, AS patterns as well as the expression of key flowering regulators were massively changed in a PTB1/2 level-dependent manner.
Collapse
Affiliation(s)
- Christina Rühl
- Center for Plant Molecular Biology, University of Tübingen, 72076 Tuebingen, Germany
| | - Eva Stauffer
- Center for Plant Molecular Biology, University of Tübingen, 72076 Tuebingen, Germany
| | - André Kahles
- Computational Biology Center, Sloan-Kettering Institute, New York, New York 10065
| | - Gabriele Wagner
- Center for Plant Molecular Biology, University of Tübingen, 72076 Tuebingen, Germany
| | - Gabriele Drechsel
- Center for Plant Molecular Biology, University of Tübingen, 72076 Tuebingen, Germany
| | - Gunnar Rätsch
- Computational Biology Center, Sloan-Kettering Institute, New York, New York 10065
| | - Andreas Wachter
- Center for Plant Molecular Biology, University of Tübingen, 72076 Tuebingen, Germany
| |
Collapse
|