1
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Gupta P, Jaiswal P. Transcriptional Modulation during Photomorphogenesis in Rice Seedlings. Genes (Basel) 2024; 15:1072. [PMID: 39202430 PMCID: PMC11353317 DOI: 10.3390/genes15081072] [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: 07/19/2024] [Revised: 08/05/2024] [Accepted: 08/07/2024] [Indexed: 09/03/2024] Open
Abstract
Light is one of the most important factors regulating plant gene expression patterns, metabolism, physiology, growth, and development. To explore how light may induce or alter transcript splicing, we conducted RNA-Seq-based transcriptome analyses by comparing the samples harvested as etiolated seedlings grown under continuous dark conditions vs. the light-treated green seedlings. The study aims to reveal differentially regulated protein-coding genes and novel long noncoding RNAs (lncRNAs), their light-induced alternative splicing, and their association with biological pathways. We identified 14,766 differentially expressed genes, of which 4369 genes showed alternative splicing. We observed that genes mapped to the plastid-localized methyl-erythritol-phosphate (MEP) pathway were light-upregulated compared to the cytosolic mevalonate (MVA) pathway genes. Many of these genes also undergo splicing. These pathways provide crucial metabolite precursors for the biosynthesis of secondary metabolic compounds needed for chloroplast biogenesis, the establishment of a successful photosynthetic apparatus, and photomorphogenesis. In the chromosome-wide survey of the light-induced transcriptome, we observed intron retention as the most predominant splicing event. In addition, we identified 1709 novel lncRNA transcripts in our transcriptome data. This study provides insights on light-regulated gene expression and alternative splicing in rice.
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Affiliation(s)
| | - Pankaj Jaiswal
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR 97331, USA;
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2
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Xu Z, Xiao Y, Guo J, Lv Z, Chen W. Relevance and regulation of alternative splicing in plant secondary metabolism: current understanding and future directions. HORTICULTURE RESEARCH 2024; 11:uhae173. [PMID: 39135731 PMCID: PMC11317897 DOI: 10.1093/hr/uhae173] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/08/2024] [Accepted: 06/14/2024] [Indexed: 08/15/2024]
Abstract
The secondary metabolism of plants is an essential life process enabling organisms to navigate various stages of plant development and cope with ever-changing environmental stresses. Secondary metabolites, abundantly found in nature, possess significant medicinal value. Among the regulatory mechanisms governing these metabolic processes, alternative splicing stands out as a widely observed post-transcriptional mechanism present in multicellular organisms. It facilitates the generation of multiple mRNA transcripts from a single gene by selecting different splicing sites. Selective splicing events in plants are widely induced by various signals, including external environmental stress and hormone signals. These events ultimately regulate the secondary metabolic processes and the accumulation of essential secondary metabolites in plants by influencing the synthesis of primary metabolites, hormone metabolism, biomass accumulation, and capillary density. Simultaneously, alternative splicing plays a crucial role in enhancing protein diversity and the abundance of the transcriptome. This paper provides a summary of the factors inducing alternative splicing events in plants and systematically describes the progress in regulating alternative splicing with respect to different secondary metabolites, including terpenoid, phenolic compounds, and nitrogen-containing compounds. Such elucidation offers critical foundational insights for understanding the role of alternative splicing in regulating plant metabolism and presents novel avenues and perspectives for bioengineering.
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Affiliation(s)
- Zihan Xu
- Research and Development Center of Chinese Medicine Resources and Biotechnology, Shanghai University of Traditional Chinese Medicine, Shanghai 201203, China
| | - Ying Xiao
- Research and Development Center of Chinese Medicine Resources and Biotechnology, Shanghai University of Traditional Chinese Medicine, Shanghai 201203, China
| | - Jinlin Guo
- College of Medical Technology, Chengdu University of Traditional Chinese Medicine, Chengdu 611103, China
- Chongqing Key Laboratory of Sichuan-Chongqing Co-construction for Diagnosis and Treatment of Infectious Diseases Integrated Traditional Chinese and Western Medicine, Chengdu University of Traditional Chinese Medicine, Chengdu 611130, China
- Key Laboratory of Characteristic Chinese Medicine Resources in Southwest China, College of Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu 611103, China
| | - Zongyou Lv
- Research and Development Center of Chinese Medicine Resources and Biotechnology, Shanghai University of Traditional Chinese Medicine, Shanghai 201203, China
| | - Wansheng Chen
- Research and Development Center of Chinese Medicine Resources and Biotechnology, Shanghai University of Traditional Chinese Medicine, Shanghai 201203, China
- Department of Pharmacy, Changzheng Hospital, Second Military Medical University, Shanghai 200003, China
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3
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Díez AR, Szakonyi D, Lozano-Juste J, Duque P. Alternative splicing as a driver of natural variation in abscisic acid response. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2024; 119:9-27. [PMID: 38659400 DOI: 10.1111/tpj.16773] [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: 10/18/2023] [Revised: 04/01/2024] [Accepted: 04/08/2024] [Indexed: 04/26/2024]
Abstract
Abscisic acid (ABA) is a crucial player in plant responses to the environment. It accumulates under stress, activating downstream signaling to implement molecular responses that restore homeostasis. Natural variance in ABA sensitivity remains barely understood, and the ABA pathway has been mainly studied at the transcriptional level, despite evidence that posttranscriptional regulation, namely, via alternative splicing, contributes to plant stress tolerance. Here, we identified the Arabidopsis accession Kn-0 as less sensitive to ABA than the reference Col-0, as shown by reduced effects of the hormone on seedling establishment, root branching, and stomatal closure, as well as by decreased induction of ABA marker genes. An in-depth comparative transcriptome analysis of the ABA response in the two variants revealed lower expression changes and fewer genes affected for the least ABA-sensitive ecotype. Notably, Kn-0 exhibited reduced levels of the ABA-signaling SnRK2 protein kinases and lower basal expression of ABA-reactivation genes, consistent with our finding that Kn-0 contains less endogenous ABA than Col-0. ABA also markedly affected alternative splicing, primarily intron retention, with Kn-0 being less responsive regarding both the number and magnitude of alternative splicing events, particularly exon skipping. We find that alternative splicing introduces a more ecotype-specific layer of ABA regulation and identify ABA-responsive splicing changes in key ABA pathway regulators that provide a functional and mechanistic link to the differential sensitivity of the two ecotypes. Our results offer new insight into the natural variation of ABA responses and corroborate a key role for alternative splicing in implementing ABA-mediated stress responses.
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Affiliation(s)
- Alba R Díez
- Instituto Gulbenkian de Ciência, 2780-156, Oeiras, Portugal
| | - Dóra Szakonyi
- Instituto Gulbenkian de Ciência, 2780-156, Oeiras, Portugal
| | - Jorge Lozano-Juste
- Instituto de Biología Molecular y Celular de Plantas (IBMCP), Universitat Politècnica de València (UPV), Consejo Superior de Investigaciones Científicas (CSIC), 46022, Valencia, Spain
| | - Paula Duque
- Instituto Gulbenkian de Ciência, 2780-156, Oeiras, Portugal
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4
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Muti RM, Barrett CF, Sinn BT. Evolution of Whirly1 in the angiosperms: sequence, splicing, and expression in a clade of early transitional mycoheterotrophic orchids. FRONTIERS IN PLANT SCIENCE 2024; 15:1241515. [PMID: 39006962 PMCID: PMC11239579 DOI: 10.3389/fpls.2024.1241515] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/16/2023] [Accepted: 06/07/2024] [Indexed: 07/16/2024]
Abstract
The plastid-targeted transcription factor Whirly1 (WHY1) has been implicated in chloroplast biogenesis, plastid genome stability, and fungal defense response, which together represent characteristics of interest for the study of autotrophic losses across the angiosperms. While gene loss in the plastid and nuclear genomes has been well studied in mycoheterotrophic plants, the evolution of the molecular mechanisms impacting genome stability is completely unknown. Here, we characterize the evolution of WHY1 in four early transitional mycoheterotrophic orchid species in the genus Corallorhiza by synthesizing the results of phylogenetic, transcriptomic, and comparative genomic analyses with WHY1 genomic sequences sampled from 21 orders of angiosperms. We found an increased number of non-canonical WHY1 isoforms assembled from all but the greenest Corallorhiza species, including intron retention in some isoforms. Within Corallorhiza, phylotranscriptomic analyses revealed the presence of tissue-specific differential expression of WHY1 in only the most photosynthetically capable species and a coincident increase in the number of non-canonical WHY1 isoforms assembled from fully mycoheterotrophic species. Gene- and codon-level tests of WHY1 selective regimes did not infer significant signal of either relaxed selection or episodic diversifying selection in Corallorhiza but did so for relaxed selection in the late-stage full mycoheterotrophic orchids Epipogium aphyllum and Gastrodia elata. Additionally, nucleotide substitutions that most likely impact the function of WHY1, such as nonsense mutations, were only observed in late-stage mycoheterotrophs. We propose that our findings suggest that splicing and expression changes may precede the selective shifts we inferred for late-stage mycoheterotrophic species, which therefore does not support a primary role for WHY1 in the transition to mycoheterotrophy in the Orchidaceae. Taken together, this study provides the most comprehensive view of WHY1 evolution across the angiosperms to date.
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Affiliation(s)
- Rachel M. Muti
- Department of Biology and Earth Science, Otterbein University, Westerville, OH, United States
- Department of Hematology and Medical Oncology, Emory University, Atlanta, GA, United States
| | - Craig F. Barrett
- Department of Biology, West Virginia University, Morgantown, WV, United States
| | - Brandon T. Sinn
- Department of Biology and Earth Science, Otterbein University, Westerville, OH, United States
- Faculty of Biology, University of Latvia, Riga, Latvia
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Abulfaraj AA, Alshareef SA. Concordant Gene Expression and Alternative Splicing Regulation under Abiotic Stresses in Arabidopsis. Genes (Basel) 2024; 15:675. [PMID: 38927612 PMCID: PMC11202685 DOI: 10.3390/genes15060675] [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: 04/16/2024] [Revised: 05/19/2024] [Accepted: 05/20/2024] [Indexed: 06/28/2024] Open
Abstract
The current investigation endeavors to identify differentially expressed alternatively spliced (DAS) genes that exhibit concordant expression with splicing factors (SFs) under diverse multifactorial abiotic stress combinations in Arabidopsis seedlings. SFs serve as the post-transcriptional mechanism governing the spatiotemporal dynamics of gene expression. The different stresses encompass variations in salt concentration, heat, intensive light, and their combinations. Clusters demonstrating consistent expression profiles were surveyed to pinpoint DAS/SF gene pairs exhibiting concordant expression. Through rigorous selection criteria, which incorporate alignment with documented gene functionalities and expression patterns observed in this study, four members of the serine/arginine-rich (SR) gene family were delineated as SFs concordantly expressed with six DAS genes. These regulated SF genes encompass cactin, SR1-like, SR30, and SC35-like. The identified concordantly expressed DAS genes encode diverse proteins such as the 26.5 kDa heat shock protein, chaperone protein DnaJ, potassium channel GORK, calcium-binding EF hand family protein, DEAD-box RNA helicase, and 1-aminocyclopropane-1-carboxylate synthase 6. Among the concordantly expressed DAS/SF gene pairs, SR30/DEAD-box RNA helicase, and SC35-like/1-aminocyclopropane-1-carboxylate synthase 6 emerge as promising candidates, necessitating further examinations to ascertain whether these SFs orchestrate splicing of the respective DAS genes. This study contributes to a deeper comprehension of the varied responses of the splicing machinery to abiotic stresses. Leveraging these DAS/SF associations shows promise for elucidating avenues for augmenting breeding programs aimed at fortifying cultivated plants against heat and intensive light stresses.
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Affiliation(s)
- Aala A. Abulfaraj
- Biological Sciences Department, College of Science & Arts, King Abdulaziz University, Rabigh 21911, Saudi Arabia
| | - Sahar A. Alshareef
- Department of Biology, College of Science and Arts at Khulis, University of Jeddah, Jeddah 21921, Saudi Arabia;
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Wu ZH, He LL, Wang CC, Liang C, Li HY, Zhong DW, Dong ZX, Zhang LJ, Zhang XQ, Ge LF, Chen S. Unveiling unique alternative splicing responses to low temperature in Zoysia japonica through ZjRTD1.0, a high-quality reference transcript dataset. PHYSIOLOGIA PLANTARUM 2024; 176:e14280. [PMID: 38644527 DOI: 10.1111/ppl.14280] [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: 10/16/2023] [Revised: 02/29/2024] [Accepted: 03/09/2024] [Indexed: 04/23/2024]
Abstract
Inadequate reference databases in RNA-seq analysis can hinder data utilization and interpretation. In this study, we have successfully constructed a high-quality reference transcript dataset, ZjRTD1.0, for Zoysia japonica, a widely-used turfgrass with exceptional tolerance to various abiotic stress, including low temperatures and salinity. This dataset comprises 113,089 transcripts from 57,143 genes. BUSCO analysis demonstrates exceptional completeness (92.4%) in ZjRTD1.0, with reduced proportions of fragmented (3.3%) and missing (4.3%) orthologs compared to prior datasets. ZjRTD1.0 enables more precise analyses, including transcript quantification and alternative splicing assessments using public datasets, which identified a substantial number of differentially expressed transcripts (DETs) and differential alternative splicing (DAS) events, leading to several novel findings on Z. japonica's responses to abiotic stresses. First, spliceosome gene expression influenced alternative splicing significantly under abiotic stress, with a greater impact observed during low-temperature stress. Then, a significant positive correlation was found between the number of differentially expressed genes (DEGs) encoding protein kinases and the frequency of DAS events, suggesting the role of protein phosphorylation in regulating alternative splicing. Additionally, our results suggest possible involvement of serine/arginine-rich (SR) proteins and heterogeneous nuclear ribonucleoproteins (hnRNPs) in generating inclusion/exclusion isoforms under low-temperature stress. Furthermore, our investigation revealed a significantly enhanced overlap between DEGs and differentially alternatively spliced genes (DASGs) in response to low-temperature stress, suggesting a unique co-regulatory mechanism governing transcription and splicing in the context of low-temperature response. In conclusion, we have proven that ZjRTD1.0 will serve as a reliable and useful resource for future transcriptomic analyses in Z. japonica.
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Affiliation(s)
- Zhi-Hao Wu
- Department of Grass Science, College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou, China
- Guangdong Engineering Research Center for Grassland Science, Guangzhou, China
| | - Liang-Liang He
- Department of Grass Science, College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou, China
- Guangdong Engineering Research Center for Grassland Science, Guangzhou, China
| | - Cong-Cong Wang
- Department of Grass Science, College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou, China
- Guangdong Engineering Research Center for Grassland Science, Guangzhou, China
| | - Chen Liang
- Department of Grass Science, College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou, China
- Guangdong Engineering Research Center for Grassland Science, Guangzhou, China
| | - Han-Ying Li
- Department of Grass Science, College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou, China
- Guangdong Engineering Research Center for Grassland Science, Guangzhou, China
| | - Dan-Wen Zhong
- Department of Grass Science, College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou, China
- Guangdong Engineering Research Center for Grassland Science, Guangzhou, China
| | - Zhao-Xia Dong
- Department of Grass Science, College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou, China
- Guangdong Engineering Research Center for Grassland Science, Guangzhou, China
| | - Li-Juan Zhang
- Shenzhen Tourism College of Jinan University, Shenzhen, Guangdong, China
| | - Xiang-Qian Zhang
- College of Food Science and Engineering, Foshan University, Foshan, Guangdong, China
| | - Liang-Fa Ge
- Department of Grass Science, College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou, China
- Guangdong Engineering Research Center for Grassland Science, Guangzhou, China
| | - Shu Chen
- Department of Grass Science, College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou, China
- Guangdong Engineering Research Center for Grassland Science, Guangzhou, China
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7
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Shamnas v M, Singh A, Kumar A, Mishra GP, Sinha SK. Exitrons: offering new roles to retained introns-the novel regulators of protein diversity and utility. AOB PLANTS 2024; 16:plae014. [PMID: 38566894 PMCID: PMC10985678 DOI: 10.1093/aobpla/plae014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/13/2023] [Accepted: 03/15/2024] [Indexed: 04/04/2024]
Abstract
Exitrons are exonic introns. This subclass of intron retention alternative splicing does not contain a Pre-Terminating stop Codon. Therefore, when retained, they are always a part of a protein. Intron retention is a frequent phenomenon predominantly found in plants, which results in either the degradation of the transcripts or can serve as a stable intermediate to be processed upon induction by specific signals or the cell status. Interestingly, exitrons have coding ability and may confer additional attributes to the proteins that retain them. Therefore, exitron-containing and exitron-spliced isoforms will be a driving force for creating protein diversity in the proteome of an organism. This review establishes a basic understanding of exitron, discussing its genesis, key features, identification methods and functions. We also try to depict its other potential roles. The present review also aims to provide a fundamental background to those who found such exitronic sequences in their gene(s) and to speculate the future course of studies.
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Affiliation(s)
- Muhammed Shamnas v
- ICAR-National Institute for Plant Biotechnology, Pusa Campus, New Delhi 110012, India
| | - Akanksha Singh
- ICAR-National Institute for Plant Biotechnology, Pusa Campus, New Delhi 110012, India
- Department of Botany and Plant Pathology, Lilly Hall of Life Sciences, Purdue University, West Lafayette 47906, Indiana, USA
| | - Anuj Kumar
- ICAR-National Institute for Plant Biotechnology, Pusa Campus, New Delhi 110012, India
| | - Gyan Prakash Mishra
- Division of Genetics, ICAR-Indian Agricultural Research Institute, Pusa Campus, New Delhi 110012, India
| | - Subodh Kumar Sinha
- ICAR-National Institute for Plant Biotechnology, Pusa Campus, New Delhi 110012, India
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Al-Dossary O, Furtado A, KharabianMasouleh A, Alsubaie B, Al-Mssallem I, Henry RJ. Long read sequencing to reveal the full complexity of a plant transcriptome by targeting both standard and long workflows. PLANT METHODS 2023; 19:112. [PMID: 37865785 PMCID: PMC10589961 DOI: 10.1186/s13007-023-01091-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/17/2022] [Accepted: 10/13/2023] [Indexed: 10/23/2023]
Abstract
BACKGROUND Long read sequencing allows the analysis of full-length transcripts in plants without the challenges of reliable transcriptome assembly. Long read sequencing of transcripts from plant genomes has often utilized sized transcript libraries. However, the value of including libraries of differing sizes has not been established. METHODS A comprehensive transcriptome of the leaves of Jojoba (Simmondsia chinensis) was generated from two different PacBio library preparations: standard workflow (SW) and long workflow (LW). RESULTS The importance of using both transcript groups in the analysis was demonstrated by the high proportion of unique sequences (74.6%) that were not shared between the groups. A total of 37.8% longer transcripts were only detected in the long dataset. The completeness of the combined transcriptome was indicated by the presence of 98.7% of genes predicted in the jojoba male reference genome. The high coverage of the transcriptome was further confirmed by BUSCO analysis showing the presence of 96.9% of the genes from the core viridiplantae_odb10 lineage. The high-quality isoforms post Cd-Hit merged dataset of the two workflows had a total of 167,866 isoforms. Most of the transcript isoforms were protein-coding sequences (71.7%) containing open reading frames (ORFs) ≥ 100 amino acids (aa). Alternative splicing and intron retention were the basis of most transcript diversity when analysed at the whole genome level and by specific analysis of the apetala2 gene families. CONCLUSION This suggests the need to specifically target the capture of longer transcripts to provide more comprehensive genome coverage in plant transcriptome analysis and reveal the high level of alternative splicing.
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Affiliation(s)
- Othman Al-Dossary
- Queensland Alliance for Agriculture and Food Innovation, University of Queensland, Brisbane, 4072, Australia
- College of Agriculture and Food Sciences, King Faisal University, 36362, Al Hofuf, Saudi Arabia
| | - Agnelo Furtado
- Queensland Alliance for Agriculture and Food Innovation, University of Queensland, Brisbane, 4072, Australia
| | - Ardashir KharabianMasouleh
- Queensland Alliance for Agriculture and Food Innovation, University of Queensland, Brisbane, 4072, Australia
| | - Bader Alsubaie
- Queensland Alliance for Agriculture and Food Innovation, University of Queensland, Brisbane, 4072, Australia
- College of Agriculture and Food Sciences, King Faisal University, 36362, Al Hofuf, Saudi Arabia
| | - Ibrahim Al-Mssallem
- College of Agriculture and Food Sciences, King Faisal University, 36362, Al Hofuf, Saudi Arabia
| | - Robert J Henry
- Queensland Alliance for Agriculture and Food Innovation, University of Queensland, Brisbane, 4072, Australia.
- ARC Centre of Excellence for Plant Success in Nature and Agriculture, University of Queensland, Brisbane, 4072, Australia.
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Marquardt S, Petrillo E, Manavella PA. Cotranscriptional RNA processing and modification in plants. THE PLANT CELL 2023; 35:1654-1670. [PMID: 36259932 PMCID: PMC10226594 DOI: 10.1093/plcell/koac309] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/25/2022] [Accepted: 10/14/2022] [Indexed: 05/30/2023]
Abstract
The activities of RNA polymerases shape the epigenetic landscape of genomes with profound consequences for genome integrity and gene expression. A fundamental event during the regulation of eukaryotic gene expression is the coordination between transcription and RNA processing. Most primary RNAs mature through various RNA processing and modification events to become fully functional. While pioneering results positioned RNA maturation steps after transcription ends, the coupling between the maturation of diverse RNA species and their transcription is becoming increasingly evident in plants. In this review, we discuss recent advances in our understanding of the crosstalk between RNA Polymerase II, IV, and V transcription and nascent RNA processing of both coding and noncoding RNAs.
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Affiliation(s)
- Sebastian Marquardt
- Department of Plant and Environmental Sciences, Copenhagen Plant Science Centre, University of Copenhagen, Frederiksberg, Denmark
| | - Ezequiel Petrillo
- Universidad de Buenos Aires, Facultad de Ciencias Exactas y Naturales, Instituto de Fisiología, Biología Molecular y Neurociencias (IFIBYNE-CONICET-UBA), Buenos Aires, C1428EHA, Argentina
| | - Pablo A Manavella
- Instituto de Agrobiotecnología del Litoral (CONICET-UNL), Cátedra de Biología Celular y Molecular, Facultad de Bioquímica y Ciencias Biológicas, Universidad Nacional del Litoral, Santa Fe 3000, Argentina
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10
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Petrillo E. Do not panic: An intron-centric guide to alternative splicing. THE PLANT CELL 2023; 35:1752-1761. [PMID: 36648241 PMCID: PMC10226583 DOI: 10.1093/plcell/koad009] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/19/2022] [Revised: 12/05/2022] [Accepted: 01/11/2023] [Indexed: 05/30/2023]
Abstract
This review is an attempt to establish concepts of splicing and alternative splicing giving proper relevance to introns, the key actors in this mechanism. It might also work as a guide for those who found their favorite gene undergoes alternative splicing and could benefit from gaining a theoretical framework to understand the possible impacts of this process. This is not a thorough review of all the work in the field, but rather a critical review of some of the most relevant work done to understand the underlying mechanisms of splicing and the key questions that remain unanswered such as: What is the physiological relevance of alternative splicing? What are the functions of the different outcomes? To what extent do different alternative splicing types contribute to the proteome? Intron retention is the most frequent alternative splicing event in plants and, although scientifically neglected, it is also common in animals. This is a heterogeneous type of alternative splicing that includes different sub-types with features that have distinctive consequences in the resulting transcripts. Remarkably, intron retention can be a dead end for a transcript, but it could also be a stable intermediate whose processing is resumed upon a particular signal or change in the cell status. New sequencing technologies combined with the study of intron lariats in different conditions might help to answer key questions and could help us to understand the actual relevance of introns in gene expression regulation.
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Affiliation(s)
- Ezequiel Petrillo
- Facultad de Ciencias Exactas y Naturales, Departamento de Fisiología, Biología, Molecular, y Celular, Universidad de Buenos Aires, 1428 Buenos Aires, Argentina
- CONICET-Universidad de Buenos Aires, Instituto de Fisiología, Biología Molecular y Neurociencias (IFIBYNE), C1428EHA Buenos Aires, Argentina
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11
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Kumar K, Sinha SK, Maity U, Kirti PB, Kumar KRR. Insights into established and emerging roles of SR protein family in plants and animals. WILEY INTERDISCIPLINARY REVIEWS. RNA 2023; 14:e1763. [PMID: 36131558 DOI: 10.1002/wrna.1763] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/19/2022] [Revised: 08/11/2022] [Accepted: 08/22/2022] [Indexed: 05/13/2023]
Abstract
Splicing of pre-mRNA is an essential part of eukaryotic gene expression. Serine-/arginine-rich (SR) proteins are highly conserved RNA-binding proteins present in all metazoans and plants. SR proteins are involved in constitutive and alternative splicing, thereby regulating the transcriptome and proteome diversity in the organism. In addition to their role in splicing, SR proteins are also involved in mRNA export, nonsense-mediated mRNA decay, mRNA stability, and translation. Due to their pivotal roles in mRNA metabolism, SR proteins play essential roles in normal growth and development. Hence, any misregulation of this set of proteins causes developmental defects in both plants and animals. SR proteins from the animal kingdom are extensively studied for their canonical and noncanonical functions. Compared with the animal kingdom, plant genomes harbor more SR protein-encoding genes and greater diversity of SR proteins, which are probably evolved for plant-specific functions. Evidence from both plants and animals confirms the essential role of SR proteins as regulators of gene expression influencing cellular processes, developmental stages, and disease conditions. This article is categorized under: RNA Processing > Splicing Mechanisms RNA Processing > Splicing Regulation/Alternative Splicing.
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Affiliation(s)
- Kundan Kumar
- Department of Biotechnology, Indira Gandhi National Tribal University (IGNTU), Amarkantak, India
| | - Shubham Kumar Sinha
- Department of Biotechnology, Indira Gandhi National Tribal University (IGNTU), Amarkantak, India
| | - Upasana Maity
- Department of Biotechnology, Indira Gandhi National Tribal University (IGNTU), Amarkantak, India
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12
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Laskar P, Hazra A, Pal A, Kundu A. Deciphering the role of alternative splicing as modulators of defense response in the MYMIV- Vigna mungo pathosystem. PHYSIOLOGIA PLANTARUM 2023; 175:e13922. [PMID: 37114622 DOI: 10.1111/ppl.13922] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/05/2023] [Revised: 04/20/2023] [Accepted: 04/24/2023] [Indexed: 06/19/2023]
Abstract
Alternative splicing (AS) is a crucial regulatory mechanism that impacts transcriptome and proteome complexity under stressful situations. Although its role in abiotic stresses is somewhat understood, our understanding of the mechanistic regulation of pre-mRNA splicing in plant-pathogen interaction is meagre. To comprehend this unexplored immune reprogramming mechanism, transcriptome profiles of Mungbean Yellow Mosaic India Virus (MYMIV)-resistant and susceptible Vigna mungo genotypes were analysed for AS genes that may underlie the resistance mechanism. Results revealed a repertoire of AS-isoforms accumulated during pathogenic infestation, with intron retention being the most common AS mechanism. Identification of 688 differential alternatively spliced (DAS) genes in the resistant host elucidates its robust antiviral response, whereas 322 DAS genes were identified in the susceptible host. Enrichment analyses confirmed DAS transcripts pertaining to stress, signalling, and immune system pathways have undergone maximal perturbations. Additionally, a strong regulation of the splicing factors has been observed both at transcriptional and post-transcriptional levels. qPCR validation of candidate DAS transcripts with induced expression upon MYMIV-infection demonstrated a competent immune response in the resistant background. The AS-impacted genes resulted either in partial/complete loss of functional domains or altered sensitivity to miRNA-mediated gene silencing. A complex regulatory module, miR7517-ATAF2, has been identified in an aberrantly spliced ATAF2 isoform that exposes an intronic miR7517 binding site, thereby suppressing the negative regulator to enhance defense reaction. The present study establishes AS as a non-canonical immune reprogramming mechanism that operates in parallel, thereby offering an alternative strategy for developing yellow mosaic-resistant V. mungo cultivars. This article is protected by copyright. All rights reserved.
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Affiliation(s)
- Parbej Laskar
- Plant Genomics and Bioinformatics Laboratory, Ramakrishna Mission Vivekananda Centenary College, Rahara, Kolkata
| | - Anjan Hazra
- Agricultural and Ecological Research Unit, Indian Statistical Institute, 203 B. T. Road, Kolkata
- Present Address: Department of Genetics, University of Calcutta, 35 Ballygunge Circular Road, Kolkata
| | - Amita Pal
- Division of Plant Biology, Bose Institute, Kolkata
| | - Anirban Kundu
- Plant Genomics and Bioinformatics Laboratory, Ramakrishna Mission Vivekananda Centenary College, Rahara, Kolkata
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13
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Zhang Y, Song X, Zhang W, Liu F, Wang C, Liu Y, Dirk LMA, Downie AB, Zhao T. Maize PIMT2 repairs damaged 3-METHYLCROTONYL COA CARBOXYLASE in mitochondria, affecting seed vigor. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2023. [PMID: 36999611 DOI: 10.1111/tpj.16225] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/05/2023] [Revised: 03/13/2023] [Accepted: 03/24/2023] [Indexed: 06/19/2023]
Abstract
PROTEIN l-ISOASPARTYL O-METHYLTRANSFERASE (PIMT) affects seed vigor by repairing damaged proteins. While PIMT is capable of isoaspartyl (isoAsp) repair in all proteins, those proteins most susceptible to isoAsp formation have not been well characterized, and the mechanisms by which PIMT affects seed vigor remain largely unknown. Using co-immunoprecipitation and LC-MS/MS, we found that maize (Zea mays) PIMT2 (ZmPIMT2) interacted predominantly with both subunits of maize 3-METHYLCROTONYL COA CARBOXYLASE (ZmMCC). ZmPIMT2 is specifically expressed in the maize embryo. Both mRNA and protein levels of ZmPIMT2 increased during seed maturation and declined during imbibition. Maize seed vigor was decreased in the zmpimt2 mutant line, while overexpression of ZmPIMT2 in maize and Arabidopsis thaliana increased seed vigor upon artificial aging. ZmPIMT2 was localized in the mitochondria, as determined by subcellular localization assays using maize protoplasts. ZmPIMT2 binding to ZmMCCα was confirmed by luciferase complementation tests in both tobacco (Nicotiana benthamiana) leaves and maize protoplasts. Knockdown of ZmMCCα decreased maize seed aging tolerance. Furthermore, overexpression of ZmPIMT2 decreased the accumulation of isoAsp of ZmMCCα protein in seed embryos that underwent accelerated aging treatment. Taken together, our results demonstrate that ZmPIMT2 binds ZmMCCα in mitochondria, repairs isoAsp damage, and positively affects maize seed vigor.
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Affiliation(s)
- Yumin Zhang
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi, 712100, China
- The Key Laboratory of Biology and Genetics Improvement of Maize in Arid Area of Northwest Region, Ministry of Agriculture, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Xianbo Song
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi, 712100, China
- The Key Laboratory of Biology and Genetics Improvement of Maize in Arid Area of Northwest Region, Ministry of Agriculture, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Wenli Zhang
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi, 712100, China
- The Key Laboratory of Biology and Genetics Improvement of Maize in Arid Area of Northwest Region, Ministry of Agriculture, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Feijun Liu
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi, 712100, China
- The Key Laboratory of Biology and Genetics Improvement of Maize in Arid Area of Northwest Region, Ministry of Agriculture, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Chunmei Wang
- Biology Experimental Teaching Center, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi, China
| | - Ying Liu
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi, 712100, China
- The Key Laboratory of Biology and Genetics Improvement of Maize in Arid Area of Northwest Region, Ministry of Agriculture, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Lynnette M A Dirk
- Department of Horticulture, Seed Biology, College of Agriculture, Food and Environment, University of Kentucky, Lexington, Kentucky, 40546, USA
| | - A Bruce Downie
- Department of Horticulture, Seed Biology, College of Agriculture, Food and Environment, University of Kentucky, Lexington, Kentucky, 40546, USA
| | - Tianyong Zhao
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi, 712100, China
- The Key Laboratory of Biology and Genetics Improvement of Maize in Arid Area of Northwest Region, Ministry of Agriculture, Northwest A&F University, Yangling, Shaanxi, 712100, China
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14
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Global Analysis of Dark- and Heat-Regulated Alternative Splicing in Arabidopsis. Int J Mol Sci 2023; 24:ijms24065299. [PMID: 36982373 PMCID: PMC10049525 DOI: 10.3390/ijms24065299] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2023] [Revised: 03/02/2023] [Accepted: 03/07/2023] [Indexed: 03/12/2023] Open
Abstract
Alternative splicing (AS) is one of the major post-transcriptional regulation mechanisms that contributes to plant responses to various environmental perturbations. Darkness and heat are two common abiotic factors affecting plant growth, yet the involvement and regulation of AS in the plant responses to these signals remain insufficiently examined. In this study, we subjected Arabidopsis seedlings to 6 h of darkness or heat stress and analyzed their transcriptome through short-read RNA sequencing. We revealed that both treatments altered the transcription and AS of a subset of genes yet with different mechanisms. Dark-regulated AS events were found enriched in photosynthesis and light signaling pathways, while heat-regulated AS events were enriched in responses to abiotic stresses but not in heat-responsive genes, which responded primarily through transcriptional regulation. The AS of splicing-related genes (SRGs) was susceptible to both treatments; while dark treatment mostly regulated the AS of these genes, heat had a strong effect on both their transcription and AS. PCR analysis showed that the AS of the Serine/Arginine-rich family gene SR30 was reversely regulated by dark and heat, and heat induced the upregulation of multiple minor SR30 isoforms with intron retention. Our results suggest that AS participates in plant responses to these two abiotic signals and reveal the regulation of splicing regulators during these processes.
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15
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Rahmatpour N, Kuo LY, Kang J, Herman E, Lei L, Li M, Srinivasan S, Zipper R, Wolniak SM, Delwiche CF, Mount S, Li FW. Analyses of Marsilea vestita genome and transcriptomes do not support widespread intron retention during spermatogenesis. THE NEW PHYTOLOGIST 2023; 237:1490-1494. [PMID: 36451524 DOI: 10.1111/nph.18652] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/25/2022] [Accepted: 11/23/2022] [Indexed: 06/17/2023]
Affiliation(s)
| | - Li-Yaung Kuo
- Institute of Molecular and Cellular Biology, National Tsing Hua University, Hsinchu, 300, Taiwan
| | - Jessica Kang
- Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, MD, 20742, USA
| | - Eliana Herman
- Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, MD, 20742, USA
| | - Lily Lei
- Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, MD, 20742, USA
| | - Muzi Li
- Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, MD, 20742, USA
| | - Sruthi Srinivasan
- Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, MD, 20742, USA
| | - Richard Zipper
- Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, MD, 20742, USA
| | - Stephen M Wolniak
- Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, MD, 20742, USA
| | - Charles F Delwiche
- Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, MD, 20742, USA
| | - Stephen Mount
- Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, MD, 20742, USA
| | - Fay-Wei Li
- Boyce Thompson Institute, Ithaca, NY, 14853, USA
- Plant Biology Section, Cornell University, Ithaca, NY, 14853, USA
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16
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Li T, Wang H, Zhang Y, Wang H, Zhang Z, Liu X, Zhang Z, Liu K, Yang D, Zhang H, Gu L. Comprehensive profiling of epigenetic modifications in fast-growing Moso bamboo shoots. PLANT PHYSIOLOGY 2023; 191:1017-1035. [PMID: 36417282 PMCID: PMC9922427 DOI: 10.1093/plphys/kiac525] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/19/2022] [Revised: 10/10/2022] [Accepted: 11/17/2022] [Indexed: 05/13/2023]
Abstract
The fast growth of Moso bamboo (Phyllostachys edulis) shoots is caused by the rapid elongation of each internode. However, the key underlying cellular processes and epigenetic mechanisms remain largely unexplored. We used microscopy and multi-omics approaches to investigate two regions (bottom and middle) of the 18th internode from shoots of two different heights (2 and 4 m). We observed that internode cells become longer, and that lignin biosynthesis and glycosyltransferase family 43 (GT43) genes are substantially upregulated with shoot height. Nanopore direct RNA sequencing (DRS) revealed a higher N6-methyladenine (m6A) modification rate in 2-m shoots than in 4-m shoots. In addition, different specific m6A modification sites were enriched at different growth stages. Global DNA methylation profiling indicated that DNA methylation levels are higher in 4-m shoots than in 2-m shoots. We also detected shorter poly(A) tail lengths (PALs) in 4-m shoots compared with 2-m shoots. Genes showing differential PAL were mainly enriched in the functional terms of protein translation and vesicle fusion. An association analysis between PALs and DNA methylation strongly suggested that gene body CG methylation levels are positively associated with PAL. This study provides valuable information to better understand post-transcriptional regulations responsible for fast-growing shoots in Moso bamboo.
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Affiliation(s)
- Tao Li
- College of Forestry, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Huihui Wang
- College of Forestry, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Yaxin Zhang
- College of Forestry, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Huiyuan Wang
- College of Forestry, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Zeyu Zhang
- College of Forestry, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Xuqing Liu
- College of Forestry, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Zekun Zhang
- College of Forestry, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Kai Liu
- College of Forestry, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Deming Yang
- College of Forestry, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Hangxiao Zhang
- Basic Forestry and Proteomics Research Center, College of Forestry, School of Future Technology, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Lianfeng Gu
- Basic Forestry and Proteomics Research Center, College of Forestry, School of Future Technology, Fujian Agriculture and Forestry University, Fuzhou 350002, China
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17
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Wei Z, Li Y, Ali F, Wang Y, Liu J, Yang Z, Wang Z, Xing Y, Li F. Transcriptomic analysis reveals the key role of histone deacetylation via mediating different phytohormone signalings in fiber initiation of cotton. Cell Biosci 2022; 12:107. [PMID: 35831870 PMCID: PMC9277824 DOI: 10.1186/s13578-022-00840-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2021] [Accepted: 06/28/2022] [Indexed: 12/04/2022] Open
Abstract
Background Histone deacetylation is one of the most important epigenetic modifications and plays diverse roles in plant development. However, the detailed functions and mechanisms of histone deacetylation in fiber development of cotton are still unclear. HDAC inhibitors (HDACi) have been commonly used to study the molecular mechanism underlying histone deacetylation or to facilitate disease therapy in humans through hindering the histone deacetylase catalytic activity. Trichostatin A (TSA)—the most widely used HDACi has been extensively employed to determine the role of histone deacetylation on different developmental stages of plants. Results Through in vitro culture of ovules, we observed that exogenous application of TSA was able to inhibit the fiber initiation development. Subsequently, we performed a transcriptomic analysis to reveal the underlying mechanisms. The data showed that TSA treatment resulted in 4209 differentially expressed genes, which were mostly enriched in plant hormone signal transduction, phenylpropanoid biosynthesis, photosynthesis, and carbon metabolism pathways. The phytohormone signal transduction pathways harbor the most differentially expressed genes. Deeper studies showed that some genes promoting auxin, Gibberellic Acid (GA) signaling were down-regulated, while some genes facilitating Abscisic Acid (ABA) and inhibiting Jasmonic Acid (JA) signaling were up-regulated after the TSA treatments. Further analysis of plant hormone contents proved that TSA significantly promoted the accumulation of ABA, JA and GA3. Conclusions Collectively, histone deacetylation can regulate some key genes involved in different phytohormone pathways, and consequently promoting the auxin, GA, and JA signaling, whereas repressing the ABA synthesis and signaling to improve the fiber cell initiation. Moreover, the genes associated with energy metabolism, phenylpropanoid, and glutathione metabolism were also regulated by histone deacetylation. The above results provided novel clues to illuminate the underlying mechanisms of epigenetic modifications as well as related different phytohormones in fiber cell differentiation, which is also very valuable for the molecular breeding of higher quality cotton. Supplementary Information The online version contains supplementary material available at 10.1186/s13578-022-00840-4.
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18
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Klodová B, Potěšil D, Steinbachová L, Michailidis C, Lindner AC, Hackenberg D, Becker JD, Zdráhal Z, Twell D, Honys D. Regulatory dynamics of gene expression in the developing male gametophyte of Arabidopsis. PLANT REPRODUCTION 2022:10.1007/s00497-022-00452-5. [PMID: 36282332 PMCID: PMC10363097 DOI: 10.1007/s00497-022-00452-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/27/2022] [Accepted: 09/26/2022] [Indexed: 06/16/2023]
Abstract
Sexual reproduction in angiosperms requires the production and delivery of two male gametes by a three-celled haploid male gametophyte. This demands synchronized gene expression in a short developmental window to ensure double fertilization and seed set. While transcriptomic changes in developing pollen are known for Arabidopsis, no studies have integrated RNA and proteomic data in this model. Further, the role of alternative splicing has not been fully addressed, yet post-transcriptional and post-translational regulation may have a key role in gene expression dynamics during microgametogenesis. We have refined and substantially updated global transcriptomic and proteomic changes in developing pollen for two Arabidopsis accessions. Despite the superiority of RNA-seq over microarray-based platforms, we demonstrate high reproducibility and comparability. We identify thousands of long non-coding RNAs as potential regulators of pollen development, hundreds of changes in alternative splicing and provide insight into mRNA translation rate and storage in developing pollen. Our analysis delivers an integrated perspective of gene expression dynamics in developing Arabidopsis pollen and a foundation for studying the role of alternative splicing in this model.
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Affiliation(s)
- Božena Klodová
- Institute of Experimental Botany of the Czech Academy of Sciences, Rozvojová 263, 165 02, Prague 6, Czech Republic
- Department of Experimental Plant Biology, Faculty of Science, Charles University, Viničná 5, Praha 2, 128 00, Czech Republic
| | - David Potěšil
- Mendel Centre for Plant Genomics and Proteomics, Central European Institute of Technology, Masaryk University, Kamenice 5, 625 00, Brno, Czech Republic
| | - Lenka Steinbachová
- Institute of Experimental Botany of the Czech Academy of Sciences, Rozvojová 263, 165 02, Prague 6, Czech Republic
| | - Christos Michailidis
- Institute of Experimental Botany of the Czech Academy of Sciences, Rozvojová 263, 165 02, Prague 6, Czech Republic
| | - Ann-Cathrin Lindner
- Instituto Gulbenkian de Ciência, Rua da Quinta Grande 6, 2780-156, Oeiras, Portugal
| | - Dieter Hackenberg
- Department of Genetics and Genome Biology, University of Leicester, Leicester, LE1 7RH, UK
- KWS SAAT SE & Co. KGaA, Grimsehlstraße 31, 37574, Einbeck, Germany
| | - Jörg D Becker
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa (ITQB NOVA), Av. da República, 2780-157, Oeiras, Portugal
- Instituto Gulbenkian de Ciência, Rua da Quinta Grande 6, 2780-156, Oeiras, Portugal
| | - Zbyněk Zdráhal
- Mendel Centre for Plant Genomics and Proteomics, Central European Institute of Technology, Masaryk University, Kamenice 5, 625 00, Brno, Czech Republic
- National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Kamenice 5, 625 00, Brno, Czech Republic
| | - David Twell
- Department of Genetics and Genome Biology, University of Leicester, Leicester, LE1 7RH, UK.
| | - David Honys
- Institute of Experimental Botany of the Czech Academy of Sciences, Rozvojová 263, 165 02, Prague 6, Czech Republic.
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19
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Zhang Y, Lou F, Chen J, Han Z, Yang T, Gao T, Song N. Single-molecule Real-time (SMRT) Sequencing Facilitates Transcriptome Research and Genome Annotation of the Fish Sillago sinica. MARINE BIOTECHNOLOGY (NEW YORK, N.Y.) 2022; 24:1002-1013. [PMID: 36083383 DOI: 10.1007/s10126-022-10163-7] [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: 05/18/2022] [Accepted: 08/30/2022] [Indexed: 06/15/2023]
Abstract
As a newly described Sillaginidae species, Chinese sillago (Sillago sinica) needs a better understanding of gene annotation information. In this study, we reported the first full-length transcriptome data of S. sinica using the PacBio isoform sequencing Iso-seq and a description of transcriptome structure analysis. A total of 454,979 high-quality full-length transcripts were obtained by single-molecule real-time (SMRT) sequencing, which was corrected by Illumina sequencing data. After that, 66,948 non-redundant full-length transcripts were generated after mapping to the reference genome of S. sinica, including 49 fusion isoforms and 9,250 novel isoforms. 63,459 isoforms were successfully annotated by one of the Nr, Nt, SwissProt, Pfam, KOG, GO, and KEGG databases. Additionally, 30,987 alternative polyadenylation (APA) sites, 451,867 alternative splicing (AS) events, 21,928 long non-coding RNAs (lncRNAs) and 12,911 transcription factors (TFs) were identified. The full-length transcripts of S. sinica would provide a precious resource for characterizing the transcriptome of S. sinica and for the further study of gene function and regulatory mechanism of this species.
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Affiliation(s)
- Yuan Zhang
- Fishery College, Ocean University of China, Qingdao, 266003, China
| | - Fangrui Lou
- School of Ocean, Yantai University, Yantai, 264005, China
| | - Jianwei Chen
- BGI-Qingdao, BGI-Shenzhen, Qingdao, 266555, China
| | - Zhiqiang Han
- Fishery College, Zhejiang Ocean University, Zhoushan, 316022, China
| | - Tianyan Yang
- Fishery College, Zhejiang Ocean University, Zhoushan, 316022, China
| | - Tianxiang Gao
- Fishery College, Zhejiang Ocean University, Zhoushan, 316022, China
| | - Na Song
- Fishery College, Ocean University of China, Qingdao, 266003, China.
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20
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de Obeso Fernández Del Valle A, Gómez-Montalvo J, Maciver SK. Acanthamoeba castellanii exhibits intron retention during encystment. Parasitol Res 2022; 121:2615-2622. [PMID: 35776211 DOI: 10.1007/s00436-022-07578-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2022] [Accepted: 06/14/2022] [Indexed: 11/24/2022]
Abstract
Intron retention (IR) refers to the mechanism of alternative splicing in which an intron is not excised from the mature transcript. IR in the cosmopolitan free-living amoeba Acanthamoeba castellanii has not been studied. We performed an analysis of RNA sequencing data during encystment to identify genes that presented differentially retained introns during this process. We show that IR increases during cyst formation, indicating a potential mechanism of gene regulation that could help downregulate metabolism. We identify 69 introns from 67 genes that are differentially retained comparing the trophozoite stage and encystment after 24 and 48 h. These genes include several hypothetical proteins. We show different patterns of IR during encystment taking as examples a lipase, a peroxin-3 protein, an Fbox domain containing protein, a proteasome subunit, a polynucleotide adenylyltransferase, and a tetratricopeptide domain containing protein. A better understanding of IR in Acanthamoeba, and even other protists, could help elucidate changes in life cycle and combat disease such as Acanthamoeba keratitis in which the cyst is key for its persistence.
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Affiliation(s)
- Alvaro de Obeso Fernández Del Valle
- Departamento de Bioingeniería, Escuela de Ingeniería y Ciencias, Tecnologico de Monterrey, Ave. Eugenio Garza Sada 2501, 64849, Monterrey, Mexico.
| | - Jesús Gómez-Montalvo
- Departamento de Bioingeniería, Escuela de Ingeniería y Ciencias, Tecnologico de Monterrey, Ave. Eugenio Garza Sada 2501, 64849, Monterrey, Mexico
| | - Sutherland K Maciver
- Centre for Discovery Brain Sciences, Edinburgh Medical School, Biomedical Sciences, University of Edinburgh, Hugh Robson Building, George Square, Edinburgh, EH8 9XD, Scotland, UK
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21
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Shao C, Cai F, Zhang Y, Bao Z, Shi G, Bao M, Zhang J. Regulation of alternative splicing of PaFT and PaFDL1, the FT and FD homologs in Platanus acerifolia. Gene 2022; 830:146506. [PMID: 35447236 DOI: 10.1016/j.gene.2022.146506] [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: 01/10/2022] [Revised: 03/16/2022] [Accepted: 04/14/2022] [Indexed: 11/04/2022]
Abstract
Alternative splicing (AS) selects different alternative splice sites and produces a variety of transcripts with different exon/intron combinations, which may result in multiple protein isoforms. The splicing signals include cis-elements and RNA structures; however, the mechanisms of AS regulation in plants have yet to be elucidated. Previous studies have shown that in Platanus acerifolia, the FLOWERING LOCUS T (FT) homolog PaFT has a unique and complex AS pattern, in which most of the splice forms of PaFT involve the first and/or second intron, and the FD homolog PaFDL1 produces two transcripts via AS, whereas the other FT homolog PaFTL is not regulated by AS. In this study, the regulatory mechanism of the AS of PaFT was demonstrated to be conserved in different plant species. To define the distribution of the AS regulatory signals, the intron-swap, site-directed mutagenesis of alternative splice sites, and deletion experiment were performed. For the PaFT gene, all the signals that regulate the AS of the first intron were located within this intron, while the usage of the first alternative splice site in the second intron was determined by the first intron. Meanwhile, the AS of PaFDL1 might be co-regulated by exons and the first intron. Additionally, the first alternative splice site and adjacent region in PaFT intron 1 might contain cis-elements and/or RNA structures that affect the use of the other sites. This study had provided a deeper insight into the distribution of AS signals in plants, namely the AS signals of different splice sites might exist in the intron where the sites were present, and might also be distributed in exons or other introns.
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Affiliation(s)
- Changsheng Shao
- Key Laboratory of Horticultural Plant Biology, Ministry of Education, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan, Hubei 430070, China.
| | - Fangfang Cai
- Key Laboratory of Horticultural Plant Biology, Ministry of Education, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan, Hubei 430070, China; Present address: Plant Genomics & Molecular Improvement of Colored Fiber Laboratory, College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou, Zhejiang 310018, China.
| | - Yanping Zhang
- Key Laboratory of Horticultural Plant Biology, Ministry of Education, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan, Hubei 430070, China.
| | - Zhiru Bao
- Key Laboratory of Horticultural Plant Biology, Ministry of Education, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan, Hubei 430070, China.
| | - Gehui Shi
- Key Laboratory of Horticultural Plant Biology, Ministry of Education, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan, Hubei 430070, China.
| | - Manzhu Bao
- Key Laboratory of Horticultural Plant Biology, Ministry of Education, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan, Hubei 430070, China.
| | - Jiaqi Zhang
- Key Laboratory of Horticultural Plant Biology, Ministry of Education, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan, Hubei 430070, China.
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22
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Rosenkranz RRE, Ullrich S, Löchli K, Simm S, Fragkostefanakis S. Relevance and Regulation of Alternative Splicing in Plant Heat Stress Response: Current Understanding and Future Directions. FRONTIERS IN PLANT SCIENCE 2022; 13:911277. [PMID: 35812973 PMCID: PMC9260394 DOI: 10.3389/fpls.2022.911277] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/02/2022] [Accepted: 05/26/2022] [Indexed: 05/26/2023]
Abstract
Alternative splicing (AS) is a major mechanism for gene expression in eukaryotes, increasing proteome diversity but also regulating transcriptome abundance. High temperatures have a strong impact on the splicing profile of many genes and therefore AS is considered as an integral part of heat stress response. While many studies have established a detailed description of the diversity of the RNAome under heat stress in different plant species and stress regimes, little is known on the underlying mechanisms that control this temperature-sensitive process. AS is mainly regulated by the activity of splicing regulators. Changes in the abundance of these proteins through transcription and AS, post-translational modifications and interactions with exonic and intronic cis-elements and core elements of the spliceosomes modulate the outcome of pre-mRNA splicing. As a major part of pre-mRNAs are spliced co-transcriptionally, the chromatin environment along with the RNA polymerase II elongation play a major role in the regulation of pre-mRNA splicing under heat stress conditions. Despite its importance, our understanding on the regulation of heat stress sensitive AS in plants is scarce. In this review, we summarize the current status of knowledge on the regulation of AS in plants under heat stress conditions. We discuss possible implications of different pathways based on results from non-plant systems to provide a perspective for researchers who aim to elucidate the molecular basis of AS under high temperatures.
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Affiliation(s)
| | - Sarah Ullrich
- Molecular Cell Biology of Plants, Goethe University Frankfurt, Frankfurt, Germany
| | - Karin Löchli
- Molecular Cell Biology of Plants, Goethe University Frankfurt, Frankfurt, Germany
| | - Stefan Simm
- Institute of Bioinformatics, University Medicine Greifswald, Greifswald, Germany
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23
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The Function of DNA Demethylase Gene ROS1a Null Mutant on Seed Development in Rice ( Oryza Sativa) Using the CRISPR/CAS9 System. Int J Mol Sci 2022; 23:ijms23126357. [PMID: 35742811 PMCID: PMC9223687 DOI: 10.3390/ijms23126357] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2022] [Revised: 06/01/2022] [Accepted: 06/04/2022] [Indexed: 02/05/2023] Open
Abstract
The endosperm is the main nutrient source in cereals for humans, as it is a highly specialized storage organ for starch, lipids, and proteins, and plays an essential role in seed growth and development. Active DNA demethylation regulates plant developmental processes and is ensured by cytosine methylation (5-meC) DNA glycosylase enzymes. To find out the role of OsROS1a in seed development, the null mutant of OsROS1a was generated using the CRISPR/Cas9 system. The null mutant of OsROS1a was stable and heritable, which affects the major agronomic traits, particularly in rice seeds. The null mutant of OsROS1a showed longer and narrower grains, and seeds were deformed containing an underdeveloped and less-starch-producing endosperm with slightly irregularly shaped embryos. In contrast to the transparent grains of the wild type, the grains of the null mutant of OsROS1a were slightly opaque and rounded starch granules, with uneven shapes, sizes, and surfaces. A total of 723 differential expression genes (DEGs) were detected in the null mutant of OsROS1a by RNA-Seq, of which 290 were downregulated and 433 were upregulated. The gene ontology (GO) terms with the top 20 enrichment factors were visualized for cellular components, biological processes, and molecular functions. The key genes that are enriched for these GO terms include starch synthesis genes (OsSSIIa and OsSSIIIa) and cellulose synthesis genes (CESA2, CESA3, CESA6, and CESA8). Genes encoding polysaccharides and glutelin were found to be downregulated in the mutant endosperm. The glutelins were further verified by SDS-PAGE, suggesting that glutelin genes could be involved in the null mutant of OsROS1a seed phenotype and OsROS1a could have the key role in the regulation of glutelins. Furthermore, 378 differentially alternative splicing (AS) genes were identified in the null mutant of OsROS1a, suggesting that the OsROS1a gene has an impact on AS events. Our findings indicated that the function on rice endosperm development in the null mutant of OsROS1a could be influenced through regulating gene expression and AS, which could provide the base to properly understand the molecular mechanism related to the OsROS1a gene in the regulation of rice seed development.
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Liu XX, Guo QH, Xu WB, Liu P, Yan K. Rapid Regulation of Alternative Splicing in Response to Environmental Stresses. FRONTIERS IN PLANT SCIENCE 2022; 13:832177. [PMID: 35310672 PMCID: PMC8931528 DOI: 10.3389/fpls.2022.832177] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/09/2021] [Accepted: 01/25/2022] [Indexed: 06/14/2023]
Abstract
Plants overcome the changing environmental conditions through diverse strategies and complex regulations. In addition to direct regulation of gene transcription, alternative splicing (AS) also acts as a crucial regulatory mechanism to cope with various stresses. Generating from the same pre-mRNA, AS events allow rapid adjustment of the abundance and function of key stress-response components. Mounting evidence has indicated the close link between AS and plant stress response. However, the mechanisms on how environmental stresses trigger AS are far from understood. The advancing high-throughput sequencing technologies have been providing useful information, whereas genetic approaches have also yielded remarkable phenotypic evidence for AS control of stress responses. It is important to study how stresses trigger AS events for both fundamental science and applications. We review current understanding of stress-responsive AS in plants and discuss research challenges for the near future, including regulation of splicing factors, epigenetic modifications, the shared targets of splice isoforms, and the stress-adjusting ratios between splicing variants.
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Affiliation(s)
- Xiao-Xiao Liu
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Tai’an, China
| | - Qian-Huan Guo
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Tai’an, China
| | - Wei-Bo Xu
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Tai’an, China
| | - Peng Liu
- Donald Danforth Plant Science Center, St. Louis, MO, United States
| | - Kang Yan
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Tai’an, China
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Ruiz-Gabarre D, Carnero-Espejo A, Ávila J, García-Escudero V. What's in a Gene? The Outstanding Diversity of MAPT. Cells 2022; 11:840. [PMID: 35269461 PMCID: PMC8909800 DOI: 10.3390/cells11050840] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2022] [Revised: 02/25/2022] [Accepted: 02/27/2022] [Indexed: 02/04/2023] Open
Abstract
Tau protein is a microtubule-associated protein encoded by the MAPT gene that carries out a myriad of physiological functions and has been linked to certain pathologies collectively termed tauopathies, including Alzheimer's disease, frontotemporal dementia, Huntington's disease, progressive supranuclear palsy, etc. Alternative splicing is a physiological process by which cells generate several transcripts from one single gene and may in turn give rise to different proteins from the same gene. MAPT transcripts have been proven to be subjected to alternative splicing, generating six main isoforms in the central nervous system. Research throughout the years has demonstrated that the splicing landscape of the MAPT gene is far more complex than that, including at least exon skipping events, the use of 3' and 5' alternative splice sites and, as has been recently discovered, also intron retention. In addition, MAPT alternative splicing has been showed to be regulated spatially and developmentally, further evidencing the complexity of the gene's splicing regulation. It is unclear what would drive the need for the existence of so many isoforms encoded by the same gene, but a wide range of functions have been ascribed to these Tau isoforms, both in physiology and pathology. In this review we offer a comprehensive up-to-date exploration of the mechanisms leading to the outstanding diversity of isoforms expressed from the MAPT gene and the functions in which such isoforms are involved, including their potential role in the onset and development of tauopathies such as Alzheimer's disease.
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Affiliation(s)
- Daniel Ruiz-Gabarre
- Anatomy, Histology and Neuroscience Department, School of Medicine, Universidad Autónoma de Madrid (UAM), 28029 Madrid, Spain; (D.R.-G.); (A.C.-E.)
- Centro de Biología Molecular Severo Ochoa (UAM-CSIC), 28049 Madrid, Spain
- Graduate Program in Neuroscience, Universidad Autónoma de Madrid (UAM), 28029 Madrid, Spain
| | - Almudena Carnero-Espejo
- Anatomy, Histology and Neuroscience Department, School of Medicine, Universidad Autónoma de Madrid (UAM), 28029 Madrid, Spain; (D.R.-G.); (A.C.-E.)
- Graduate Program in Neuroscience, Universidad Autónoma de Madrid (UAM), 28029 Madrid, Spain
| | - Jesús Ávila
- Centro de Biología Molecular Severo Ochoa (UAM-CSIC), 28049 Madrid, Spain
- Networking Research Center on Neurodegenerative Diseases (CIBERNED), Instituto de Salud Carlos III, 28031 Madrid, Spain
| | - Vega García-Escudero
- Anatomy, Histology and Neuroscience Department, School of Medicine, Universidad Autónoma de Madrid (UAM), 28029 Madrid, Spain; (D.R.-G.); (A.C.-E.)
- Centro de Biología Molecular Severo Ochoa (UAM-CSIC), 28049 Madrid, Spain
- Graduate Program in Neuroscience, Universidad Autónoma de Madrid (UAM), 28029 Madrid, Spain
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Meng Y, Ma X, Li J, Ito H, Oracz K, Cai J, Shao C. The novel activity of Argonautes in intron splicing: A transcriptome-wide survey in plants. JOURNAL OF PLANT PHYSIOLOGY 2022; 270:153632. [PMID: 35114616 DOI: 10.1016/j.jplph.2022.153632] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/12/2021] [Revised: 01/24/2022] [Accepted: 01/24/2022] [Indexed: 06/14/2023]
Abstract
The importance of the evolutionarily conserved Argonaute (AGO) proteins has been well recognized for their involvement in the RNA interference pathways. Recent discoveries in animals demonstrated that AGOs also participate in alternative splicing (AS). Motivated by the question whether the AGO proteins are also functional in RNA splicing in plants, we searched for the introns excised through an AGO-dependent manner in Arabidopsis (Arabidopsis thaliana). RNA sequencing (RNA-seq) data analysis uncovered hundreds of the introns up- or down-regulated in the ago1 and ago4 mutants, respectively. For different genes, AGOs might play either a positive or a negative role in intron excision, which was further validated by reverse transcription-polymerase chain reaction (RT-PCR). Some introns were specifically regulated by one of the AGO proteins, while some were regulated by both AGOs. Besides, a large portion of the AGO-dependent introns were organ-specifically regulated. RNA immunoprecipitation combined with high-throughput sequencing (RIP-seq) revealed that both AGOs preferentially bound to the intronic regions, supporting their high intron binding affinities. Immunoprecipitation followed by mass spectrometry (IP-MS) was performed to identify the proteins potentially interacting with the two AGOs. Six novel interactors (two interacting with AGO1 and four with both AGOs) involved in mRNA binding were uncovered, which might facilitate AGO-intron recognition. Analysis of the RNA-seq data from the rice (Oryza sativa) ago18 mutants revealed that hundreds of the introns were expressed in an AGO18-dependent manner. In summary, our results point to the novel role of the plant AGOs in intron splicing, paving a way for further studies on the mechanisms underlying AGO-mediated RNA splicing.
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Affiliation(s)
- Yijun Meng
- College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, 311121, China.
| | - Xiaoxia Ma
- College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, 311121, China; School of Pharmacy, Hangzhou Normal University, Hangzhou, 311121, China
| | - Jie Li
- College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, 311121, China
| | - Hidetaka Ito
- Faculty of Science, Hokkaido University, Sapporo, 060-0810, Japan
| | - Krystyna Oracz
- Department of Plant Physiology, Institute of Biology, Warsaw University of Life Sciences-SGGW, Warsaw, 02-776, Poland
| | - Jiahui Cai
- College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, 311121, China
| | - Chaogang Shao
- College of Life Sciences, Huzhou University, Huzhou, 313000, China
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Luo X, Zhang M, Xu P, Liu G, Wei S. The Intron Retention Variant CsClpP3m Is Involved in Leaf Chlorosis in Some Tea Cultivars. FRONTIERS IN PLANT SCIENCE 2022; 12:804428. [PMID: 35154195 PMCID: PMC8831552 DOI: 10.3389/fpls.2021.804428] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/29/2021] [Accepted: 12/16/2021] [Indexed: 06/14/2023]
Abstract
Tea products made from chlorotic or albino leaves are very popular for their unique flavor. Probing into the molecular mechanisms underlying the chlorotic leaf phenotype is required to better understand the formation of these tea cultivars and aid in future practical breeding. In this study, transcriptional alterations of multiple subunit genes of the caseinolytic protease complex (Clp) in the chlorotic tea cultivar 'Yu-Jin-Xiang' (YJX) were found. Cultivar YJX possessed the intron retention variant of ClpP3, named as CsClpP3m, in addition to the non-mutated ClpP3. The mutated variant results in a truncated protein containing only 166 amino acid residues and lacks the catalytic triad S182-H206-D255. Quantitative analysis of two CsClpP3 variants in different leaves with varying degrees of chlorosis in YJX and analyses of different chlorotic tea cultivars revealed that the transcript ratios of CsClpP3m over CsClpP3 were negatively correlated with leaf chlorophyll contents. The chlorotic young leaf phenotype was also generated in the transgenic tobacco by suppressing ClpP3 using the RNAi method; complementation with non-mutated CsClpP3 rescued the wild-type phenotype, whereas CsClpP3m failed to complement. Taken together, CsClpP3m is involved in leaf chlorosis in YJX and some other tea cultivars in a dose-dependent manner, likely resulting from the failure of Clp complex assembly due to the truncated sequence of CsClpP3m. Our data shed light on the mechanisms controlling leaf chlorosis in tea plants.
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Affiliation(s)
- Xueyin Luo
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei, China
| | - Mengxian Zhang
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei, China
| | - Pei Xu
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei, China
| | - Guofeng Liu
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei, China
- Henan Provincial Key Laboratory of Tea Plant Biology, Xinyang Normal University, Xinyang, China
| | - Shu Wei
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei, China
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Abstract
BACKGROUND: Alternative splicing is a mechanism to produce different proteins with diverse functions from one gene. Many splicing factors play an important role in cancer progression. PRPF8 is a core protein component of the spliceosome complex, U4/U6-U5 tri-snRNP. OBJECTIVE: However, PRPF8 involved in mRNA alternative splicing are rarely included in the prognosis. METHODS: We found that PRPF8 was expressed in all examined cancer types. Further analyses found that PRPF8 expression was significantly different between the breast cancer and paracancerous tissues. RESULTS: Survival analyses showed that PRPF8-high patients had a poor prognosis, and the expression of PRPF8 is associated with distant metastasis-free survival (DMFS) and post progression survival (PPS). Gene Set Enrichment Analysis (GSEA) has revealed that PRPF8 expression is correlated with TGF-β, JAK-STAT, and cell cycle control pathways. Consistent with these results, upon PRPF8 silencing, the growth of MCF-7 cells was reduced, the ability of cell clone formation was weakened, and p21 expression was increased. CONCLUSIONS: These results have revealed that PRPF8 is a significant factor for splicing in breast cancer progression.
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Affiliation(s)
- Difei Cao
- Institute of Advanced Technology, Heilongjiang Academy of Sciences, Harbin, Heilongjiang, China
| | - Jiaying Xue
- Institute of Advanced Technology, Heilongjiang Academy of Sciences, Harbin, Heilongjiang, China
| | - Guoqing Huang
- Institute of Advanced Technology, Heilongjiang Academy of Sciences, Harbin, Heilongjiang, China
| | - Jing An
- Institute of Cancer Prevention and Treatment, Heilongjiang Province Academy of Medical Sciences, Harbin, Heilongjiang, China
| | - Weiwei An
- Institute of Cancer Prevention and Treatment, Heilongjiang Province Academy of Medical Sciences, Harbin, Heilongjiang, China
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Pootakham W, Sonthirod C, Naktang C, Kongkachana W, Sangsrakru D, U‐thoomporn S, Maknual C, Meepol W, Promchoo W, Maprasop P, Phormsin N, Tangphatsornruang S. A chromosome‐scale reference genome assembly of yellow mangrove (
Bruguiera parviflora
) reveals a whole genome duplication event associated with the Rhizophoraceae lineage. Mol Ecol Resour 2022; 22:1939-1953. [DOI: 10.1111/1755-0998.13587] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2021] [Revised: 01/06/2022] [Accepted: 01/12/2022] [Indexed: 11/27/2022]
Affiliation(s)
- Wirulda Pootakham
- National Omics Center National Science and Technology Development Agency (NSTDA) Pathum Thani Thailand
| | - Chutima Sonthirod
- National Omics Center National Science and Technology Development Agency (NSTDA) Pathum Thani Thailand
| | - Chaiwat Naktang
- National Omics Center National Science and Technology Development Agency (NSTDA) Pathum Thani Thailand
| | - Wasitthee Kongkachana
- National Omics Center National Science and Technology Development Agency (NSTDA) Pathum Thani Thailand
| | - Duangjai Sangsrakru
- National Omics Center National Science and Technology Development Agency (NSTDA) Pathum Thani Thailand
| | - Sonicha U‐thoomporn
- National Omics Center National Science and Technology Development Agency (NSTDA) Pathum Thani Thailand
| | - Chatree Maknual
- Department of Marine and Coastal Resources 120 The Government Complex, Chaengwatthana Rd. Thung Song Hong, Bangkok 10210 Thailand
| | - Wijarn Meepol
- Department of Marine and Coastal Resources 120 The Government Complex, Chaengwatthana Rd. Thung Song Hong, Bangkok 10210 Thailand
| | - Waratthaya Promchoo
- Department of Marine and Coastal Resources 120 The Government Complex, Chaengwatthana Rd. Thung Song Hong, Bangkok 10210 Thailand
| | - Pasin Maprasop
- Department of Marine and Coastal Resources 120 The Government Complex, Chaengwatthana Rd. Thung Song Hong, Bangkok 10210 Thailand
| | - Nawin Phormsin
- Department of Marine and Coastal Resources 120 The Government Complex, Chaengwatthana Rd. Thung Song Hong, Bangkok 10210 Thailand
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Wang X, Liu X, Hu Z, Bao S, Xia H, Feng B, Ma L, Zhao G, Zhang D, Hu Y. Essentiality for rice fertility and alternative splicing of OsSUT1. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2022; 314:111065. [PMID: 34895534 DOI: 10.1016/j.plantsci.2021.111065] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/21/2020] [Revised: 08/20/2021] [Accepted: 09/17/2021] [Indexed: 06/14/2023]
Abstract
Sucrose-proton symporters play important roles in carbohydrate transport during plant growth and development. Their physiological functions have only been partly characterized and their regulation mechanism is largely unclear. Here we report that the knockout of a sucrose transporter gene, OsSUT1, by CRISPR-Cas9 mediated gene editing resulted in a slightly dwarf size and complete infertility of the gene's homozygous mutants. Observation of caryopsis development revealed that the endosperm of OsSUT1 mutants failed to cellularize and did not show any sign of seed-filling. Consistently, OsSUT1 was identified to express strongly in developing caryopsis of wild-type rice, particularly in the nucellar epidermis and aleurone which are critical for the uptake of nutrients into the endosperm. These results indicate that OsSUT1 is indispensable during the rice reproductive stage particularly for caryopsis development. Interestingly, OsSUT1 possesses at least 6 alternative splicing transcripts, including the 4 transcripts deposited previously and the other two identified by us. The differences among these transcripts primarily lie in their coding region of the 3' end and 3' UTR region. Real-time PCR showed that 4 of the 6 transcripts had different expressional patterns during rice vegetative and reproductive growth stages. Given the versatility of the gene, addressing its alternative splicing mechanism may expand our understanding of SUT's function substantially.
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Affiliation(s)
- Xiaowen Wang
- College of Resources & Environmental Sciences, Nanjing Agricultural University, Nanjing, 210095, China; College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China
| | - Xiuli Liu
- College of Resources & Environmental Sciences, Nanjing Agricultural University, Nanjing, 210095, China; State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Institute of Virology and Biotechnology, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China
| | - Zhi Hu
- College of Resources & Environmental Sciences, Nanjing Agricultural University, Nanjing, 210095, China
| | - Shuhui Bao
- College of Resources & Environmental Sciences, Nanjing Agricultural University, Nanjing, 210095, China
| | - Huihuang Xia
- College of Resources & Environmental Sciences, Nanjing Agricultural University, Nanjing, 210095, China
| | - Bing Feng
- College of Resources & Environmental Sciences, Nanjing Agricultural University, Nanjing, 210095, China
| | - Lai Ma
- College of Resources & Environmental Sciences, Nanjing Agricultural University, Nanjing, 210095, China
| | - Gengmao Zhao
- College of Resources & Environmental Sciences, Nanjing Agricultural University, Nanjing, 210095, China
| | - Dechun Zhang
- Bio-technology Research Center, China Three Gorges University, Yichang, 443002, China
| | - Yibing Hu
- College of Resources & Environmental Sciences, Nanjing Agricultural University, Nanjing, 210095, China.
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Kumari A, Sedehizadeh S, Brook JD, Kozlowski P, Wojciechowska M. Differential fates of introns in gene expression due to global alternative splicing. Hum Genet 2022; 141:31-47. [PMID: 34907472 PMCID: PMC8758631 DOI: 10.1007/s00439-021-02409-6] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2021] [Accepted: 12/02/2021] [Indexed: 02/06/2023]
Abstract
The discovery of introns over four decades ago revealed a new vision of genes and their interrupted arrangement. Throughout the years, it has appeared that introns play essential roles in the regulation of gene expression. Unique processing of excised introns through the formation of lariats suggests a widespread role for these molecules in the structure and function of cells. In addition to rapid destruction, these lariats may linger on in the nucleus or may even be exported to the cytoplasm, where they remain stable circular RNAs (circRNAs). Alternative splicing (AS) is a source of diversity in mature transcripts harboring retained introns (RI-mRNAs). Such RNAs may contain one or more entire retained intron(s) (RIs), but they may also have intron fragments resulting from sequential excision of smaller subfragments via recursive splicing (RS), which is characteristic of long introns. There are many potential fates of RI-mRNAs, including their downregulation via nuclear and cytoplasmic surveillance systems and the generation of new protein isoforms with potentially different functions. Various reports have linked the presence of such unprocessed transcripts in mammals to important roles in normal development and in disease-related conditions. In certain human neurological-neuromuscular disorders, including myotonic dystrophy type 2 (DM2), frontotemporal dementia/amyotrophic lateral sclerosis (FTD/ALS) and Duchenne muscular dystrophy (DMD), peculiar processing of long introns has been identified and is associated with their pathogenic effects. In this review, we discuss different mechanisms involved in the processing of introns during AS and the functions of these large sections of the genome in our biology.
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Affiliation(s)
- Anjani Kumari
- Queen's Medical Centre, School of Life Sciences, University of Nottingham, Nottingham, NG7 2UH, UK
| | - Saam Sedehizadeh
- Queen's Medical Centre, School of Life Sciences, University of Nottingham, Nottingham, NG7 2UH, UK
| | - John David Brook
- Queen's Medical Centre, School of Life Sciences, University of Nottingham, Nottingham, NG7 2UH, UK
| | - Piotr Kozlowski
- Department of Molecular Genetics, Institute of Bioorganic Chemistry, Polish Academy of Sciences, 61-704, Poznan, Poland
| | - Marzena Wojciechowska
- Department of Molecular Genetics, Institute of Bioorganic Chemistry, Polish Academy of Sciences, 61-704, Poznan, Poland.
- Department of Rare Human Diseases, Institute of Bioorganic Chemistry, Polish Academy of Sciences, 61-704, Poznan, Poland.
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Cui Y, Bian J, Guan Y, Xu F, Han X, Deng X, Liu X. Genome-Wide Analysis and Expression Profiles of Ethylene Signal Genes and Apetala2/Ethylene-Responsive Factors in Peanut ( Arachis hypogaea L.). FRONTIERS IN PLANT SCIENCE 2022; 13:828482. [PMID: 35371146 PMCID: PMC8968948 DOI: 10.3389/fpls.2022.828482] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/15/2021] [Accepted: 02/14/2022] [Indexed: 05/05/2023]
Abstract
Peanut is an important oil and economic crop widely cultivated in the world. It has special characteristics such as blooming on the ground but bearing fruits underground. During the peg penetrating into the ground, it is subjected to mechanical stress from the soil at the same time. It has been proved that mechanical stress affects plant growth and development by regulating the ethylene signaling-related genes. In this study, we identified some genes related to ethylene signal of peanut, including 10 ethylene sensors, two constitutive triple responses (CTRs), four ethylene insensitive 2 (EIN2s), four ethylene insensitive 3 (EIN3s), six EIN3-binding F-box proteins (EBFs), and 188 Apetala2/ethylene-responsive factors (AP2/ERFs). One hundred and eighty-eight AP2/ERFs were further divided into four subfamilies, 123 ERFs, 56 AP2s, 6 Related to ABI3/VP1 (RAVs), and three Soloists, of them one hundred and seventy AP2/ERF gene pairs were clustered into segmental duplication events in genome of Arachis hypogaea. A total of 134, 138, 97, and 150 AhAP2/ERF genes formed 210, 195, 166, and 525 orthologous gene pairs with Arachis duranensis, Arachis ipaensis, Arabidopsis thaliana, and Glycine max, respectively. Our transcriptome results showed that two EIN3s (Arahy.J729H0 and Arahy.S7XF8N) and one EBFs (Arahy.G4JMEM) were highly expressed when mechanical stress increased. Among the 188 AhAP2/ERF genes, there were 31 genes with the fragments per kilobase of exon model per million mapped fragments (FPKM) ≥ 100 at least one of the 15 samples of Tifrunner. Among them, three AhAP2/ERFs (Arahy.15RATX, Arahy.FAI7YU, and Arahy.452FBF) were specifically expressed in seeds and five AhAP2/ERFs (Arahy.HGAZ7D, Arahy.ZW7540, Arahy.4XS3FZ, Arahy.QGFJ76, and Arahy.AS0C7C) were highly expressed in the tissues, which responded mechanical stress, suggesting that they might sense mechanical stress. Mechanical stress simulation experiment showed that three AhAP2/ERFs (Arahy.QGFJ76, Arahy.AS0C7C, and Arahy.HGAZ7D) were sensitive to mechanical stress changes and they all had the conservative repressor motif (DLNXXP) in the C-terminus, indicated that they might transmit mechanical stress signals through transcriptional inhibition. This study reveals the regulatory landscape of ethylene signal-related genes in peanut, providing valuable information for the mining of target genes for further study.
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Affiliation(s)
- Yuanyuan Cui
- Institute of Advanced Agricultural Science, Peking University, Weifang, China
- School of Advanced Agricultural Sciences, Peking University, Beijing, China
| | - Jianxin Bian
- Institute of Advanced Agricultural Science, Peking University, Weifang, China
| | - Yu Guan
- Institute of Advanced Agricultural Science, Peking University, Weifang, China
| | - Fangtao Xu
- Institute of Advanced Agricultural Science, Peking University, Weifang, China
| | - Xue Han
- Institute of Advanced Agricultural Science, Peking University, Weifang, China
- School of Advanced Agricultural Sciences, Peking University, Beijing, China
| | - Xingwang Deng
- Institute of Advanced Agricultural Science, Peking University, Weifang, China
- School of Advanced Agricultural Sciences, Peking University, Beijing, China
- *Correspondence: Xingwang Deng,
| | - Xiaoqin Liu
- Institute of Advanced Agricultural Science, Peking University, Weifang, China
- Xiaoqin Liu,
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33
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Genome-Scale Computational Identification and Characterization of UTR Introns in Atalantia buxifolia. HORTICULTURAE 2021. [DOI: 10.3390/horticulturae7120556] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Accumulated evidence has shown that CDS introns (CIs) play important roles in regulating gene expression. However, research on UTR introns (UIs) is limited. In this study, UIs (including 5′UTR and 3′UTR introns (5UIs and 3UIs)) were identified from the Atalantia buxifolia genome. The length and nucleotide distribution characteristics of both 5UIs and 3UIs and the distributions of cis-acting elements and transcription factor binding sites (TFBSs) in 5UIs were investigated. Moreover, PageMan enrichment analysis was applied to show the possible roles of transcripts containing UIs (UI-Ts). In total, 1077 5UIs and 866 3UIs were identified from 897 5UI-Ts and 670 3UI-Ts, respectively. Among them, 765 (85.28%) 5UI-Ts and 527 (78.66%) 3UI-Ts contained only one UI, and 94 (6.38%) UI-Ts contained both 5UI and 3UI. The UI density was lower than that of CDS introns, but their mean and median intron sizes were ~2 times those of the CDS introns. The A. buxifolia 5UIs were rich in gene-expression-enhancement-related elements and contained many TFBSs for BBR-BPC, MIKC_MADS, AP2 and Dof TFs, indicating that 5UIs play a role in regulating or enhancing the expression of downstream genes. Enrichment analysis revealed that UI-Ts involved in ‘not assigned’ and ‘RNA’ pathways were significantly enriched. Noteworthily, 119 (85.61%) of the 3UI-Ts were genes encoding pentatricopeptide (PPR) repeat-containing proteins. These results will be helpful for the future study of the regulatory roles of UIs in A. buxifolia.
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Ding X, Zhang T, Ma L. Rapidly evolving genetic features for desert adaptations in Stipagrostis pennata. BMC Genomics 2021; 22:846. [PMID: 34814836 PMCID: PMC8609760 DOI: 10.1186/s12864-021-08124-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2021] [Accepted: 10/26/2021] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Stipagrostis pennata is distributed in the mobile and semi-mobile sand dunes which can adapt well to extreme environments such as drought and high temperature. It is a pioneer plant species with potential for stabilizing sand dunes and ecological restoration. It can settle on moving sand dunes earlier than other desert plants. It can effectively improve the stability of sand dunes and help more plants settle down and increase plant diversity. However, despite its important ecological value, the genetic resources available for this species are limited. RESULTS We used single-molecule real-time sequencing technology to obtain the complete full-length transcriptome of Stipagrostis pennata, including 90,204 unigenes with an average length of 2624 bp. In addition, the 5436 transcription factors identified in these unigenes are rich in stress resistance genes, such as MYB-related, C3H, bHLH, GRAS and HSF, etc., which may play a role in adapting to desert drought and strong wind stress. Intron retention events are abundant alternative splicing events. Stipagrostis pennata has experienced stronger positive selection, accelerating the fixation of advantageous variants. Thirty-eight genes, such as CPP/TSO1-like gene, have evolved rapidly and may play a role in material transportation, flowering and seed formation. CONCLUSIONS The present study captures the complete full-length transcriptome of Stipagrostis pennata and reveals its rapid evolution. The desert adaptation in Stipagrostis pennata is reflected in the regulation of gene expression and the adaptability of gene function. Our findings provide a wealth of knowledge for the evolutionary adaptability of desert grass species.
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Affiliation(s)
- Xixu Ding
- College of Life Sciences, Shihezi University, Shihezi City, Xinjiang, China
| | - Tingting Zhang
- College of Life Sciences, Shihezi University, Shihezi City, Xinjiang, China.
| | - Lei Ma
- College of Life Sciences, Shihezi University, Shihezi City, Xinjiang, China.
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Zhao X, Tan L, Wang S, Shen Y, Guo L, Ye X, Liu S, Feng Y, Wu W. The SR Splicing Factors: Providing Perspectives on Their Evolution, Expression, Alternative Splicing, and Function in Populus trichocarpa. Int J Mol Sci 2021; 22:ijms222111369. [PMID: 34768799 PMCID: PMC8583155 DOI: 10.3390/ijms222111369] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2021] [Revised: 10/15/2021] [Accepted: 10/18/2021] [Indexed: 12/11/2022] Open
Abstract
Serine/arginine-rich (SR) proteins are important splicing factors in plant development and abiotic/hormone-related stresses. However, evidence that SR proteins contribute to the process in woody plants has been lacking. Using phylogenetics, gene synteny, transgenic experiments, and RNA-seq analysis, we identified 24 PtSR genes and explored their evolution, expression, and function in Popolus trichocarpa. The PtSR genes were divided into six subfamilies, generated by at least two events of genome triplication and duplication. Notably, they were constitutively expressed in roots, stems, and leaves, demonstrating their fundamental role in P. trichocarpa. Additionally, most PtSR genes (~83%) responded to at least one stress (cold, drought, salt, SA, MeJA, or ABA), and, especially, cold stress induced a dramatic perturbation in the expression and/or alternative splicing (AS) of 18 PtSR genes (~75%). Evidentially, the overexpression of PtSCL30 in Arabidopsis decreased freezing tolerance, which probably resulted from AS changes of the genes (e.g., ICE2 and COR15A) critical for cold tolerance. Moreover, the transgenic plants were salt-hypersensitive at the germination stage. These indicate that PtSCL30 may act as a negative regulator under cold and salt stress. Altogether, this study sheds light on the evolution, expression, and AS of PtSR genes, and the functional mechanisms of PtSCL30 in woody plants.
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Affiliation(s)
- Xijuan Zhao
- State Key Laboratory of Subtropical Silviculture, School of Forestry and Biotechnology, Zhejiang Agriculture and Forestry University, Hangzhou 311300, China; (X.Z.); (L.T.); (S.W.); (Y.S.); (L.G.); (S.L.)
| | - Lingling Tan
- State Key Laboratory of Subtropical Silviculture, School of Forestry and Biotechnology, Zhejiang Agriculture and Forestry University, Hangzhou 311300, China; (X.Z.); (L.T.); (S.W.); (Y.S.); (L.G.); (S.L.)
| | - Shuo Wang
- State Key Laboratory of Subtropical Silviculture, School of Forestry and Biotechnology, Zhejiang Agriculture and Forestry University, Hangzhou 311300, China; (X.Z.); (L.T.); (S.W.); (Y.S.); (L.G.); (S.L.)
| | - Yirong Shen
- State Key Laboratory of Subtropical Silviculture, School of Forestry and Biotechnology, Zhejiang Agriculture and Forestry University, Hangzhou 311300, China; (X.Z.); (L.T.); (S.W.); (Y.S.); (L.G.); (S.L.)
| | - Liangyu Guo
- State Key Laboratory of Subtropical Silviculture, School of Forestry and Biotechnology, Zhejiang Agriculture and Forestry University, Hangzhou 311300, China; (X.Z.); (L.T.); (S.W.); (Y.S.); (L.G.); (S.L.)
| | - Xiaoxue Ye
- Institute of Tropical Biosciences and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China;
| | - Shenkui Liu
- State Key Laboratory of Subtropical Silviculture, School of Forestry and Biotechnology, Zhejiang Agriculture and Forestry University, Hangzhou 311300, China; (X.Z.); (L.T.); (S.W.); (Y.S.); (L.G.); (S.L.)
| | - Ying Feng
- State Key Laboratory of Subtropical Silviculture, School of Forestry and Biotechnology, Zhejiang Agriculture and Forestry University, Hangzhou 311300, China; (X.Z.); (L.T.); (S.W.); (Y.S.); (L.G.); (S.L.)
- Key Laboratory of Nutrition, Metabolism and Food Safety, Shanghai Institute of Nutrition and Health (SINH), Chinese Academy of Sciences (CAS), Shanghai 200032, China
- Correspondence: (Y.F.); (W.W.)
| | - Wenwu Wu
- State Key Laboratory of Subtropical Silviculture, School of Forestry and Biotechnology, Zhejiang Agriculture and Forestry University, Hangzhou 311300, China; (X.Z.); (L.T.); (S.W.); (Y.S.); (L.G.); (S.L.)
- Correspondence: (Y.F.); (W.W.)
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Gao P, Quilichini TD, Zhai C, Qin L, Nilsen KT, Li Q, Sharpe AG, Kochian LV, Zou J, Reddy AS, Wei Y, Pozniak C, Patterson N, Gillmor CS, Datla R, Xiang D. Alternative splicing dynamics and evolutionary divergence during embryogenesis in wheat species. PLANT BIOTECHNOLOGY JOURNAL 2021; 19:1624-1643. [PMID: 33706417 PMCID: PMC8384600 DOI: 10.1111/pbi.13579] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/15/2020] [Revised: 02/25/2021] [Accepted: 03/08/2021] [Indexed: 05/07/2023]
Abstract
Among polyploid species with complex genomic architecture, variations in the regulation of alternative splicing (AS) provide opportunities for transcriptional and proteomic plasticity and the potential for generating trait diversities. However, the evolution of AS and its influence on grain development in diploid grass and valuable polyploid wheat crops are poorly understood. To address this knowledge gap, we developed a pipeline for the analysis of alternatively spliced transcript isoforms, which takes the high sequence similarity among polyploid wheat subgenomes into account. Through analysis of synteny and detection of collinearity of homoeologous subgenomes, conserved and specific AS events across five wheat and grass species were identified. A global analysis of the regulation of AS in diploid grass and polyploid wheat grains revealed diversity in AS events not only between the endosperm, pericarp and embryo overdevelopment, but also between subgenomes. Analysis of AS in homoeologous triads of polyploid wheats revealed evolutionary divergence between gene-level and transcript-level regulation of embryogenesis. Evolutionary age analysis indicated that the generation of novel transcript isoforms has occurred in young genes at a more rapid rate than in ancient genes. These findings, together with the development of comprehensive AS resources for wheat and grass species, advance understanding of the evolution of regulatory features of AS during embryogenesis and grain development in wheat.
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Affiliation(s)
- Peng Gao
- Global Institute for Food SecurityUniversity of SaskatchewanSaskatoonSKCanada
| | - Teagen D. Quilichini
- Aquatic and Crop Resource DevelopmentNational Research Council CanadaSaskatoonSKCanada
| | - Chun Zhai
- Agriculture and Agri‐Food CanadaSaskatoon Research and Development CentreSaskatoonSKCanada
| | - Li Qin
- College of Art & ScienceUniversity of SaskatchewanSaskatoonSKCanada
| | - Kirby T. Nilsen
- Agriculture and Agri‐Food CanadaBrandon Research and Development CentreBrandonMBCanada
| | - Qiang Li
- National Key Laboratory of Crop Genetic ImprovementHuazhong Agricultural UniversityWuhanChina
| | - Andrew G. Sharpe
- Global Institute for Food SecurityUniversity of SaskatchewanSaskatoonSKCanada
| | - Leon V. Kochian
- Global Institute for Food SecurityUniversity of SaskatchewanSaskatoonSKCanada
| | - Jitao Zou
- Aquatic and Crop Resource DevelopmentNational Research Council CanadaSaskatoonSKCanada
| | - Anireddy S.N. Reddy
- Department of Biology and Program in Cell and Molecular BiologyColorado State UniversityFort CollinsCOUSA
| | - Yangdou Wei
- College of Art & ScienceUniversity of SaskatchewanSaskatoonSKCanada
| | - Curtis Pozniak
- Crop Development CentreUniversity of SaskatchewanSaskatoonSKCanada
| | - Nii Patterson
- Aquatic and Crop Resource DevelopmentNational Research Council CanadaSaskatoonSKCanada
| | - C. Stewart Gillmor
- Laboratorio Nacional de Genómica para la Biodiversidad (Langebio)Unidad de Genómica AvanzadaCentro de Investigación y Estudios Avanzados del IPN (CINVESTAV‐IPN)IrapuatoGuanajuatoMexico
| | - Raju Datla
- Global Institute for Food SecurityUniversity of SaskatchewanSaskatoonSKCanada
| | - Daoquan Xiang
- Aquatic and Crop Resource DevelopmentNational Research Council CanadaSaskatoonSKCanada
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Nayar S, Thangavel G. CsubMADS1, a lag phase transcription factor, controls development of polar eukaryotic microalga Coccomyxa subellipsoidea C-169. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2021; 107:1228-1242. [PMID: 34160095 DOI: 10.1111/tpj.15380] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/10/2021] [Revised: 05/30/2021] [Accepted: 06/19/2021] [Indexed: 06/13/2023]
Abstract
MADS-box transcription factors (TFs) have not been functionally delineated in microalgae. In this study, the role of CsubMADS1 from microalga Coccomyxa subellipsoidea C-169 has been explored. Unlike Type II MADS-box proteins of seed plants with MADS, Intervening, K-box, and C domains, CsubMADS1 only has MADS and Intervening domains. It forms a group with MADS TFs from algae in the phylogenetic tree within the Type II MIKCC clade. CsubMADS1 is expressed strongly in the lag phase of growth. The CsubMADS1 monomer does not have a specific localization in the nucleus, and it forms homodimers to localize exclusively in the nucleus. The monomer has two nuclear localization signals (NLSs): an N-terminal NLS and an internal NLS. The internal NLS is functional, and the homodimer requires two NLSs for specific nuclear localization. Overexpression (OX) of CsubMADS1 slows down the growth of the culture and leads to the creation of giant polyploid multinucleate cells, resembling autospore mother cells. This implies that the release of autospores from autospore mother cells may be delayed. Thus, in wild-type (WT) cells, CsubMADS1 may play a crucial role in slowing down growth during the lag phase. Due to starvation in 2-month-old colonies on solid media, the WT colonies produce mucilage, whereas OX colonies produce significantly less mucilage. Thus, CsubMADS1 also negatively regulates stress-induced mucilage production and probably plays a role in stress tolerance during the lag phase. Taken together, our results reveal that CsubMADS1 is a key TF involved in the development and stress tolerance of this polar microalga.
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Affiliation(s)
- Saraswati Nayar
- Division of Plant Molecular Biology, Rajiv Gandhi Centre for Biotechnology, Thiruvananthapuram, 695014, India
| | - Gokilavani Thangavel
- Division of Plant Molecular Biology, Rajiv Gandhi Centre for Biotechnology, Thiruvananthapuram, 695014, India
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Provart NJ, Brady SM, Parry G, Schmitz RJ, Queitsch C, Bonetta D, Waese J, Schneeberger K, Loraine AE. Anno genominis XX: 20 years of Arabidopsis genomics. THE PLANT CELL 2021; 33:832-845. [PMID: 33793861 PMCID: PMC8226293 DOI: 10.1093/plcell/koaa038] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/21/2020] [Accepted: 12/09/2020] [Indexed: 05/04/2023]
Abstract
Twenty years ago, the Arabidopsis thaliana genome sequence was published. This was an important moment as it was the first sequenced plant genome and explicitly brought plant science into the genomics era. At the time, this was not only an outstanding technological achievement, but it was characterized by a superb global collaboration. The Arabidopsis genome was the seed for plant genomic research. Here, we review the development of numerous resources based on the genome that have enabled discoveries across plant species, which has enhanced our understanding of how plants function and interact with their environments.
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Affiliation(s)
- Nicholas J Provart
- Department of Cell & Systems Biology/Centre for the Analysis of Genome Evolution and Function, University of Toronto, Toronto, Ontario, M5S 3B2, Canada
| | - Siobhan M Brady
- Department of Plant Biology and Genome Center, University of California, Davis, California, 95616, USA
| | - Geraint Parry
- GARNet, School of Biosciences, Cardiff University, Cardiff, CF10 3AX, UK
| | - Robert J Schmitz
- Department of Genetics, University of Georgia, Georgia, 30602, USA
| | - Christine Queitsch
- Department of Genome Sciences, School of Medicine, University of Washington, Seattle, Washington, 98195, USA
- Brotman Baty Institute for Precision Medicine, Seattle, Washington, 98195, USA
| | - Dario Bonetta
- Faculty of Science, Ontario Tech University, Oshawa, Ontario, L1G 0C5, Canada
| | - Jamie Waese
- Department of Cell & Systems Biology/Centre for the Analysis of Genome Evolution and Function, University of Toronto, Toronto, Ontario, M5S 3B2, Canada
| | - Korbinian Schneeberger
- Department of Chromosome Biology, Max Planck Institute for Plant Breeding Research, D-50829, Cologne, Germany
- Faculty of Biology, LMU Munich, 82152 Munich, Germany
| | - Ann E Loraine
- Department of Bioinformatics and Genomics, University of North Carolina at Charlotte, Charlotte, NC, 28223, USA
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Dent CI, Singh S, Mukherjee S, Mishra S, Sarwade RD, Shamaya N, Loo KP, Harrison P, Sureshkumar S, Powell D, Balasubramanian S. Quantifying splice-site usage: a simple yet powerful approach to analyze splicing. NAR Genom Bioinform 2021; 3:lqab041. [PMID: 34017946 PMCID: PMC8121094 DOI: 10.1093/nargab/lqab041] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2020] [Revised: 03/24/2021] [Accepted: 04/28/2021] [Indexed: 02/07/2023] Open
Abstract
RNA splicing, and variations in this process referred to as alternative splicing, are critical aspects of gene regulation in eukaryotes. From environmental responses in plants to being a primary link between genetic variation and disease in humans, splicing differences confer extensive phenotypic changes across diverse organisms (1–3). Regulation of splicing occurs through differential selection of splice sites in a splicing reaction, which results in variation in the abundance of isoforms and/or splicing events. However, genomic determinants that influence splice-site selection remain largely unknown. While traditional approaches for analyzing splicing rely on quantifying variant transcripts (i.e. isoforms) or splicing events (i.e. intron retention, exon skipping etc.) (4), recent approaches focus on analyzing complex/mutually exclusive splicing patterns (5–8). However, none of these approaches explicitly measure individual splice-site usage, which can provide valuable information about splice-site choice and its regulation. Here, we present a simple approach to quantify the empirical usage of individual splice sites reflecting their strength, which determines their selection in a splicing reaction. Splice-site strength/usage, as a quantitative phenotype, allows us to directly link genetic variation with usage of individual splice-sites. We demonstrate the power of this approach in defining the genomic determinants of splice-site choice through GWAS. Our pilot analysis with more than a thousand splice sites hints that sequence divergence in cis rather than trans is associated with variations in splicing among accessions of Arabidopsis thaliana. This approach allows deciphering principles of splicing and has broad implications from agriculture to medicine.
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Affiliation(s)
- Craig I Dent
- School of Biological Sciences, Monash University, VIC 3800, Australia
| | - Shilpi Singh
- School of Biological Sciences, Monash University, VIC 3800, Australia
| | | | - Shikhar Mishra
- School of Biological Sciences, Monash University, VIC 3800, Australia
| | - Rucha D Sarwade
- School of Biological Sciences, Monash University, VIC 3800, Australia
| | - Nawar Shamaya
- School of Biological Sciences, Monash University, VIC 3800, Australia
| | - Kok Ping Loo
- School of Biological Sciences, Monash University, VIC 3800, Australia
| | - Paul Harrison
- Monash Bioinformatics Platform, Monash University, VIC 3800, Australia
| | | | - David Powell
- Monash Bioinformatics Platform, Monash University, VIC 3800, Australia
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Mahadani P, Hazra A. Expression and splicing dynamics of WRKY family genes along physiological exigencies of tea plant (Camellia sinensis). Biologia (Bratisl) 2021. [DOI: 10.1007/s11756-021-00784-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
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Yu H, Du Q, Campbell M, Yu B, Walia H, Zhang C. Genome-wide discovery of natural variation in pre-mRNA splicing and prioritising causal alternative splicing to salt stress response in rice. THE NEW PHYTOLOGIST 2021; 230:1273-1287. [PMID: 33453070 PMCID: PMC8048671 DOI: 10.1111/nph.17189] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/13/2020] [Accepted: 01/04/2021] [Indexed: 05/14/2023]
Abstract
Pre-mRNA splicing is an essential step for the regulation of gene expression. In order to specifically capture splicing variants in plants for genome-wide association studies (GWAS), we developed a software tool to quantify and visualise Variations of Splicing in Population (VaSP). VaSP can quantify splicing variants from short-read RNA-seq datasets and discover genotype-specific splicing (GSS) events, which can be used to prioritise causal pre-mRNA splicing events in GWAS. We applied our method to an RNA-seq dataset with 328 samples from 82 genotypes from a rice diversity panel exposed to optimal and saline growing conditions. In total, 764 significant GSS events were identified in salt stress conditions. GSS events were used as markers for a GWAS with the shoot Na+ accumulation, which identified six GSS events in five genes significantly associated with the shoot Na+ content. Two of these genes, OsNUC1 and OsRAD23 emerged as top candidate genes with splice variants that exhibited significant divergence between the variants for shoot growth under salt stress conditions. VaSP is a versatile tool for alternative splicing analysis in plants and a powerful tool for prioritising candidate causal pre-mRNA splicing and corresponding genomic variations in GWAS.
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Affiliation(s)
- Huihui Yu
- School of Biological SciencesUniversity of NebraskaLincolnNE68588USA
| | - Qian Du
- School of Biological SciencesUniversity of NebraskaLincolnNE68588USA
| | - Malachy Campbell
- Department of Agronomy and HorticultureUniversity of NebraskaLincolnNE68583USA
- Department of Plant BiologyCornell UniversityIthacaNY14850USA
| | - Bin Yu
- School of Biological SciencesUniversity of NebraskaLincolnNE68588USA
- Center for Plant Science and InnovationUniversity of NebraskaLincolnNE68588USA
| | - Harkamal Walia
- Department of Agronomy and HorticultureUniversity of NebraskaLincolnNE68583USA
- Center for Plant Science and InnovationUniversity of NebraskaLincolnNE68588USA
| | - Chi Zhang
- School of Biological SciencesUniversity of NebraskaLincolnNE68588USA
- Center for Plant Science and InnovationUniversity of NebraskaLincolnNE68588USA
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Ganie SA, Reddy ASN. Stress-Induced Changes in Alternative Splicing Landscape in Rice: Functional Significance of Splice Isoforms in Stress Tolerance. BIOLOGY 2021; 10:309. [PMID: 33917813 PMCID: PMC8068108 DOI: 10.3390/biology10040309] [Citation(s) in RCA: 35] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/07/2021] [Revised: 04/01/2021] [Accepted: 04/06/2021] [Indexed: 12/20/2022]
Abstract
Improvements in yield and quality of rice are crucial for global food security. However, global rice production is substantially hindered by various biotic and abiotic stresses. Making further improvements in rice yield is a major challenge to the rice research community, which can be accomplished through developing abiotic stress-resilient rice varieties and engineering durable agrochemical-independent pathogen resistance in high-yielding elite rice varieties. This, in turn, needs increased understanding of the mechanisms by which stresses affect rice growth and development. Alternative splicing (AS), a post-transcriptional gene regulatory mechanism, allows rapid changes in the transcriptome and can generate novel regulatory mechanisms to confer plasticity to plant growth and development. Mounting evidence indicates that AS has a prominent role in regulating rice growth and development under stress conditions. Several regulatory and structural genes and splicing factors of rice undergo different types of stress-induced AS events, and the functional significance of some of them in stress tolerance has been defined. Both rice and its pathogens use this complex regulatory mechanism to devise strategies against each other. This review covers the current understanding and evidence for the involvement of AS in biotic and abiotic stress-responsive genes, and its relevance to rice growth and development. Furthermore, we discuss implications of AS for the virulence of different rice pathogens and highlight the areas of further research and potential future avenues to develop climate-smart and disease-resistant rice varieties.
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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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Tang Y, Abdelrahman M, Li J, Wang F, Ji Z, Qi H, Wang C, Zhao K. CRISPR/Cas9 induces exon skipping that facilitates development of fragrant rice. PLANT BIOTECHNOLOGY JOURNAL 2021; 19:642-644. [PMID: 33217139 PMCID: PMC8051596 DOI: 10.1111/pbi.13514] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/09/2020] [Revised: 10/24/2020] [Accepted: 11/11/2020] [Indexed: 05/07/2023]
Affiliation(s)
- Yongchao Tang
- National Key Facility for Crop Gene Resources and Genetic ImprovementInstitute of Crop SciencesChinese Academy of Agricultural SciencesBeijingChina
| | - Mohamed Abdelrahman
- National Key Facility for Crop Gene Resources and Genetic ImprovementInstitute of Crop SciencesChinese Academy of Agricultural SciencesBeijingChina
- Rice Research and Training CenterField Crop Research InstituteAgricultural Research CenterKafrelsheikhEgypt
| | - Jinbo Li
- Food Crop Research InstituteHubei Academy of Agriculture SciencesWuhanChina
| | - Fujun Wang
- National Key Facility for Crop Gene Resources and Genetic ImprovementInstitute of Crop SciencesChinese Academy of Agricultural SciencesBeijingChina
- Institute of Rice ResearchGuangdong Academy of Agricultural SciencesGuangzhouChina
| | - Zhiyuan Ji
- National Key Facility for Crop Gene Resources and Genetic ImprovementInstitute of Crop SciencesChinese Academy of Agricultural SciencesBeijingChina
| | - Huaxiong Qi
- Food Crop Research InstituteHubei Academy of Agriculture SciencesWuhanChina
| | - Chunlian Wang
- National Key Facility for Crop Gene Resources and Genetic ImprovementInstitute of Crop SciencesChinese Academy of Agricultural SciencesBeijingChina
| | - Kaijun Zhao
- National Key Facility for Crop Gene Resources and Genetic ImprovementInstitute of Crop SciencesChinese Academy of Agricultural SciencesBeijingChina
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Yu X, Yu K, Chen B, Liao Z, Qin Z, Yao Q, Huang Y, Liang J, Huang W. Nanopore long-read RNAseq reveals regulatory mechanisms of thermally variable reef environments promoting heat tolerance of scleractinian coral Pocillopora damicornis. ENVIRONMENTAL RESEARCH 2021; 195:110782. [PMID: 33503412 DOI: 10.1016/j.envres.2021.110782] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/16/2020] [Revised: 01/15/2021] [Accepted: 01/19/2021] [Indexed: 06/12/2023]
Abstract
Some scleractinian corals exhibit high thermal adaptability to climate changes, although the mechanism of their adaptation is unclear. This study investigated the adaptability of scleractinian coral Pocillopora damicornis to thermally variable reef environments by applying a nanopore-based RNA sequencing method to characterize different transcription responses that promote heat tolerance of P. damicornis. We identified 1414 novel genes and optimized 6256 mis-annotated loci. Based on full-length transcriptome data, we identified complex alternative polyadenylation and alternative splicing events, which can improve our understanding of the genome annotation and gene structures of P. damicornis. Furthermore, we constructed differentially expressed lncRNA-mRNA co-expression networks, which may play a crucial role in the P. damicornis thermal adaptive response. KEGG function enrichment analysis revealed that P. damicornis from the high-temperature pool had a lower metabolic rate than that from the low-temperature pool. We hypothesize that metabolic readjustment, in the form of a lower metabolic rate, positively correlated with increased heat tolerance in P. damicornis in thermally variable reef environments. Our study provides novel insights into lncRNAs that promote thermally tolerance of scleractinian corals in the thermally variable reef environment, suggesting potential mechanisms for their adaptation to global warming in the future.
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Affiliation(s)
- Xiaopeng Yu
- Guangxi Laboratory on the Study of Coral Reefs in the South China Sea, Coral Reef Research Center of China, School of Marine Sciences, Guangxi University, Nanning, China
| | - Kefu Yu
- Guangxi Laboratory on the Study of Coral Reefs in the South China Sea, Coral Reef Research Center of China, School of Marine Sciences, Guangxi University, Nanning, China; Southern Marine Science and Engineering Guangdong Laboratory, Zhuhai, China.
| | - Biao Chen
- Guangxi Laboratory on the Study of Coral Reefs in the South China Sea, Coral Reef Research Center of China, School of Marine Sciences, Guangxi University, Nanning, China
| | - Zhiheng Liao
- Guangxi Laboratory on the Study of Coral Reefs in the South China Sea, Coral Reef Research Center of China, School of Marine Sciences, Guangxi University, Nanning, China
| | - Zhenjun Qin
- Guangxi Laboratory on the Study of Coral Reefs in the South China Sea, Coral Reef Research Center of China, School of Marine Sciences, Guangxi University, Nanning, China
| | - Qiucui Yao
- Guangxi Laboratory on the Study of Coral Reefs in the South China Sea, Coral Reef Research Center of China, School of Marine Sciences, Guangxi University, Nanning, China
| | - Yanhua Huang
- Guangxi Laboratory on the Study of Coral Reefs in the South China Sea, Coral Reef Research Center of China, School of Marine Sciences, Guangxi University, Nanning, China
| | - Jiayuan Liang
- Guangxi Laboratory on the Study of Coral Reefs in the South China Sea, Coral Reef Research Center of China, School of Marine Sciences, Guangxi University, Nanning, China
| | - Wen Huang
- Guangxi Laboratory on the Study of Coral Reefs in the South China Sea, Coral Reef Research Center of China, School of Marine Sciences, Guangxi University, Nanning, China
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Combined Transcriptome Analysis Reveals the Ovule Abortion Regulatory Mechanisms in the Female Sterile Line of Pinus tabuliformis Carr. Int J Mol Sci 2021; 22:ijms22063138. [PMID: 33808669 PMCID: PMC8003466 DOI: 10.3390/ijms22063138] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2020] [Revised: 03/16/2021] [Accepted: 03/16/2021] [Indexed: 11/17/2022] Open
Abstract
Ovule abortion is a common phenomenon in plants that has an impact on seed production. Previous studies of ovule and female gametophyte (FG) development have mainly focused on angiosperms, especially in Arabidopsis thaliana. However, because it is difficult to acquire information about ovule development in gymnosperms, this remains unclear. Here, we investigated the transcriptomic data of natural ovule abortion mutants (female sterile line, STE) and the wild type (female fertile line, FER) of Pinus tabuliformis Carr. to evaluate the mechanism of ovule abortion during the process of free nuclear mitosis (FNM). Using single-molecule real-time (SMRT) sequencing and next-generation sequencing (NGS), 18 cDNA libraries via Illumina and two normalized libraries via PacBio, with a total of almost 400,000 reads, were obtained. Our analysis showed that the numbers of isoforms and alternative splicing (AS) patterns were significantly variable between FER and STE. The functional annotation results demonstrate that genes involved in the auxin response, energy metabolism, signal transduction, cell division, and stress response were differentially expressed in different lines. In particular, AUX/IAA, ARF2, SUS, and CYCB had significantly lower expression in STE, showing that auxin might be insufficient in STE, thus hindering nuclear division and influencing metabolism. Apoptosis in STE might also have affected the expression levels of these genes. To confirm the transcriptomic analysis results, nine pairs were confirmed by quantitative real-time PCR. Taken together, these results provide new insights into ovule abortion in gymnosperms and further reveal the regulatory mechanisms of ovule development.
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Li X, Xiang F, Zhang W, Yan J, Li X, Zhong M, Yang P, Chen C, Liu X, Mao D, Zhao X. Characterization and fine mapping of a new dwarf mutant in Brassica napus. BMC PLANT BIOLOGY 2021; 21:117. [PMID: 33637037 PMCID: PMC7908660 DOI: 10.1186/s12870-021-02885-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/06/2020] [Accepted: 02/10/2021] [Indexed: 06/12/2023]
Abstract
BACKGROUND Plant height is an important plant characteristic closely related to yield performance of many crops. Reasonable reduction of plant height of crops is beneficial for improving yield and enhancing lodging resistance. RESULTS In the present study, we described the Brassica napus dwarf mutant bnd2 that was isolated using ethyl methanesulfonate (EMS) mutagenesis. Compared to wild type (WT), bnd2 exhibited reduced height and shorter hypocotyl and petiole leaves. By crossing the bnd2 mutant with the WT strain, we found that the ratio of the mutant to the WT in the F2 population was close to 1:3, indicating that bnd2 is a recessive mutation of a single locus. Following bulked segregant analysis (BSA) by resequencing, BND2 was found to be located in the 13.77-18.08 Mb interval of chromosome A08, with a length of 4.31 Mb. After fine mapping with single nucleotide polymorphism (SNP) and insertion/deletion (InDel) markers, the gene was narrowed to a 140-Kb interval ranging from 15.62 Mb to 15.76 Mb. According to reference genome annotation, there were 27 genes in the interval, of which BnaA08g20960D had an SNP type variation in the intron between the mutant and its parent, which may be the candidate gene corresponding to BND2. The hybrid line derived from a cross between the mutant bnd2 and the commercial cultivar L329 had similar plant height but higher grain yield compared to the commercial cultivar, suggesting that the allele bnd2 is beneficial for hybrid breeding of lodging resistant and high yield rapeseed. CONCLUSION In this study, we identified a novel dwarf mutant of rapeseed with a new locus, which may be useful for functional analyses of genetic mechanisms of plant architecture and grain yield in rapeseed.
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Affiliation(s)
- Xin Li
- College of Biology, Hunan Hybrid Rape Engineering and Technology Research Center, Hunan University, Changsha, 410082, China
- Shenzhen Institute, Hunan University, Shenzhen, 518057, China
- Key Laboratory of Agro-Ecological Processes in Subtropical Region, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Changsha, 410125, China
| | - Fujiang Xiang
- College of Biology, Hunan Hybrid Rape Engineering and Technology Research Center, Hunan University, Changsha, 410082, China
- Shenzhen Institute, Hunan University, Shenzhen, 518057, China
| | - Wei Zhang
- College of Agronnomy, Hunan Agricultural University, Changsha, 410128, China
| | - Jindong Yan
- College of Biology, Hunan Hybrid Rape Engineering and Technology Research Center, Hunan University, Changsha, 410082, China
- Shenzhen Institute, Hunan University, Shenzhen, 518057, China
| | - Xinmei Li
- College of Biology, Hunan Hybrid Rape Engineering and Technology Research Center, Hunan University, Changsha, 410082, China
- Shenzhen Institute, Hunan University, Shenzhen, 518057, China
| | - Ming Zhong
- College of Biology, Hunan Hybrid Rape Engineering and Technology Research Center, Hunan University, Changsha, 410082, China
- Shenzhen Institute, Hunan University, Shenzhen, 518057, China
| | - Piao Yang
- College of Biology, Hunan Hybrid Rape Engineering and Technology Research Center, Hunan University, Changsha, 410082, China
- Shenzhen Institute, Hunan University, Shenzhen, 518057, China
| | - Caiyan Chen
- Key Laboratory of Agro-Ecological Processes in Subtropical Region, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Changsha, 410125, China
| | - Xuanming Liu
- College of Biology, Hunan Hybrid Rape Engineering and Technology Research Center, Hunan University, Changsha, 410082, China
| | - Donghai Mao
- Key Laboratory of Agro-Ecological Processes in Subtropical Region, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Changsha, 410125, China.
| | - Xiaoying Zhao
- College of Biology, Hunan Hybrid Rape Engineering and Technology Research Center, Hunan University, Changsha, 410082, China.
- Shenzhen Institute, Hunan University, Shenzhen, 518057, China.
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Cucinotta M, Cavalleri A, Guazzotti A, Astori C, Manrique S, Bombarely A, Oliveto S, Biffo S, Weijers D, Kater MM, Colombo L. Alternative Splicing Generates a MONOPTEROS Isoform Required for Ovule Development. Curr Biol 2021; 31:892-899.e3. [PMID: 33275890 DOI: 10.1016/j.cub.2020.11.026] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2019] [Revised: 11/06/2020] [Accepted: 11/11/2020] [Indexed: 10/22/2022]
Abstract
The plant hormone auxin is a fundamental regulator of organ patterning and development that regulates gene expression via the canonical AUXIN RESPONSE FACTOR (ARF) and AUXIN/INDOLE-3-ACETIC ACID (Aux/IAA) combinatorial system. ARF and Aux/IAA factors interact, but at high auxin concentrations, the Aux/IAA transcriptional repressor is degraded, allowing ARF-containing complexes to activate gene expression. ARF5/MONOPTEROS (MP) is an important integrator of auxin signaling in Arabidopsis development and activates gene transcription in cells with elevated auxin levels. Here, we show that in ovules, MP is expressed in cells with low levels of auxin and can activate the expression of direct target genes. We identified and characterized a splice variant of MP that encodes a biologically functional isoform that lacks the Aux/IAA interaction domain. This MP11ir isoform was able to complement inflorescence, floral, and ovule developmental defects in mp mutants, suggesting that it was fully functional. Our findings describe a novel scenario in which ARF post-transcriptional regulation controls the formation of an isoform that can function as a transcriptional activator in regions of subthreshold auxin concentration.
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Affiliation(s)
- Mara Cucinotta
- Dipartimento di BioScienze, Università degli Studi di Milano, Via Celoria 26, 20133 Milano, Italy
| | - Alex Cavalleri
- Dipartimento di BioScienze, Università degli Studi di Milano, Via Celoria 26, 20133 Milano, Italy
| | - Andrea Guazzotti
- Dipartimento di BioScienze, Università degli Studi di Milano, Via Celoria 26, 20133 Milano, Italy
| | - Chiara Astori
- Dipartimento di BioScienze, Università degli Studi di Milano, Via Celoria 26, 20133 Milano, Italy
| | - Silvia Manrique
- Dipartimento di BioScienze, Università degli Studi di Milano, Via Celoria 26, 20133 Milano, Italy
| | - Aureliano Bombarely
- Dipartimento di BioScienze, Università degli Studi di Milano, Via Celoria 26, 20133 Milano, Italy
| | - Stefania Oliveto
- Dipartimento di BioScienze, Università degli Studi di Milano, Via Celoria 26, 20133 Milano, Italy; INGM, National Institute of Molecular Genetics "Romeo ed Enrica Invernizzi," 20122 Milano, Italy
| | - Stefano Biffo
- Dipartimento di BioScienze, Università degli Studi di Milano, Via Celoria 26, 20133 Milano, Italy; INGM, National Institute of Molecular Genetics "Romeo ed Enrica Invernizzi," 20122 Milano, Italy
| | - Dolf Weijers
- Laboratory of Biochemistry, Wageningen University, Dreijenlaan 3, 6703 HA Wageningen, the Netherlands
| | - Martin M Kater
- Dipartimento di BioScienze, Università degli Studi di Milano, Via Celoria 26, 20133 Milano, Italy
| | - Lucia Colombo
- Dipartimento di BioScienze, Università degli Studi di Milano, Via Celoria 26, 20133 Milano, Italy.
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Martín G, Márquez Y, Mantica F, Duque P, Irimia M. Alternative splicing landscapes in Arabidopsis thaliana across tissues and stress conditions highlight major functional differences with animals. Genome Biol 2021; 22:35. [PMID: 33446251 PMCID: PMC7807721 DOI: 10.1186/s13059-020-02258-y] [Citation(s) in RCA: 77] [Impact Index Per Article: 25.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2020] [Accepted: 12/22/2020] [Indexed: 12/15/2022] Open
Abstract
BACKGROUND Alternative splicing (AS) is a widespread regulatory mechanism in multicellular organisms. Numerous transcriptomic and single-gene studies in plants have investigated AS in response to specific conditions, especially environmental stress, unveiling substantial amounts of intron retention that modulate gene expression. However, a comprehensive study contrasting stress-response and tissue-specific AS patterns and directly comparing them with those of animal models is still missing. RESULTS We generate a massive resource for Arabidopsis thaliana, PastDB, comprising AS and gene expression quantifications across tissues, development and environmental conditions, including abiotic and biotic stresses. Harmonized analysis of these datasets reveals that A. thaliana shows high levels of AS, similar to fruitflies, and that, compared to animals, disproportionately uses AS for stress responses. We identify core sets of genes regulated specifically by either AS or transcription upon stresses or among tissues, a regulatory specialization that is tightly mirrored by the genomic features of these genes. Unexpectedly, non-intron retention events, including exon skipping, are overrepresented across regulated AS sets in A. thaliana, being also largely involved in modulating gene expression through NMD and uORF inclusion. CONCLUSIONS Non-intron retention events have likely been functionally underrated in plants. AS constitutes a distinct regulatory layer controlling gene expression upon internal and external stimuli whose target genes and master regulators are hardwired at the genomic level to specifically undergo post-transcriptional regulation. Given the higher relevance of AS in the response to different stresses when compared to animals, this molecular hardwiring is likely required for a proper environmental response in A. thaliana.
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Affiliation(s)
- Guiomar Martín
- Instituto Gulbenkian de Ciência, Rua da Quinta Grande, 6, 2780-156, Oeiras, Portugal.
| | - Yamile Márquez
- Centre for Genomic Regulation, Barcelona Institute of Science and Technology, Dr. Aiguader, 88, Barcelona, 08003, Spain
| | - Federica Mantica
- Centre for Genomic Regulation, Barcelona Institute of Science and Technology, Dr. Aiguader, 88, Barcelona, 08003, Spain
| | - Paula Duque
- Instituto Gulbenkian de Ciência, Rua da Quinta Grande, 6, 2780-156, Oeiras, Portugal
| | - Manuel Irimia
- Centre for Genomic Regulation, Barcelona Institute of Science and Technology, Dr. Aiguader, 88, Barcelona, 08003, Spain. .,Universitat Pompeu Fabra, Dr. Aiguader, 88, Barcelona, 08003, Spain. .,ICREA, Passeig de Lluís Companys, 23, 08010, Barcelona, Spain.
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Rosenkranz RRE, Bachiri S, Vraggalas S, Keller M, Simm S, Schleiff E, Fragkostefanakis S. Identification and Regulation of Tomato Serine/Arginine-Rich Proteins Under High Temperatures. FRONTIERS IN PLANT SCIENCE 2021; 12:645689. [PMID: 33854522 PMCID: PMC8039515 DOI: 10.3389/fpls.2021.645689] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/23/2020] [Accepted: 03/03/2021] [Indexed: 05/15/2023]
Abstract
Alternative splicing is an important mechanism for the regulation of gene expression in eukaryotes during development, cell differentiation or stress response. Alterations in the splicing profiles of genes under high temperatures that cause heat stress (HS) can impact the maintenance of cellular homeostasis and thermotolerance. Consequently, information on factors involved in HS-sensitive alternative splicing is required to formulate the principles of HS response. Serine/arginine-rich (SR) proteins have a central role in alternative splicing. We aimed for the identification and characterization of SR-coding genes in tomato (Solanum lycopersicum), a plant extensively used in HS studies. We identified 17 canonical SR and two SR-like genes. Several SR-coding genes show differential expression and altered splicing profiles in different organs as well as in response to HS. The transcriptional induction of five SR and one SR-like genes is partially dependent on the master regulator of HS response, HS transcription factor HsfA1a. Cis-elements in the promoters of these SR genes were predicted, which can be putatively recognized by HS-induced transcription factors. Further, transiently expressed SRs show reduced or steady-state protein levels in response to HS. Thus, the levels of SRs under HS are regulated by changes in transcription, alternative splicing and protein stability. We propose that the accumulation or reduction of SRs under HS can impact temperature-sensitive alternative splicing.
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Affiliation(s)
- Remus R. E. Rosenkranz
- Department of Biosciences, Molecular Cell Biology of Plants, Goethe University, Frankfurt am Main, Germany
| | - Samia Bachiri
- Department of Biosciences, Molecular Cell Biology of Plants, Goethe University, Frankfurt am Main, Germany
| | - Stavros Vraggalas
- Department of Biosciences, Molecular Cell Biology of Plants, Goethe University, Frankfurt am Main, Germany
| | - Mario Keller
- Department of Biosciences, Molecular Cell Biology of Plants, Goethe University, Frankfurt am Main, Germany
- Buchmann Institute for Molecular Life Sciences, Goethe University, Frankfurt am Main, Germany
| | - Stefan Simm
- Institute of Bioinformatics, University Medicine Greifswald, Greifswald, Germany
| | - Enrico Schleiff
- Department of Biosciences, Molecular Cell Biology of Plants, Goethe University, Frankfurt am Main, Germany
- Buchmann Institute for Molecular Life Sciences, Goethe University, Frankfurt am Main, Germany
- Frankfurt Institute of Advanced Studies, Frankfurt am Main, Germany
- *Correspondence: Enrico Schleiff
| | - Sotirios Fragkostefanakis
- Department of Biosciences, Molecular Cell Biology of Plants, Goethe University, Frankfurt am Main, Germany
- Sotirios Fragkostefanakis
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50
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Schmitz U, Monteuuis G, Petrova V, Shah JS, Rasko JE. Computational Methods for Intron Retention Identification and Quantification. SYSTEMS MEDICINE 2021. [DOI: 10.1016/b978-0-12-801238-3.11567-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022] Open
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