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Hou Y, Li Q, Zhou H, Kafle S, Li W, Tan L, Liang J, Meng L, Xin H. SMRT sequencing of a full-length transcriptome reveals cold induced alternative splicing in Vitis amurensis root. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2024; 213:108863. [PMID: 38917739 DOI: 10.1016/j.plaphy.2024.108863] [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: 03/02/2024] [Revised: 05/31/2024] [Accepted: 06/19/2024] [Indexed: 06/27/2024]
Abstract
Alternative splicing enhances diversity at the transcriptional and protein levels that widely involved in plant response to biotic and abiotic stresses. V. amurensis is an extremely cold-tolerant wild grape variety, however, studies on alternative splicing (AS) in amur grape at low temperatures are currently poorly understood. In this study, we analyzed full-length transcriptome and RNA seq data at 0, 2, and 24 h after cold stress in V. amurensis roots. Following quality control and correction, 221,170 high-quality full-length non-concatemer (FLNC) reads were identified. A total of 16,181 loci and 30,733 isoforms were identified. These included 22,868 novel isoforms from annotated genes and 2815 isoforms from 2389 novel genes. Among the distinguished novel isoforms, 673 Long non-coding RNAs (LncRNAs) and 18,164 novel isoforms open reading frame (ORF) region were found. A total of 2958 genes produced 8797 AS events, of which 189 genes were involved in the low-temperature response. Twelve transcription factors show AS during cold treatment and VaMYB108 was selected for initial exploration. Two transcripts, Chr05.63.1 (VaMYB108short) and Chr05.63.2 (VaMYB108normal) of VaMYB108, display up-regulated expression after cold treatment in amur grape roots and are both localized in the nucleus. Only VaMYB108normal exhibits transcriptional activation activity. Overexpression of either VaMYB108short or VaMYB108normal in grape roots leads to increased expression of the other transcript and both increased chilling resistance of amur grape roots. The results improve and supplement the genome annotations and provide insights for further investigation into AS mechanisms during cold stress in V. amurensis.
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Affiliation(s)
- Yujun Hou
- State Key Laboratory of Plant Diversity and Specialty Crops, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, 430074, China; University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Qingyun Li
- State Key Laboratory of Plant Diversity and Specialty Crops, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, 430074, China; University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Huimin Zhou
- State Key Laboratory of Plant Diversity and Specialty Crops, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, 430074, China; University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Subash Kafle
- State Key Laboratory of Plant Diversity and Specialty Crops, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, 430074, China; University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Wenjuan Li
- State Key Laboratory of Plant Diversity and Specialty Crops, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, 430074, China; University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Lisha Tan
- State Key Laboratory of Plant Diversity and Specialty Crops, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, 430074, China
| | - Ju Liang
- Turpan Institute of Agricultural Sciences, Xinjiang Academy of Agricultural Sciences, Xinjiang, 830091, China
| | - Lin Meng
- State Key Laboratory of Plant Diversity and Specialty Crops, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, 430074, China
| | - Haiping Xin
- State Key Laboratory of Plant Diversity and Specialty Crops, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, 430074, China; Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, 430074, China.
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Punzo P, Suede Cigliano R, Aversano R, Grillo S, Batelli G. Determination of Differential Alternative Splicing Under Stress Conditions. Methods Mol Biol 2024; 2832:67-79. [PMID: 38869788 DOI: 10.1007/978-1-0716-3973-3_5] [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] [Indexed: 06/14/2024]
Abstract
Alternative splicing (AS) is an important mechanism contributing to stress-induced regulation of gene expression and proteome diversity. Massive sequencing technologies allow the identification of transcripts generated via stress-responsive AS, potentially important for adaptation to stress conditions. Several bioinformatics tools have been developed to identify differentially expressed alternative splicing events/transcripts from RNA-sequencing results. This chapter describes a detailed protocol for differential alternative splicing analysis using the rMATS tool. In addition, we provide guidelines for validation of the detected splice variants by qRT-PCR based on the obtained output files.
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Affiliation(s)
- Paola Punzo
- CNR Institute of Biosciences and Bioresources, Research Division Portici, Portici, Italy
- Department of Agricultural Sciences, University of Naples "Federico II", Portici, Italy
| | | | - Riccardo Aversano
- Department of Agricultural Sciences, University of Naples "Federico II", Portici, Italy
| | - Stefania Grillo
- CNR Institute of Biosciences and Bioresources, Research Division Portici, Portici, Italy
| | - Giorgia Batelli
- CNR Institute of Biosciences and Bioresources, Research Division Portici, Portici, Italy.
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Larran AS, Pajoro A, Qüesta JI. Is winter coming? Impact of the changing climate on plant responses to cold temperature. PLANT, CELL & ENVIRONMENT 2023; 46:3175-3193. [PMID: 37438895 DOI: 10.1111/pce.14669] [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: 05/03/2023] [Revised: 06/23/2023] [Accepted: 07/03/2023] [Indexed: 07/14/2023]
Abstract
Climate change is causing alterations in annual temperature regimes worldwide. Important aspects of this include the reduction of winter chilling temperatures as well as the occurrence of unpredicted frosts, both significantly affecting plant growth and yields. Recent studies advanced the knowledge of the mechanisms underlying cold responses and tolerance in the model plant Arabidopsis thaliana. However, how these cold-responsive pathways will readjust to ongoing seasonal temperature variation caused by global warming remains an open question. In this review, we highlight the plant developmental programmes that depend on cold temperature. We focus on the molecular mechanisms that plants have evolved to adjust their development and stress responses upon exposure to cold. Covering both genetic and epigenetic aspects, we present the latest insights into how alternative splicing, noncoding RNAs and the formation of biomolecular condensates play key roles in the regulation of cold responses. We conclude by commenting on attractive targets to accelerate the breeding of increased cold tolerance, bringing up biotechnological tools that might assist in overcoming current limitations. Our aim is to guide the reflection on the current agricultural challenges imposed by a changing climate and to provide useful information for improving plant resilience to unpredictable cold regimes.
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Affiliation(s)
- Alvaro Santiago Larran
- Centre for Research in Agricultural Genomics (CRAG) IRTA-CSIC-UAB-UB, Campus UAB, Barcelona, Spain
| | - Alice Pajoro
- National Research Council, Institute of Molecular Biology and Pathology, Rome, Italy
| | - Julia I Qüesta
- Centre for Research in Agricultural Genomics (CRAG) IRTA-CSIC-UAB-UB, Campus UAB, Barcelona, Spain
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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: 0] [Impact Index Per Article: 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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Wang L, Xu F, Yu F. Two environmental signal-driven RNA metabolic processes: Alternative splicing and translation. PLANT, CELL & ENVIRONMENT 2023; 46:718-732. [PMID: 36609800 DOI: 10.1111/pce.14537] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/18/2022] [Revised: 12/29/2022] [Accepted: 01/06/2023] [Indexed: 06/17/2023]
Abstract
Plants live in fixed locations and have evolved adaptation mechanisms that integrate multiple responses to various environmental signals. Among the different components of these response pathways, receptors/sensors represent nodes that recognise environmental signals. Additionally, RNA metabolism plays an essential role in the regulation of gene expression and protein synthesis. With the development of RNA biotechnology, recent advances have been made in determining the roles of RNA metabolism in response to different environmental signals-especially the roles of alternative splicing and translation. In this review, we discuss recent progress in research on how the environmental adaptation mechanisms in plants are affected at the posttranscriptional level. These findings improve our understanding of the mechanism through which plants adapt to environmental changes by regulating the posttranscriptional level and are conducive for breeding stress-tolerant plants to cope with dynamic and rapidly changing environments.
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Affiliation(s)
- Long Wang
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Biology, Hunan Key Laboratory of Plant Functional Genomics and Developmental Regulation, Hunan University, Changsha, China
| | - Fan Xu
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Biology, Hunan Key Laboratory of Plant Functional Genomics and Developmental Regulation, Hunan University, Changsha, China
| | - Feng Yu
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Biology, Hunan Key Laboratory of Plant Functional Genomics and Developmental Regulation, Hunan University, Changsha, China
- State Key Laboratory of Hybrid Rice, Hunan Hybrid Rice Research Center, Changsha, China
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6
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Sahoo DK, Hegde C, Bhattacharyya MK. Identification of multiple novel genetic mechanisms that regulate chilling tolerance in Arabidopsis. FRONTIERS IN PLANT SCIENCE 2023; 13:1094462. [PMID: 36714785 PMCID: PMC9878698 DOI: 10.3389/fpls.2022.1094462] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/10/2022] [Accepted: 12/28/2022] [Indexed: 06/18/2023]
Abstract
INTRODUCTION Cold stress adversely affects the growth and development of plants and limits the geographical distribution of many plant species. Accumulation of spontaneous mutations shapes the adaptation of plant species to diverse climatic conditions. METHODS The genome-wide association study of the phenotypic variation gathered by a newly designed phenomic platform with the over six millions single nucleotide polymorphic (SNP) loci distributed across the genomes of 417 Arabidopsis natural variants collected from various geographical regions revealed 33 candidate cold responsive genes. RESULTS Investigation of at least two independent insertion mutants for 29 genes identified 16 chilling tolerance genes governing diverse genetic mechanisms. Five of these genes encode novel leucine-rich repeat domain-containing proteins including three nucleotide-binding site-leucine-rich repeat (NBS-LRR) proteins. Among the 16 identified chilling tolerance genes, ADS2 and ACD6 are the only two chilling tolerance genes identified earlier. DISCUSSION The 12.5% overlap between the genes identified in this genome-wide association study (GWAS) of natural variants with those discovered previously through forward and reverse genetic approaches suggests that chilling tolerance is a complex physiological process governed by a large number of genetic mechanisms.
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Affiliation(s)
- Dipak Kumar Sahoo
- Department of Agronomy, Iowa State University, Ames, IA, United States
| | - Chinmay Hegde
- Department of Electrical and Computer Engineering, Iowa State University, Ames, IA, United States
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Rodriguez Gallo MC, Li Q, Mehta D, Uhrig RG. Genome-scale analysis of Arabidopsis splicing-related protein kinase families reveals roles in abiotic stress adaptation. BMC PLANT BIOLOGY 2022; 22:496. [PMID: 36273172 PMCID: PMC9587599 DOI: 10.1186/s12870-022-03870-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/25/2022] [Accepted: 10/04/2022] [Indexed: 05/24/2023]
Abstract
Nearly 60 - 80 % of intron-containing plant genes undergo alternative splicing in response to either stress or plant developmental cues. RNA splicing is performed by a large ribonucleoprotein complex called the spliceosome in conjunction with associated subunits such as serine arginine (SR) proteins, all of which undergo extensive phosphorylation. In plants, there are three main protein kinase families suggested to phosphorylate core spliceosome subunits and related splicing factors based on orthology to human splicing-related kinases: the SERINE/ARGININE PROTEIN KINASES (SRPK), ARABIDOPSIS FUS3 COMPLEMENT (AFC), and Pre-mRNA PROCESSING FACTOR 4 (PRP4K) protein kinases. To better define the conservation and role(s) of these kinases in plants, we performed a genome-scale analysis of the three families across photosynthetic eukaryotes, followed by extensive transcriptomic and bioinformatic analysis of all Arabidopsis thaliana SRPK, AFC, and PRP4K protein kinases to elucidate their biological functions. Unexpectedly, this revealed the existence of SRPK and AFC phylogenetic groups with distinct promoter elements and patterns of transcriptional response to abiotic stress, while PRP4Ks possess no phylogenetic sub-divisions, suggestive of functional redundancy. We also reveal splicing-related kinase families are both diel and photoperiod regulated, implicating different orthologs as discrete time-of-day RNA splicing regulators. This foundational work establishes a number of new hypotheses regarding how reversible spliceosome phosphorylation contributes to both diel plant cell regulation and abiotic stress adaptation in plants.
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Affiliation(s)
- M C Rodriguez Gallo
- Department of Biological Sciences, University of Alberta, Edmonton, AB, T6G 2E9, Canada
| | - Q Li
- Department of Biological Sciences, University of Alberta, Edmonton, AB, T6G 2E9, Canada
| | - D Mehta
- Department of Biological Sciences, University of Alberta, Edmonton, AB, T6G 2E9, Canada
| | - R G Uhrig
- Department of Biological Sciences, University of Alberta, Edmonton, AB, T6G 2E9, Canada.
- Department of Biochemistry, University of Alberta, Edmonton, AB, Canada.
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OsTBP2.1, a TATA-Binding Protein, Alters the Ratio of OsNRT2.3b to OsNRT2.3a and Improves Rice Grain Yield. Int J Mol Sci 2022; 23:ijms231810795. [PMID: 36142708 PMCID: PMC9503026 DOI: 10.3390/ijms231810795] [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: 07/30/2022] [Revised: 09/06/2022] [Accepted: 09/08/2022] [Indexed: 11/30/2022] Open
Abstract
The OsNRT2.3a and OsNRT2.3b isoforms play important roles in the uptake and transport of nitrate during rice growth. However, it is unclear which cis-acting element controls the transcription of OsNRT2.3 into these specific isoforms. In this study, we used a yeast one-hybrid assay to obtain the TATA-box binding protein OsTBP2.1, which binds to the TATA-box of OsNRT2.3, and verified its important role through transient expression and RNA-seq. We found that the TATA-box of OsNRT2.3 mutants and binding protein OsTBP2.1 together increased the transcription ratio of OsNRT2.3b to OsNRT2.3a. The overexpression of OsTBP2.1 promoted nitrogen uptake and increased rice yield compared with the wild-type; however, the OsTBP2.1 T-DNA mutant lines exhibited the opposite trend. Detailed analyses demonstrated that the TATA-box was the key cis-regulatory element for OsNRT2.3 to be transcribed into OsNRT2.3a and OsNRT2.3b. Additionally, this key cis-regulatory element, together with the binding protein OsTBP2.1, promoted the development of rice and increased grain yield.
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9
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Liu Y, Cai Y, Li Y, Zhang X, Shi N, Zhao J, Yang H. Dynamic changes in the transcriptome landscape of Arabidopsis thaliana in response to cold stress. FRONTIERS IN PLANT SCIENCE 2022; 13:983460. [PMID: 36110360 PMCID: PMC9468617 DOI: 10.3389/fpls.2022.983460] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/01/2022] [Accepted: 08/04/2022] [Indexed: 06/15/2023]
Abstract
Plants must reprogram gene expression to adapt constantly changing environmental temperatures. With the increased occurrence of extremely low temperatures, the negative effects on plants, especially on growth and development, from cold stress are becoming more and more serious. In this research, strand-specific RNA sequencing (ssRNA-seq) was used to explore the dynamic changes in the transcriptome landscape of Arabidopsis thaliana exposed to cold temperatures (4°C) at different times. In total, 7,623 differentially expressed genes (DEGs) exhibited dynamic temporal changes during the cold treatments. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis showed that the DEGs were enriched in cold response, secondary metabolic processes, photosynthesis, glucosinolate biosynthesis, and plant hormone signal transduction pathways. Meanwhile, long non-coding RNAs (lncRNAs) were identified after the assembly of the transcripts, from which 247 differentially expressed lncRNAs (DElncRNAs) and their potential target genes were predicted. 3,621 differentially alternatively spliced (DAS) genes related to RNA splicing and spliceosome were identified, indicating enhanced transcriptome complexity due to the alternative splicing (AS) in the cold. In addition, 739 cold-regulated transcription factors (TFs) belonging to 52 gene families were identified as well. This research analyzed the dynamic changes of the transcriptome landscape in response to cold stress, which reveals more complete transcriptional patterns during short- and long-term cold treatment and provides new insights into functional studies of that how plants are affected by cold stress.
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Affiliation(s)
- Yue Liu
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, China
- Hubei Hongshan Laboratory, Wuhan, China
| | - Yajun Cai
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, China
- Hubei Hongshan Laboratory, Wuhan, China
| | - Yanzhuo Li
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, China
- Hubei Hongshan Laboratory, Wuhan, China
| | - Xiaoling Zhang
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, China
- Hubei Hongshan Laboratory, Wuhan, China
| | - Nan Shi
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, China
- Hubei Hongshan Laboratory, Wuhan, China
| | - Jingze Zhao
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, China
- Hubei Hongshan Laboratory, Wuhan, China
| | - Hongchun Yang
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, China
- Hubei Hongshan Laboratory, Wuhan, China
- RNA Institute, Wuhan University, Wuhan, China
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10
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ABA Mediates Plant Development and Abiotic Stress via Alternative Splicing. Int J Mol Sci 2022; 23:ijms23073796. [PMID: 35409156 PMCID: PMC8998868 DOI: 10.3390/ijms23073796] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2022] [Revised: 03/25/2022] [Accepted: 03/27/2022] [Indexed: 02/01/2023] Open
Abstract
Alternative splicing (AS) exists in eukaryotes to increase the complexity and adaptability of systems under biophysiological conditions by increasing transcriptional and protein diversity. As a classic hormone, abscisic acid (ABA) can effectively control plant growth, improve stress resistance, and promote dormancy. At the transcriptional level, ABA helps plants respond to the outside world by regulating transcription factors through signal transduction pathways to regulate gene expression. However, at the post-transcriptional level, the mechanism by which ABA can regulate plant biological processes by mediating alternative splicing is not well understood. Therefore, this paper briefly introduces the mechanism of ABA-induced alternative splicing and the role of ABA mediating AS in plant response to the environment and its own growth.
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11
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Experimental Design for Time-Series RNA-Seq Analysis of Gene Expression and Alternative Splicing. Methods Mol Biol 2021. [PMID: 34674176 DOI: 10.1007/978-1-0716-1912-4_14] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/29/2023]
Abstract
RNA-sequencing (RNA-seq) is currently the method of choice for analysis of differential gene expression. To fully exploit the wealth of data generated from genome-wide transcriptomic approaches, the initial design of the experiment is of paramount importance. Biological rhythms in nature are pervasive and are driven by endogenous gene networks collectively known as circadian clocks. Measuring circadian gene expression requires time-course experiments which take into account time-of-day factors influencing variability in expression levels. We describe here an approach for characterizing diurnal changes in expression and alternative splicing for plants undergoing cooling. The method uses inexpensive everyday laboratory equipment and utilizes an RNA-seq application (3D RNA-seq) that can handle complex experimental designs and requires little or no prior bioinformatics expertise.
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12
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Alternative splicing in plant abiotic stress responses. Biochem Soc Trans 2021; 48:2117-2126. [PMID: 32869832 DOI: 10.1042/bst20200281] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2020] [Revised: 08/05/2020] [Accepted: 08/07/2020] [Indexed: 02/06/2023]
Abstract
Modifications of the cellular proteome pool upon stress allow plants to tolerate environmental changes. Alternative splicing is the most significant mechanism responsible for the production of multiple protein isoforms from a single gene. The spliceosome, a large ribonucleoprotein complex, together with several associated proteins, controls this pre-mRNA processing, adding an additional level of regulation to gene expression. Deep sequencing of transcriptomes revealed that this co- or post-transcriptional mechanism is highly induced by abiotic stress, and concerns vast numbers of stress-related genes. Confirming the importance of splicing in plant stress adaptation, key players of stress signaling have been shown to encode alternative transcripts, whereas mutants lacking splicing factors or associated components show a modified sensitivity and defective responses to abiotic stress. Here, we examine recent literature on alternative splicing and splicing alterations in response to environmental stresses, focusing on its role in stress adaptation and analyzing the future perspectives and directions for research.
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Fuchs A, Riegler S, Ayatollahi Z, Cavallari N, Giono LE, Nimeth BA, Mutanwad KV, Schweighofer A, Lucyshyn D, Barta A, Petrillo E, Kalyna M. Targeting alternative splicing by RNAi: from the differential impact on splice variants to triggering artificial pre-mRNA splicing. Nucleic Acids Res 2021; 49:1133-1151. [PMID: 33406240 PMCID: PMC7826280 DOI: 10.1093/nar/gkaa1260] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2018] [Revised: 12/08/2020] [Accepted: 12/17/2020] [Indexed: 12/25/2022] Open
Abstract
Alternative splicing generates multiple transcript and protein isoforms from a single gene and controls transcript intracellular localization and stability by coupling to mRNA export and nonsense-mediated mRNA decay (NMD). RNA interference (RNAi) is a potent mechanism to modulate gene expression. However, its interactions with alternative splicing are poorly understood. We used artificial microRNAs (amiRNAs, also termed shRNAmiR) to knockdown all splice variants of selected target genes in Arabidopsis thaliana. We found that splice variants, which vary by their protein-coding capacity, subcellular localization and sensitivity to NMD, are affected differentially by an amiRNA, although all of them contain the target site. Particular transcript isoforms escape amiRNA-mediated degradation due to their nuclear localization. The nuclear and NMD-sensitive isoforms mask RNAi action in alternatively spliced genes. Interestingly, Arabidopsis SPL genes, which undergo alternative splicing and are targets of miR156, are regulated in the same manner. Moreover, similar results were obtained in mammalian cells using siRNAs, indicating cross-kingdom conservation of these interactions among RNAi and splicing isoforms. Furthermore, we report that amiRNA can trigger artificial alternative splicing, thus expanding the RNAi functional repertoire. Our findings unveil novel interactions between different post-transcriptional processes in defining transcript fates and regulating gene expression.
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Affiliation(s)
- Armin Fuchs
- Max Perutz Labs, Medical University of Vienna, Vienna 1030, Austria
| | - Stefan Riegler
- Max Perutz Labs, Medical University of Vienna, Vienna 1030, Austria.,Department of Applied Genetics and Cell Biology, University of Natural Resources and Life Sciences Vienna, Vienna 1190, Austria
| | - Zahra Ayatollahi
- Max Perutz Labs, Medical University of Vienna, Vienna 1030, Austria
| | - Nicola Cavallari
- Max Perutz Labs, Medical University of Vienna, Vienna 1030, Austria
| | - Luciana E Giono
- Instituto de Fisiología, Biología Molecular y Neurociencias (IFIBYNE), CONICET-Universidad de Buenos Aires, C1428EHA, Buenos Aires, Argentina
| | - Barbara A Nimeth
- Department of Applied Genetics and Cell Biology, University of Natural Resources and Life Sciences Vienna, Vienna 1190, Austria
| | - Krishna V Mutanwad
- Department of Applied Genetics and Cell Biology, University of Natural Resources and Life Sciences Vienna, Vienna 1190, Austria
| | | | - Doris Lucyshyn
- Department of Applied Genetics and Cell Biology, University of Natural Resources and Life Sciences Vienna, Vienna 1190, Austria
| | - Andrea Barta
- Max Perutz Labs, Medical University of Vienna, Vienna 1030, Austria
| | - Ezequiel Petrillo
- Max Perutz Labs, Medical University of Vienna, Vienna 1030, Austria.,Instituto de Fisiología, Biología Molecular y Neurociencias (IFIBYNE), CONICET-Universidad de Buenos Aires, C1428EHA, Buenos Aires, Argentina
| | - Maria Kalyna
- Department of Applied Genetics and Cell Biology, University of Natural Resources and Life Sciences Vienna, Vienna 1190, Austria
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14
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Chen X, Huang S, Jiang M, Chen Y, XuHan X, Zhang Z, Lin Y, Lai Z. Genome-wide identification and expression analysis of the SR gene family in longan (Dimocarpus longan Lour.). PLoS One 2020; 15:e0238032. [PMID: 32841304 PMCID: PMC7447046 DOI: 10.1371/journal.pone.0238032] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2020] [Accepted: 08/07/2020] [Indexed: 12/05/2022] Open
Abstract
Longan (Dimocarpus longan Lour.) is an important commercial fruit tree in southern China. The embryogenesis of longan affects the quality and yield of fruit. A large number of alternative splicing events occurs during somatic embryogenesis (SE), which is regulated by serine/arginine-rich (SR) proteins. However, the functions of SR proteins in longan are poorly understood. In this study, 21 Dlo-SR gene family members belonging to six subfamilies were identified, among which Dlo-RSZ20a, Dlo-SR30, Dlo-SR17, Dlo-SR53 and Dlo-SR32 were localized in the nucleus, Dlo-RSZ20b, Dlo-RSZ20c, Dlo-RSZ20d, Dlo-SC18, Dlo-RS2Z29, Dlo-SCL41, and Dlo-SR33 were localized in chloroplasts, and Dlo-RS43, Dlo-SC33, Dlo-SC37, Dlo-RS2Z33, Dlo-RS2Z16, Dlo-RS2Z24, Dlo-SCL43, Dlo-SR112, and Dlo-SR59 were localized in the nucleus and chloroplasts. The Dlo-SR genes exhibited differential expression patterns in different tissues of longan. The transcript levels of Dlo-RSZ20a, Dlo-SC18, Dlo-RS2Z29, DLo-SR59, Dlo-SR53, and Dlo-SR17 were low in all analyzed tissues, whereas Dlo-RS43, Dlo-RS2Z16, Dlo-RS2Z24, and Dlo-SR30 were highly expressed in all tissues. To clarify their function during SE, the transcript levels of Dlo-SR genes were analyzed at different four stages of SE, comprising non-embryonic callus (NEC), friable-embryogenic callus (EC), incomplete compact pro-embryogenic culture (ICpEC) and globular embryo (GE). Interestingly, the transcript levels of Dlo-RS2Z29 and Dlo-SR112 were increased in embryogenic cells compared with the NEC stage, whereas transcript levels of Dlo-RSZ20a, Dlo-RS43, Dlo-SC37, and Dlo-RS2Z16 were especially increased at the GE stage compared with the other stages. Alternative splicing events of Dlo-SR mRNA precursors (pre-mRNAs) was detected during SE, with totals of 41, 29, 35, and 44 events detected during NEC, EC, ICpEC, and GE respectively. Protein–protein interaction analysis showed that SR proteins were capable of interaction with each other. The results indicate that the alternative splicing of Dlo-SR pre-mRNAs occurs during SE and that Dlo-SR proteins may interact to regulate embryogenesis of longan.
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Affiliation(s)
- Xiaodong Chen
- Institute of horticultural biotechnology, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Shuqi Huang
- Institute of horticultural biotechnology, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Mengqi Jiang
- Institute of horticultural biotechnology, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Yukun Chen
- Institute of horticultural biotechnology, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Xu XuHan
- Institute of horticultural biotechnology, Fujian Agriculture and Forestry University, Fuzhou, China
- Institute de la Recherche Interdisciplinaire de Toulouse, Toulouse, France
| | - Zihao Zhang
- Institute of horticultural biotechnology, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Yuling Lin
- Institute of horticultural biotechnology, Fujian Agriculture and Forestry University, Fuzhou, China
- * E-mail: (YL); (ZL)
| | - Zhongxiong Lai
- Institute of horticultural biotechnology, Fujian Agriculture and Forestry University, Fuzhou, China
- * E-mail: (YL); (ZL)
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15
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First Come, First Served: Sui Generis Features of the First Intron. PLANTS 2020; 9:plants9070911. [PMID: 32707681 PMCID: PMC7411622 DOI: 10.3390/plants9070911] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/31/2020] [Revised: 07/15/2020] [Accepted: 07/17/2020] [Indexed: 02/07/2023]
Abstract
Most of the transcribed genes in eukaryotic cells are interrupted by intervening sequences called introns that are co-transcriptionally removed from nascent messenger RNA through the process of splicing. In Arabidopsis, 79% of genes contain introns and more than 60% of intron-containing genes undergo alternative splicing (AS), which ostensibly is considered to increase protein diversity as one of the intrinsic mechanisms for fitness to the varying environment or the internal developmental program. In addition, recent findings have prevailed in terms of overlooked intron functions. Here, we review recent progress in the underlying mechanisms of intron function, in particular by focusing on unique features of the first intron that is located in close proximity to the transcription start site. The distinct deposition of epigenetic marks and nucleosome density on the first intronic DNA sequence, the impact of the first intron on determining the transcription start site and elongation of its own expression (called intron-mediated enhancement, IME), translation control in 5′-UTR, and the new mechanism of the trans-acting function of the first intron in regulating gene expression at the post-transcriptional level are summarized.
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16
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Li Y, Mi X, Zhao S, Zhu J, Guo R, Xia X, Liu L, Liu S, Wei C. Comprehensive profiling of alternative splicing landscape during cold acclimation in tea plant. BMC Genomics 2020; 21:65. [PMID: 31959105 PMCID: PMC6971990 DOI: 10.1186/s12864-020-6491-6] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2019] [Accepted: 01/13/2020] [Indexed: 11/11/2022] Open
Abstract
BACKGROUND Alternative splicing (AS) may generate multiple mRNA splicing isoforms from a single mRNA precursor using different splicing sites, leading to enhanced diversity of transcripts and proteins. AS has been implicated in cold acclimation by affecting gene expression in various ways, yet little information is known about how AS influences cold responses in tea plant (Camellia sinensis). RESULTS In this study, the AS transcriptional landscape was characterized in the tea plant genome using high-throughput RNA-seq during cold acclimation. We found that more than 41% (14,103) of genes underwent AS events. We summarize the possible existence of 11 types of AS events, including the four common types of intron retention (IR), exon skipping (ES), alternative 5' splice site (A5SS), and alternative 3' splice site (A3SS); of these, IR was the major type in all samples. The number of AS events increased rapidly during cold treatment, but decreased significantly following de-acclimation (DA). It is notable that the number of differential AS genes gradually increased during cold acclimation, and these genes were enriched in pathways relating to oxidoreductase activity and sugar metabolism during acclimation and de-acclimation. Remarkably, the AS isoforms of bHLH transcription factors showed higher expression levels than their full-length ones during cold acclimation. Interestingly, the expression pattern of some AS transcripts of raffinose and sucrose synthase genes were significantly correlated with sugar contents. CONCLUSION Our findings demonstrated that changes in AS numbers and transcript expression may contribute to rapid changes in gene expression and metabolite profile during cold acclimation, suggesting that AS events play an important regulatory role in response to cold acclimation in tea plant.
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Affiliation(s)
- Yeyun Li
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, West 130 Changjiang Road, Hefei, Anhui, 230036, People's Republic of China
| | - Xiaozeng Mi
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, West 130 Changjiang Road, Hefei, Anhui, 230036, People's Republic of China
| | - Shiqi Zhao
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, West 130 Changjiang Road, Hefei, Anhui, 230036, People's Republic of China
| | - Junyan Zhu
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, West 130 Changjiang Road, Hefei, Anhui, 230036, People's Republic of China
| | - Rui Guo
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, West 130 Changjiang Road, Hefei, Anhui, 230036, People's Republic of China
| | - Xiaobo Xia
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, West 130 Changjiang Road, Hefei, Anhui, 230036, People's Republic of China
| | - Lu Liu
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, West 130 Changjiang Road, Hefei, Anhui, 230036, People's Republic of China
| | - Shengrui Liu
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, West 130 Changjiang Road, Hefei, Anhui, 230036, People's Republic of China.
| | - Chaoling Wei
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, West 130 Changjiang Road, Hefei, Anhui, 230036, People's Republic of China.
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17
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Lu CA, Huang CK, Huang WS, Huang TS, Liu HY, Chen YF. DEAD-Box RNA Helicase 42 Plays a Critical Role in Pre-mRNA Splicing under Cold Stress. PLANT PHYSIOLOGY 2020; 182:255-271. [PMID: 31753844 PMCID: PMC6945872 DOI: 10.1104/pp.19.00832] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/10/2019] [Accepted: 11/13/2019] [Indexed: 05/24/2023]
Abstract
Low temperature is an important environmental stress that adversely affects rice (Oryza sativa) growth and productivity. Splicing of pre-mRNA is a crucial posttranscriptional regulatory step in gene expression in plants and is sensitive to temperature. DEAD-box RNA helicases belong to an RNA helicase family involved in the rearrangement of ribonucleoprotein complexes and the modification of RNA structure and are therefore involved in all aspects of RNA metabolism. In this study, we demonstrate that the rate of pre-mRNA splicing is reduced in rice at low temperatures and that the DEAD-box RNA Helicase42 (OsRH42) is necessary to support effective splicing of pre-mRNA during mRNA maturation at low temperatures. OsRH42 expression is tightly coupled to temperature fluctuation, and OsRH42 is localized in the splicing speckles and interacts directly with U2 small nuclear RNA. Retarded pre-mRNA splicing and plant growth defects were exhibited by OsRH42-knockdown transgenic lines at low temperatures, thus indicating that OsRH42 performs an essential role in ensuring accurate pre-mRNA splicing and normal plant growth under low ambient temperature. Unexpectedly, our results show that OsRH42 overexpression significantly disrupts the pre-mRNA splicing pathway, causing retarded plant growth and reducing plant cold tolerance. Combined, these results indicate that accurate control of OsRH42 homeostasis is essential for rice plants to respond to changes in ambient temperature. In addition, our study presents the molecular mechanism of DEAD-box RNA helicase function in pre-mRNA splicing, which is required for adaptation to cold stress in rice.
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Affiliation(s)
- Chung-An Lu
- Department of Life Sciences, National Central University, Jhongli City, Taoyuan County 320, Taiwan, Republic of China
| | - Chun-Kai Huang
- Department of Life Sciences, National Central University, Jhongli City, Taoyuan County 320, Taiwan, Republic of China
| | - Wen-Shan Huang
- Department of Life Sciences, National Central University, Jhongli City, Taoyuan County 320, Taiwan, Republic of China
| | - Tian-Sheng Huang
- Department of Life Sciences, National Central University, Jhongli City, Taoyuan County 320, Taiwan, Republic of China
| | - Hsin-Yi Liu
- Department of Life Sciences, National Central University, Jhongli City, Taoyuan County 320, Taiwan, Republic of China
| | - Yu-Fu Chen
- Department of Life Sciences, National Central University, Jhongli City, Taoyuan County 320, Taiwan, Republic of China
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18
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Nimeth BA, Riegler S, Kalyna M. Alternative Splicing and DNA Damage Response in Plants. FRONTIERS IN PLANT SCIENCE 2020; 11:91. [PMID: 32140165 PMCID: PMC7042379 DOI: 10.3389/fpls.2020.00091] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/29/2019] [Accepted: 01/21/2020] [Indexed: 05/06/2023]
Abstract
Plants are exposed to a variety of abiotic and biotic stresses that may result in DNA damage. Endogenous processes - such as DNA replication, DNA recombination, respiration, or photosynthesis - are also a threat to DNA integrity. It is therefore essential to understand the strategies plants have developed for DNA damage detection, signaling, and repair. Alternative splicing (AS) is a key post-transcriptional process with a role in regulation of gene expression. Recent studies demonstrate that the majority of intron-containing genes in plants are alternatively spliced, highlighting the importance of AS in plant development and stress response. Not only does AS ensure a versatile proteome and influence the abundance and availability of proteins greatly, it has also emerged as an important player in the DNA damage response (DDR) in animals. Despite extensive studies of DDR carried out in plants, its regulation at the level of AS has not been comprehensively addressed. Here, we provide some insights into the interplay between AS and DDR in plants.
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19
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Li MH, Liu DK, Zhang GQ, Deng H, Tu XD, Wang Y, Lan SR, Liu ZJ. A perspective on crassulacean acid metabolism photosynthesis evolution of orchids on different continents: Dendrobium as a case study. JOURNAL OF EXPERIMENTAL BOTANY 2019; 71:422-434. [PMID: 31625570 DOI: 10.1093/jxb/erz444] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/21/2019] [Accepted: 09/24/2019] [Indexed: 05/24/2023]
Abstract
Members of the Orchidaceae, one of the largest families of flowering plants, evolved the crassulacean acid metabolism (CAM) photosynthesis strategy. It is thought that CAM triggers adaptive radiation into new niche spaces, yet very little is known about its origin and diversification on different continents. Here, we assess the prevalence of CAM in Dendrobium, which is one of the largest genera of flowering plants and found in a wide range of environments, from the high altitudes of the Himalayas to relatively arid habitats in Australia. Based on phylogenetic time trees, we estimated that CAM, as determined by δ 13C values less negative than -20.0‰, evolved independently at least eight times in Dendrobium. The oldest lineage appeared in the Asian clade during the middle Miocene, indicating the origin of CAM was associated with a pronounced climatic cooling that followed a period of aridity. Divergence of the four CAM lineages in the Asian clade appeared to be earlier than divergence of those in the Australasian clade. However, CAM species in the Asian clade are much less diverse (25.6%) than those in the Australasian clade (57.9%). These findings shed new light on CAM evolutionary history and the aridity levels of the paleoclimate on different continents.
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Affiliation(s)
- Ming-He Li
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization at College of Landscape Architecture, Fujian Agriculture and Forestry University, Fuzhou, China
- Fujian Colleges and Universities Engineering Research Institute of Conservation and Utilization of Natural Bioresources, College of Forestry, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Ding-Kun Liu
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization at College of Landscape Architecture, Fujian Agriculture and Forestry University, Fuzhou, China
- Fujian Colleges and Universities Engineering Research Institute of Conservation and Utilization of Natural Bioresources, College of Forestry, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Guo-Qiang Zhang
- Shenzhen Key Laboratory for Orchid Conservation and Utilization, the Orchid Conservation & Research Center of Shenzhen, Shenzhen, China
| | - Hua Deng
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of State Forestry Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, China
| | - Xiong-De Tu
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization at College of Landscape Architecture, Fujian Agriculture and Forestry University, Fuzhou, China
- Fujian Colleges and Universities Engineering Research Institute of Conservation and Utilization of Natural Bioresources, College of Forestry, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Yan Wang
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of State Forestry Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, China
| | - Si-Ren Lan
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization at College of Landscape Architecture, Fujian Agriculture and Forestry University, Fuzhou, China
- Fujian Colleges and Universities Engineering Research Institute of Conservation and Utilization of Natural Bioresources, College of Forestry, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Zhong-Jian Liu
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization at College of Landscape Architecture, Fujian Agriculture and Forestry University, Fuzhou, China
- Fujian Colleges and Universities Engineering Research Institute of Conservation and Utilization of Natural Bioresources, College of Forestry, Fujian Agriculture and Forestry University, Fuzhou, China
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20
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Zhou K. The alternative splicing of SKU5-Similar3 in Arabidopsis. PLANT SIGNALING & BEHAVIOR 2019; 14:e1651182. [PMID: 31397618 PMCID: PMC6768224 DOI: 10.1080/15592324.2019.1651182] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/02/2019] [Accepted: 07/18/2019] [Indexed: 05/29/2023]
Abstract
Alternative splicing largely enhanced the diversity of transcriptome and proteome in eukaryas. Along with technological development, more and more genes are reported to be alternatively spliced during mRNA maturation. Here, I report the alternative splicing of SKU5-Similar 3 (SKS3) and its special splicing site in Arabidopsis. SKS3 was predicted to be alternatively transcribed into two variants, SKS3.1 and SKS3.2, which encoded a GPI-anchored protein and a soluble secretory protein, respectively. But, according to experimental data, instead of SKS3.2, a novel variant, SKS3.3, which encodes a protein with a transmembrane region at its C-terminus, was demonstrated. Interestingly, it exhibites a different organ-specific expression pattern with SKS3.1, and an unusual intron splicing site not following 'GT-AG' rule or any reported rule.
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Affiliation(s)
- Ke Zhou
- FAFU-UCR Joint Center for Horticultural Biology and Metabolomics, Haixia Institute of Science and Technology, Fujian Agriculture and Forestry University, Fuzhou, China
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21
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Nakaminami K, Seki M. RNA Regulation in Plant Cold Stress Response. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2019; 1081:23-44. [PMID: 30288702 DOI: 10.1007/978-981-13-1244-1_2] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
In addition to plants, all organisms react to environmental stimuli via the perception of signals and subsequently respond through alterations of gene expression. However, genes/mRNAs are usually not the functional unit themselves, and instead, resultant protein products with individual functions result in various acquired phenotypes. In order to fully characterize the adaptive responses of plants to environmental stimuli, it is essential to determine the level of proteins, in addition to the regulation of mRNA expression. This regulatory step, which is referred to as "mRNA posttranscriptional regulation," occurs subsequent to mRNA transcription and prior to translation. Although these RNA regulatory mechanisms have been well-studied in many organisms, including plants, it is not fully understood how plants respond to environmental stimuli, such as cold stress, via these RNA regulations.A recent study described several RNA regulatory factors in relation to environmental stress responses, including plant cold stress tolerance. In this chapter, the functions of RNA regulatory factors and comprehensive analyses related to the RNA regulations involved in cold stress response are summarized, such as mRNA maturation, including capping, splicing, polyadenylation of mRNA, and the quality control system of mRNA; mRNA degradation, including the decapping step; and mRNA stabilization. In addition, the putative roles of messenger ribonucleoprotein (mRNP) granules, such as processing bodies (PBs) and stress granules (SGs), which are cytoplasmic particles, are described in relation to RNA regulations under stress conditions. These RNA regulatory systems are important for adjusting or fine-tuning and determining the final levels of mRNAs and proteins in order to adapt or respond to environmental stresses. Collectively, these new areas of study revealed that plants possess precise novel regulatory mechanisms which specifically function in the response to cold stress.
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Affiliation(s)
- Kentaro Nakaminami
- Plant Genomic Network Research Team, RIKEN Center for Sustainable Resource Science, Yokohama, Kanagawa, Japan.
| | - Motoaki Seki
- Plant Genomic Network Research Team, RIKEN Center for Sustainable Resource Science, Yokohama, Kanagawa, Japan
- Plant Epigenome Regulation Laboratory, Cluster for Pioneering Research, RIKEN, Wako, Saitama, Japan
- Kihara Institute for Biological Research, Yokohama City University, Yokohama, Kanagawa, Japan
- Core Research for Evolutional Science and Technology (CREST), Japan Science and Technology (JST), Kawaguchi, Saitama, Japan
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22
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Calixto CPG, Tzioutziou NA, James AB, Hornyik C, Guo W, Zhang R, Nimmo HG, Brown JWS. Cold-Dependent Expression and Alternative Splicing of Arabidopsis Long Non-coding RNAs. FRONTIERS IN PLANT SCIENCE 2019; 10:235. [PMID: 30891054 PMCID: PMC6413719 DOI: 10.3389/fpls.2019.00235] [Citation(s) in RCA: 48] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/23/2018] [Accepted: 02/12/2019] [Indexed: 05/07/2023]
Abstract
Plants re-program their gene expression when responding to changing environmental conditions. Besides differential gene expression, extensive alternative splicing (AS) of pre-mRNAs and changes in expression of long non-coding RNAs (lncRNAs) are associated with stress responses. RNA-sequencing of a diel time-series of the initial response of Arabidopsis thaliana rosettes to low temperature showed massive and rapid waves of both transcriptional and AS activity in protein-coding genes. We exploited the high diversity of transcript isoforms in AtRTD2 to examine regulation and post-transcriptional regulation of lncRNA gene expression in response to cold stress. We identified 135 lncRNA genes with cold-dependent differential expression (DE) and/or differential alternative splicing (DAS) of lncRNAs including natural antisense RNAs, sORF lncRNAs, and precursors of microRNAs (miRNAs) and trans-acting small-interfering RNAs (tasiRNAs). The high resolution (HR) of the time-series allowed the dynamics of changes in transcription and AS to be determined and identified early and adaptive transcriptional and AS changes in the cold response. Some lncRNA genes were regulated only at the level of AS and using plants grown at different temperatures and a HR time-course of the first 3 h of temperature reduction, we demonstrated that the AS of some lncRNAs is highly sensitive to small temperature changes suggesting tight regulation of expression. In particular, a splicing event in TAS1a which removed an intron that contained the miR173 processing and phased siRNAs generation sites was differentially alternatively spliced in response to cold. The cold-induced reduction of the spliced form of TAS1a and of the tasiRNAs suggests that splicing may enhance production of the siRNAs. Our results identify candidate lncRNAs that may contribute to the regulation of expression that determines the physiological processes essential for acclimation and freezing tolerance.
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Affiliation(s)
- Cristiane P. G. Calixto
- Plant Sciences Division, School of Life Sciences, University of Dundee, Dundee, United Kingdom
| | - Nikoleta A. Tzioutziou
- Plant Sciences Division, School of Life Sciences, University of Dundee, Dundee, United Kingdom
| | - Allan B. James
- Institute of Molecular, Cell and Systems Biology, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, United Kingdom
| | - Csaba Hornyik
- Cell and Molecular Sciences, The James Hutton Institute, Dundee, United Kingdom
| | - Wenbin Guo
- Plant Sciences Division, School of Life Sciences, University of Dundee, Dundee, United Kingdom
- Information and Computational Sciences, The James Hutton Institute, Dundee, United Kingdom
| | - Runxuan Zhang
- Information and Computational Sciences, The James Hutton Institute, Dundee, United Kingdom
| | - Hugh G. Nimmo
- Institute of Molecular, Cell and Systems Biology, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, United Kingdom
| | - John W. S. Brown
- Plant Sciences Division, School of Life Sciences, University of Dundee, Dundee, United Kingdom
- Cell and Molecular Sciences, The James Hutton Institute, Dundee, United Kingdom
- *Correspondence: John W. S. Brown,
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23
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Nibau C, Gallemí M, Dadarou D, Doonan JH, Cavallari N. Thermo-Sensitive Alternative Splicing of FLOWERING LOCUS M Is Modulated by Cyclin-Dependent Kinase G2. FRONTIERS IN PLANT SCIENCE 2019; 10:1680. [PMID: 32038671 PMCID: PMC6987439 DOI: 10.3389/fpls.2019.01680] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/29/2019] [Accepted: 11/29/2019] [Indexed: 05/05/2023]
Abstract
The ability to sense environmental temperature and to coordinate growth and development accordingly, is critical to the reproductive success of plants. Flowering time is regulated at the level of gene expression by a complex network of factors that integrate environmental and developmental cues. One of the main players, involved in modulating flowering time in response to changes in ambient temperature is FLOWERING LOCUS M (FLM). FLM transcripts can undergo extensive alternative splicing producing multiple variants, of which FLM-β and FLM-δ are the most representative. While FLM-β codes for the flowering repressor FLM protein, translation of FLM-δ has the opposite effect on flowering. Here we show that the cyclin-dependent kinase G2 (CDKG2), together with its cognate cyclin, CYCLYN L1 (CYCL1) affects the alternative splicing of FLM, balancing the levels of FLM-β and FLM-δ across the ambient temperature range. In the absence of the CDKG2/CYCL1 complex, FLM-β expression is reduced while FLM-δ is increased in a temperature dependent manner and these changes are associated with an early flowering phenotype in the cdkg2 mutant lines. In addition, we found that transcript variants retaining the full FLM intron 1 are sequestered in the cell nucleus. Strikingly, FLM intron 1 splicing is also regulated by CDKG2/CYCL1. Our results provide evidence that temperature and CDKs regulate the alternative splicing of FLM, contributing to flowering time definition.
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Affiliation(s)
- Candida Nibau
- Institute of Biological, Environmental, and Rural Sciences, Aberystwyth University, Aberystwyth, United Kingdom
- *Correspondence: Nicola Cavallari, ; Candida Nibau,
| | - Marçal Gallemí
- Institute of Science and Technology Austria, Klosterneuburg, Austria
| | - Despoina Dadarou
- Institute of Biological, Environmental, and Rural Sciences, Aberystwyth University, Aberystwyth, United Kingdom
| | - John H. Doonan
- Institute of Biological, Environmental, and Rural Sciences, Aberystwyth University, Aberystwyth, United Kingdom
| | - Nicola Cavallari
- Institute of Science and Technology Austria, Klosterneuburg, Austria
- Max F. Perutz Laboratories, Medical University of Vienna, Vienna, Austria
- *Correspondence: Nicola Cavallari, ; Candida Nibau,
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Catalá R, Carrasco-López C, Perea-Resa C, Hernández-Verdeja T, Salinas J. Emerging Roles of LSM Complexes in Posttranscriptional Regulation of Plant Response to Abiotic Stress. FRONTIERS IN PLANT SCIENCE 2019; 10:167. [PMID: 30873189 PMCID: PMC6401655 DOI: 10.3389/fpls.2019.00167] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/08/2018] [Accepted: 01/31/2019] [Indexed: 05/04/2023]
Abstract
It has long been assumed that the wide reprogramming of gene expression that modulates plant response to unfavorable environmental conditions is mainly controlled at the transcriptional level. A growing body of evidence, however, indicates that posttranscriptional regulatory mechanisms also play a relevant role in this control. Thus, the LSMs, a family of proteins involved in mRNA metabolism highly conserved in eukaryotes, have emerged as prominent regulators of plant tolerance to abiotic stress. Arabidopsis contains two main LSM ring-shaped heteroheptameric complexes, LSM1-7 and LSM2-8, with different subcellular localization and function. The LSM1-7 ring is part of the cytoplasmic decapping complex that regulates mRNA stability. On the other hand, the LSM2-8 complex accumulates in the nucleus to ensure appropriate levels of U6 snRNA and, therefore, correct pre-mRNA splicing. Recent studies reported unexpected results that led to a fundamental change in the assumed consideration that LSM complexes are mere components of the mRNA decapping and splicing cellular machineries. Indeed, these data have demonstrated that LSM1-7 and LSM2-8 rings operate in Arabidopsis by selecting specific RNA targets, depending on the environmental conditions. This specificity allows them to actively imposing particular gene expression patterns that fine-tune plant responses to abiotic stresses. In this review, we will summarize current and past knowledge on the role of LSM rings in modulating plant physiology, with special focus on their function in abiotic stress responses.
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Genome-wide identification and characterization of mRNAs and lncRNAs involved in cold stress in the wild banana (Musa itinerans). PLoS One 2018; 13:e0200002. [PMID: 29985922 PMCID: PMC6037364 DOI: 10.1371/journal.pone.0200002] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2017] [Accepted: 06/18/2018] [Indexed: 12/19/2022] Open
Abstract
Cold stress seriously affects banana growth, yield and fruit quality. Long noncoding RNAs (lncRNAs) have been demonstrated as key regulators of biotic and abiotic stress in plants, but the identification and prediction of cold responsive mRNAs and lncRNAs in wild banana remains unexplored. In present study, a cold resistant wild banana line from China was used to profile the cold-responsive mRNAs and lncRNAs by RNA-seq under cold stress conditions, i.e. 13°C (critical growth temperature), 4°C (chilling temperature), 0°C (freezing temperature) and normal growing condition, i.e. 28°C (control group). A total of 12,462 lncRNAs were identified in cold-stressed wild banana. In mRNA, much more alternative splicing events occurred in wild banana under the cold stress conditions compared with that in the normal growing condition. The GO analysis of differential expression genes (DEGs) showed the biochemical processes and membrane related genes responded positively to the cold stress. The KEGG pathway enrichment analysis of the DEGs showed that the pathways of photosynthesis, photosynthesis–antenna proteins, circadian rhythm–plant, glutathione metabolism, starch and sucrose metabolism, cutin/suberine/biosynthesis were altered or affected by the cold stress conditions. Our analyses of the generated transcriptome and lncRNAs provide new insights into regulating expression of genes and lncRNAs that respond to cold stress in the wild banana.
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Calixto CPG, Guo W, James AB, Tzioutziou NA, Entizne JC, Panter PE, Knight H, Nimmo HG, Zhang R, Brown JWS. Rapid and Dynamic Alternative Splicing Impacts the Arabidopsis Cold Response Transcriptome. THE PLANT CELL 2018; 30:1424-1444. [PMID: 29764987 PMCID: PMC6096597 DOI: 10.1105/tpc.18.00177] [Citation(s) in RCA: 182] [Impact Index Per Article: 30.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/26/2018] [Revised: 04/20/2018] [Accepted: 05/10/2018] [Indexed: 05/18/2023]
Abstract
Plants have adapted to tolerate and survive constantly changing environmental conditions by reprogramming gene expression The dynamics of the contribution of alternative splicing (AS) to stress responses are unknown. RNA-sequencing of a time-series of Arabidopsis thaliana plants exposed to cold determines the timing of significant AS changes. This shows a massive and rapid AS response with coincident waves of transcriptional and AS activity occurring in the first few hours of temperature reduction and further AS throughout the cold. In particular, hundreds of genes showed changes in expression due to rapidly occurring AS in response to cold ("early AS" genes); these included numerous novel cold-responsive transcription factors and splicing factors/RNA binding proteins regulated only by AS. The speed and sensitivity to small temperature changes of AS of some of these genes suggest that fine-tuning expression via AS pathways contributes to the thermo-plasticity of expression. Four early AS splicing regulatory genes have been shown previously to be required for freezing tolerance and acclimation; we provide evidence of a fifth gene, U2B"-LIKE Such factors likely drive cascades of AS of downstream genes that, alongside transcription, modulate transcriptome reprogramming that together govern the physiological and survival responses of plants to low temperature.
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Affiliation(s)
- Cristiane P G Calixto
- Plant Sciences Division, School of Life Sciences, University of Dundee, Dundee DD2 5DA, United Kingdom
| | - Wenbin Guo
- Plant Sciences Division, School of Life Sciences, University of Dundee, Dundee DD2 5DA, United Kingdom
- Information and Computational Sciences, The James Hutton Institute, Dundee DD2 5DA, United Kingdom
| | - Allan B James
- Institute of Molecular, Cell, and Systems Biology, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow G12 8QQ, United Kingdom
| | - Nikoleta A Tzioutziou
- Plant Sciences Division, School of Life Sciences, University of Dundee, Dundee DD2 5DA, United Kingdom
| | - Juan Carlos Entizne
- Plant Sciences Division, School of Life Sciences, University of Dundee, Dundee DD2 5DA, United Kingdom
- Cell and Molecular Sciences, The James Hutton Institute, Dundee DD2 5DA, United Kingdom
| | - Paige E Panter
- Department of Biosciences, Durham University, Durham DH1 3LE, United Kingdom
| | - Heather Knight
- Department of Biosciences, Durham University, Durham DH1 3LE, United Kingdom
| | - Hugh G Nimmo
- Institute of Molecular, Cell, and Systems Biology, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow G12 8QQ, United Kingdom
| | - Runxuan Zhang
- Information and Computational Sciences, The James Hutton Institute, Dundee DD2 5DA, United Kingdom
| | - John W S Brown
- Plant Sciences Division, School of Life Sciences, University of Dundee, Dundee DD2 5DA, United Kingdom
- Cell and Molecular Sciences, The James Hutton Institute, Dundee DD2 5DA, United Kingdom
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27
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Calixto CPG, Guo W, James AB, Tzioutziou NA, Entizne JC, Panter PE, Knight H, Nimmo HG, Zhang R, Brown JWS. Rapid and Dynamic Alternative Splicing Impacts the Arabidopsis Cold Response Transcriptome. THE PLANT CELL 2018; 30:1424-1444. [PMID: 29764987 DOI: 10.1101/251876] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/26/2018] [Revised: 04/20/2018] [Accepted: 05/10/2018] [Indexed: 05/20/2023]
Abstract
Plants have adapted to tolerate and survive constantly changing environmental conditions by reprogramming gene expression The dynamics of the contribution of alternative splicing (AS) to stress responses are unknown. RNA-sequencing of a time-series of Arabidopsis thaliana plants exposed to cold determines the timing of significant AS changes. This shows a massive and rapid AS response with coincident waves of transcriptional and AS activity occurring in the first few hours of temperature reduction and further AS throughout the cold. In particular, hundreds of genes showed changes in expression due to rapidly occurring AS in response to cold ("early AS" genes); these included numerous novel cold-responsive transcription factors and splicing factors/RNA binding proteins regulated only by AS. The speed and sensitivity to small temperature changes of AS of some of these genes suggest that fine-tuning expression via AS pathways contributes to the thermo-plasticity of expression. Four early AS splicing regulatory genes have been shown previously to be required for freezing tolerance and acclimation; we provide evidence of a fifth gene, U2B"-LIKE Such factors likely drive cascades of AS of downstream genes that, alongside transcription, modulate transcriptome reprogramming that together govern the physiological and survival responses of plants to low temperature.
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Affiliation(s)
- Cristiane P G Calixto
- Plant Sciences Division, School of Life Sciences, University of Dundee, Dundee DD2 5DA, United Kingdom
| | - Wenbin Guo
- Plant Sciences Division, School of Life Sciences, University of Dundee, Dundee DD2 5DA, United Kingdom
- Information and Computational Sciences, The James Hutton Institute, Dundee DD2 5DA, United Kingdom
| | - Allan B James
- Institute of Molecular, Cell, and Systems Biology, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow G12 8QQ, United Kingdom
| | - Nikoleta A Tzioutziou
- Plant Sciences Division, School of Life Sciences, University of Dundee, Dundee DD2 5DA, United Kingdom
| | - Juan Carlos Entizne
- Plant Sciences Division, School of Life Sciences, University of Dundee, Dundee DD2 5DA, United Kingdom
- Cell and Molecular Sciences, The James Hutton Institute, Dundee DD2 5DA, United Kingdom
| | - Paige E Panter
- Department of Biosciences, Durham University, Durham DH1 3LE, United Kingdom
| | - Heather Knight
- Department of Biosciences, Durham University, Durham DH1 3LE, United Kingdom
| | - Hugh G Nimmo
- Institute of Molecular, Cell, and Systems Biology, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow G12 8QQ, United Kingdom
| | - Runxuan Zhang
- Information and Computational Sciences, The James Hutton Institute, Dundee DD2 5DA, United Kingdom
| | - John W S Brown
- Plant Sciences Division, School of Life Sciences, University of Dundee, Dundee DD2 5DA, United Kingdom
- Cell and Molecular Sciences, The James Hutton Institute, Dundee DD2 5DA, United Kingdom
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28
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Zeng X, Xu Y, Jiang J, Zhang F, Ma L, Wu D, Wang Y, Sun W. Identification of cold stress responsive microRNAs in two winter turnip rape (Brassica rapa L.) by high throughput sequencing. BMC PLANT BIOLOGY 2018; 18:52. [PMID: 29587648 PMCID: PMC5870505 DOI: 10.1186/s12870-018-1242-4] [Citation(s) in RCA: 47] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/12/2017] [Accepted: 01/17/2018] [Indexed: 05/21/2023]
Abstract
BACKGROUND Low temperature is a major abiotic stress affecting the production of rapeseed in China by impeding plant growth and development. A comprehensive knowledge of small-RNA expression pattern in Brassica rapa under cold stress could improve our knowledge of microRNA-mediated stress responses. RESULTS A total of 353 cold-responsive miRNAs, 84 putative novel and 269 conserved miRNAs, were identified from the leaves and roots of two winter turnip rape varieties 'Longyou 7' (cold-tolerant) and 'Tianyou 4' (cold-sensitive), which were stressed under - 4 °C for 8 h. Eight conserved (miR166h-3p-1, miR398b-3p, miR398b-3p-1, miR408d, miR156a-5p, miR396h, miR845a-1, miR166u) and two novel miRNAs (Bra-novel-miR3153-5p and Bra-novel-miR3172-5p) were differentially expressed in leaves of 'Longyou 7' under cold stress. Bra-novel-miR3936-5p was up-regulated in roots of 'Longyou 7' under cold stress. Four and five conserved miRNAs were differentially expressed in leaves and roots of 'Tianyou 4' after cold stress. Besides, we found two conserved miRNAs (miR319e and miR166m-2) were down-regulated in non-stressed roots of 'Longyou 7' compared with 'Tianyou 4'. After cold stress, we found two and eight miRNAs were differentially expressed in leaves and roots of 'Longyou 7' compared with 'Tianyou 4'. The differentially expressed miRNAs between two cultivars under cold stress include novel miRNAs and the members of the miR166 and miR319 families. A total of 211 target genes for 15 known miRNAs and two novel miRNAs were predicted by bioinformatic analysis, mainly involved in metabolic processes and stress responses. Five differentially expressed miRNAs and predicted target genes were confirmed by quantitative reverse transcription PCR, and the expressional changes of target genes were negatively correlated to differentially expressed miRNAs. Our data indicated that some candidate miRNAs (e.g., miR166e, miR319, and Bra-novel-miR3936-5p) may play important roles in plant response to cold stress. CONCLUSIONS Our work indicates that miRNA and putative target genes mediated metabolic processes and stress responses are significant to cold tolerance in B. rapa.
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Affiliation(s)
- Xiucun Zeng
- College of Agronomy and Biotechnology, Hexi University, Zhangye, 734000 China
| | - Yaozhao Xu
- College of Agronomy and Biotechnology, Hexi University, Zhangye, 734000 China
- College of Agronomy, Gansu Agricultural University, Lanzhou, 730070 China
| | - Jinjin Jiang
- Jiangsu Provincial Key Laboratory of Crop Genetics and Physiology, Yangzhou University, Yangzhou, 225009 China
| | - Fenqin Zhang
- College of Agronomy and Biotechnology, Hexi University, Zhangye, 734000 China
| | - Li Ma
- College of Agronomy and Biotechnology, Hexi University, Zhangye, 734000 China
| | - Dewei Wu
- Jiangsu Provincial Key Laboratory of Crop Genetics and Physiology, Yangzhou University, Yangzhou, 225009 China
| | - Youping Wang
- Jiangsu Provincial Key Laboratory of Crop Genetics and Physiology, Yangzhou University, Yangzhou, 225009 China
| | - Wancang Sun
- College of Agronomy, Gansu Agricultural University, Lanzhou, 730070 China
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29
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Zhang R, Calixto CPG, Marquez Y, Venhuizen P, Tzioutziou NA, Guo W, Spensley M, Entizne JC, Lewandowska D, Ten Have S, Frei Dit Frey N, Hirt H, James AB, Nimmo HG, Barta A, Kalyna M, Brown JWS. A high quality Arabidopsis transcriptome for accurate transcript-level analysis of alternative splicing. Nucleic Acids Res 2017; 45:5061-5073. [PMID: 28402429 PMCID: PMC5435985 DOI: 10.1093/nar/gkx267] [Citation(s) in RCA: 169] [Impact Index Per Article: 24.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2016] [Accepted: 04/04/2017] [Indexed: 12/30/2022] Open
Abstract
Alternative splicing generates multiple transcript and protein isoforms from the same gene and thus is important in gene expression regulation. To date, RNA-sequencing (RNA-seq) is the standard method for quantifying changes in alternative splicing on a genome-wide scale. Understanding the current limitations of RNA-seq is crucial for reliable analysis and the lack of high quality, comprehensive transcriptomes for most species, including model organisms such as Arabidopsis, is a major constraint in accurate quantification of transcript isoforms. To address this, we designed a novel pipeline with stringent filters and assembled a comprehensive Reference Transcript Dataset for Arabidopsis (AtRTD2) containing 82,190 non-redundant transcripts from 34 212 genes. Extensive experimental validation showed that AtRTD2 and its modified version, AtRTD2-QUASI, for use in Quantification of Alternatively Spliced Isoforms, outperform other available transcriptomes in RNA-seq analysis. This strategy can be implemented in other species to build a pipeline for transcript-level expression and alternative splicing analyses.
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Affiliation(s)
- Runxuan Zhang
- Informatics and Computational Sciences, The James Hutton Institute, Invergowrie, Dundee DD2 5DA, UK
| | - Cristiane P G Calixto
- Plant Sciences Division, College of Life Sciences, University of Dundee, Invergowrie, Dundee DD2 5DA, UK
| | - Yamile Marquez
- Max F. Perutz Laboratories, Medical University of Vienna, Dr. Bohrgasse 9/3, 1030 Vienna, Austria
| | - Peter Venhuizen
- Max F. Perutz Laboratories, Medical University of Vienna, Dr. Bohrgasse 9/3, 1030 Vienna, Austria
| | - Nikoleta A Tzioutziou
- Plant Sciences Division, College of Life Sciences, University of Dundee, Invergowrie, Dundee DD2 5DA, UK
| | - Wenbin Guo
- Informatics and Computational Sciences, The James Hutton Institute, Invergowrie, Dundee DD2 5DA, UK.,Plant Sciences Division, College of Life Sciences, University of Dundee, Invergowrie, Dundee DD2 5DA, UK
| | - Mark Spensley
- The Donnelly Centre, University of Toronto, 160 College Street, Toronto, Ontario, Canada
| | - Juan Carlos Entizne
- Plant Sciences Division, College of Life Sciences, University of Dundee, Invergowrie, Dundee DD2 5DA, UK
| | - Dominika Lewandowska
- Cell and Molecular Sciences, The James Hutton Institute, Invergowrie, Dundee DD2 5DA, UK
| | - Sara Ten Have
- Centre for Gene Regulation and Expression, School of Life Sciences, University of Dundee, Dundee, UK
| | | | - Heribert Hirt
- Institute of Plant Sciences Paris Saclay, INRA-CNRS-UEVE, Orsay 91405, France
| | - Allan B James
- Institute of Molecular, Cell and Systems Biology, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow G12 8QQ, UK
| | - Hugh G Nimmo
- Institute of Molecular, Cell and Systems Biology, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow G12 8QQ, UK
| | - Andrea Barta
- Max F. Perutz Laboratories, Medical University of Vienna, Dr. Bohrgasse 9/3, 1030 Vienna, Austria
| | - Maria Kalyna
- Department of Applied Genetics and Cell Biology, University of Natural Resources and Life Sciences - BOKU, Muthgasse 18, 1190 Vienna, Austria
| | - John W S Brown
- Plant Sciences Division, College of Life Sciences, University of Dundee, Invergowrie, Dundee DD2 5DA, UK.,Cell and Molecular Sciences, The James Hutton Institute, Invergowrie, Dundee DD2 5DA, UK
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30
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Chanroj V, Rattanawong R, Phumichai T, Tangphatsornruang S, Ukoskit K. Genome-wide association mapping of latex yield and girth in Amazonian accessions of Hevea brasiliensis grown in a suboptimal climate zone. Genomics 2017; 109:475-484. [PMID: 28751185 DOI: 10.1016/j.ygeno.2017.07.005] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2017] [Revised: 07/07/2017] [Accepted: 07/21/2017] [Indexed: 12/29/2022]
Abstract
Latex yield and growth are the key complex traits in commercial rubber production. The present study is the first to report genome-wide association mapping of latex yield and girth, for 170 Amazonian accessions grown in a suboptimal area characterized by limited rainfall and a lengthy dry season. Targeted sequence enrichment to capture gene transcripts generated 14,155 high quality filtered single nucleotide polymorphisms (SNPs) of which 94.3% resided in coding regions. The rapid decay of linkage disequilibrium over physical and genetic distance found in the accessions was comparable to those previously reported for several outcrossing species. A mixed linear model detected three significant SNPs in three candidate genes involved in plant adaptation to drought stress, individually explaining 12.7-15.7% of the phenotypic variance. The SNPs identified in the study will help to extend understanding, and to support genetic improvement of rubber trees grown in drought-affected regions.
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Affiliation(s)
- Vipavee Chanroj
- Department of Biotechnology, Faculty of Science and Technology, Thammasat University, Rangsit Campus, Klong Luang, Pathumtani 12121, Thailand
| | - Ratchanee Rattanawong
- Nong Khai Rubber Research Center, Rubber Research Institute of Thailand, Rattanawapi District, Nong Khai, 43120, Thailand
| | | | - Sithichoke Tangphatsornruang
- National Center for Genetic Engineering and Biotechnology, 113 Phaholyothin Rd., Klong 1, Klong Luang, Pathumthani 12120, Thailand
| | - Kittipat Ukoskit
- Department of Biotechnology, Faculty of Science and Technology, Thammasat University, Rangsit Campus, Klong Luang, Pathumtani 12121, Thailand.
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31
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Nájera VA, González MC, Pérez-Ruiz JM, Cejudo FJ. An event of alternative splicing affects the expression of the NTRC gene, encoding NADPH-thioredoxin reductase C, in seed plants. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2017; 258:21-28. [PMID: 28330560 DOI: 10.1016/j.plantsci.2017.02.001] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/17/2016] [Revised: 01/31/2017] [Accepted: 02/02/2017] [Indexed: 06/06/2023]
Abstract
The NTRC gene encodes a NADPH-dependent thioredoxin reductase with a joint thioredoxin domain, exclusive of photosynthetic organisms. An updated search shows that although most species harbor a single copy of the NTRC gene, two copies were identified in different species of the genus Solanum, Glycine max and the moss Physcomitrella patens. The phylogenetic analysis of NTRCs from different sources produced a tree with the major groups of photosynthetic organisms: cyanobacteria, algae and land plants, indicating the evolutionary success of the NTRC gene among photosynthetic eukaryotes. An event of alternative splicing affecting the expression of the NTRC gene was identified, which is conserved in seed plants but not in algae, bryophytes and lycophytes. The alternative splicing event results in a transcript with premature stop codon, which would produce a truncated form of the enzyme. The standard splicing/alternative splicing (SS/AS) transcripts ratio was higher in photosynthetic tissues from Arabidopsis, Brachypodium and tomato, in line with the higher content of the NTRC polypeptide in these tissues. Moreover, environmental stresses such as cold or high salt affected the SS/AS ratio of the NTRC gene transcripts in Brachypodium seedlings. These results suggest that the alternative splicing of the NTRC gene might be an additional mechanism for modulating the content of NTRC in photosynthetic and non-photosynthetic tissues of seed plants.
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Affiliation(s)
- Victoria A Nájera
- Instituto de Bioquímica Vegetal y Fotosíntesis, Universidad de Sevilla and CSIC, Avda Américo Vespucio 49, 41092, Sevilla, Spain.
| | - María Cruz González
- Instituto de Bioquímica Vegetal y Fotosíntesis, Universidad de Sevilla and CSIC, Avda Américo Vespucio 49, 41092, Sevilla, Spain.
| | - Juan Manuel Pérez-Ruiz
- Instituto de Bioquímica Vegetal y Fotosíntesis, Universidad de Sevilla and CSIC, Avda Américo Vespucio 49, 41092, Sevilla, Spain.
| | - Francisco Javier Cejudo
- Instituto de Bioquímica Vegetal y Fotosíntesis, Universidad de Sevilla and CSIC, Avda Américo Vespucio 49, 41092, Sevilla, Spain.
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32
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AlShareef S, Ling Y, Butt H, Mariappan KG, Benhamed M, Mahfouz MM. Herboxidiene triggers splicing repression and abiotic stress responses in plants. BMC Genomics 2017; 18:260. [PMID: 28347276 PMCID: PMC5369228 DOI: 10.1186/s12864-017-3656-z] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2016] [Accepted: 03/22/2017] [Indexed: 12/28/2022] Open
Abstract
Background Constitutive and alternative splicing of pre-mRNAs from multiexonic genes controls the diversity of the proteome; these precisely regulated processes also fine-tune responses to cues related to growth, development, and stresses. Small-molecule inhibitors that perturb splicing provide invaluable tools for use as chemical probes to uncover the molecular underpinnings of splicing regulation and as potential anticancer compounds. Results Here, we show that herboxidiene (GEX1A) inhibits both constitutive and alternative splicing. Moreover, GEX1A activates genome-wide transcriptional patterns involved in abiotic stress responses in plants. GEX1A treatment -activated ABA-inducible promoters, and led to stomatal closure. Interestingly, GEX1A and pladienolide B (PB) elicited similar cellular changes, including alterations in the patterns of transcription and splicing, suggesting that these compounds might target the same spliceosome complex in plant cells. Conclusions Our study establishes GEX1A as a potent splicing inhibitor in plants that can be used to probe the assembly, dynamics, and molecular functions of the spliceosome and to study the interplay between splicing stress and abiotic stresses, as well as having potential biotechnological applications. Electronic supplementary material The online version of this article (doi:10.1186/s12864-017-3656-z) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Sahar AlShareef
- Laboratory for Genome Engineering, Division of Biological Sciences, 4700 King Abdullah University of Science and Technology, Thuwal, 23955-6900, Saudi Arabia
| | - Yu Ling
- Laboratory for Genome Engineering, Division of Biological Sciences, 4700 King Abdullah University of Science and Technology, Thuwal, 23955-6900, Saudi Arabia
| | - Haroon Butt
- Laboratory for Genome Engineering, Division of Biological Sciences, 4700 King Abdullah University of Science and Technology, Thuwal, 23955-6900, Saudi Arabia
| | - Kiruthiga G Mariappan
- Laboratory for Genome Engineering, Division of Biological Sciences, 4700 King Abdullah University of Science and Technology, Thuwal, 23955-6900, Saudi Arabia
| | - Moussa Benhamed
- Laboratory for Genome Engineering, Division of Biological Sciences, 4700 King Abdullah University of Science and Technology, Thuwal, 23955-6900, Saudi Arabia
| | - Magdy M Mahfouz
- Laboratory for Genome Engineering, Division of Biological Sciences, 4700 King Abdullah University of Science and Technology, Thuwal, 23955-6900, Saudi Arabia.
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33
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Splicing-related genes are alternatively spliced upon changes in ambient temperatures in plants. PLoS One 2017; 12:e0172950. [PMID: 28257507 PMCID: PMC5336241 DOI: 10.1371/journal.pone.0172950] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2016] [Accepted: 02/13/2017] [Indexed: 11/19/2022] Open
Abstract
Plants adjust their development and architecture to small variations in ambient temperature. In a time in which temperatures are rising world-wide, the mechanism by which plants are able to sense temperature fluctuations and adapt to it, is becoming of special interest. By performing RNA-sequencing on two Arabidopsis accession and one Brassica species exposed to temperature alterations, we showed that alternative splicing is an important mechanism in ambient temperature sensing and adaptation. We found that amongst the differentially alternatively spliced genes, splicing related genes are enriched, suggesting that the splicing machinery itself is targeted for alternative splicing when temperature changes. Moreover, we showed that many different components of the splicing machinery are targeted for ambient temperature regulated alternative splicing. Mutant analysis of a splicing related gene that was differentially spliced in two of the genotypes showed an altered flowering time response to different temperatures. We propose a two-step mechanism where temperature directly influences alternative splicing of the splicing machinery genes, followed by a second step where the altered splicing machinery affects splicing of downstream genes involved in the adaptation to altered temperatures.
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34
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Shao MR, Kumar Kenchanmane Raju S, Laurie JD, Sanchez R, Mackenzie SA. Stress-responsive pathways and small RNA changes distinguish variable developmental phenotypes caused by MSH1 loss. BMC PLANT BIOLOGY 2017; 17:47. [PMID: 28219335 PMCID: PMC5319189 DOI: 10.1186/s12870-017-0996-4] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/19/2016] [Accepted: 02/08/2017] [Indexed: 05/03/2023]
Abstract
BACKGROUND Proper regulation of nuclear-encoded, organelle-targeted genes is crucial for plastid and mitochondrial function. Among these genes, MutS Homolog 1 (MSH1) is notable for generating an assortment of mutant phenotypes with varying degrees of penetrance and pleiotropy. Stronger phenotypes have been connected to stress tolerance and epigenetic changes, and in Arabidopsis T-DNA mutants, two generations of homozygosity with the msh1 insertion are required before severe phenotypes begin to emerge. These observations prompted us to examine how msh1 mutants contrast according to generation and phenotype by profiling their respective transcriptomes and small RNA populations. RESULTS Using RNA-seq, we analyze pathways that are associated with MSH1 loss, including abiotic stresses such as cold response, pathogen defense and immune response, salicylic acid, MAPK signaling, and circadian rhythm. Subtle redox and environment-responsive changes also begin in the first generation, in the absence of strong phenotypes. Using small RNA-seq we further identify miRNA changes, and uncover siRNA trends that indicate modifications at the chromatin organization level. In all cases, the magnitude of changes among protein-coding genes, transposable elements, and small RNAs increases according to generation and phenotypic severity. CONCLUSION Loss of MSH1 is sufficient to cause large-scale regulatory changes in pathways that have been individually linked to one another, but rarely described all together within a single mutant background. This study enforces the recognition of organelles as critical integrators of both internal and external cues, and highlights the relationship between organelle and nuclear regulation in fundamental aspects of plant development and stress signaling. Our findings also encourage further investigation into potential connections between organelle state and genome regulation vis-á-vis small RNA feedback.
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Affiliation(s)
- Mon-Ray Shao
- Department of Agronomy and Horticulture, University of Nebraska-Lincoln, Lincoln, NE USA
| | | | - John D. Laurie
- Department of Agronomy and Horticulture, University of Nebraska-Lincoln, Lincoln, NE USA
- Sainsbury Laboratory, University of Cambridge, Cambridge, UK
| | - Robersy Sanchez
- Department of Agronomy and Horticulture, University of Nebraska-Lincoln, Lincoln, NE USA
| | - Sally A. Mackenzie
- Department of Agronomy and Horticulture, University of Nebraska-Lincoln, Lincoln, NE USA
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35
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Ling Y, Alshareef S, Butt H, Lozano-Juste J, Li L, Galal AA, Moustafa A, Momin AA, Tashkandi M, Richardson DN, Fujii H, Arold S, Rodriguez PL, Duque P, Mahfouz MM. Pre-mRNA splicing repression triggers abiotic stress signaling in plants. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2017; 89:291-309. [PMID: 27664942 DOI: 10.1111/tpj.13383] [Citation(s) in RCA: 58] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/10/2016] [Revised: 09/15/2016] [Accepted: 09/21/2016] [Indexed: 05/24/2023]
Abstract
Alternative splicing (AS) of precursor RNAs enhances transcriptome plasticity and proteome diversity in response to diverse growth and stress cues. Recent work has shown that AS is pervasive across plant species, with more than 60% of intron-containing genes producing different isoforms. Mammalian cell-based assays have discovered various inhibitors of AS. Here, we show that the macrolide pladienolide B (PB) inhibits constitutive splicing and AS in plants. Also, our RNA sequencing (RNA-seq) data revealed that PB mimics abiotic stress signals including salt, drought and abscisic acid (ABA). PB activates the abiotic stress- and ABA-responsive reporters RD29A::LUC and MAPKKK18::uidA in Arabidopsis thaliana and mimics the effects of ABA on stomatal aperture. Genome-wide analysis of AS by RNA-seq revealed that PB perturbs the splicing machinery and leads to a striking increase in intron retention and a reduction in other forms of AS. Interestingly, PB treatment activates the ABA signaling pathway by inhibiting the splicing of clade A PP2C phosphatases while still maintaining to some extent the splicing of ABA-activated SnRK2 kinases. Taken together, our data establish PB as an inhibitor and modulator of splicing and a mimic of abiotic stress signals in plants. Thus, PB reveals the molecular underpinnings of the interplay between stress responses, ABA signaling and post-transcriptional regulation in plants.
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Affiliation(s)
- Yu Ling
- Laboratory for Genome Engineering, Division of Biological Sciences, 4700 King Abdullah University of Science and Technology, Thuwal, 23955-6900, Saudi Arabia
| | - Sahar Alshareef
- Laboratory for Genome Engineering, Division of Biological Sciences, 4700 King Abdullah University of Science and Technology, Thuwal, 23955-6900, Saudi Arabia
| | - Haroon Butt
- Laboratory for Genome Engineering, Division of Biological Sciences, 4700 King Abdullah University of Science and Technology, Thuwal, 23955-6900, Saudi Arabia
| | - Jorge Lozano-Juste
- Instituto de Biologia Molecular y Celular de Plantas, Consejo Superior de Investigaciones Cientificas-Universidad Politecnica de Valencia, ES-46022, Valencia, Spain
| | - Lixin Li
- Laboratory for Genome Engineering, Division of Biological Sciences, 4700 King Abdullah University of Science and Technology, Thuwal, 23955-6900, Saudi Arabia
| | - Aya A Galal
- Department of Biology and Biotechnology Graduate Program, American University in Cairo, New Cairo, 11835, Egypt
| | - Ahmed Moustafa
- Department of Biology and Biotechnology Graduate Program, American University in Cairo, New Cairo, 11835, Egypt
| | - Afaque A Momin
- Division of Biological and Environmental Sciences and Engineering, King Abdullah University of Science and Technology, Thuwal, 23955-6900, Saudi Arabia
| | - Manal Tashkandi
- Laboratory for Genome Engineering, Division of Biological Sciences, 4700 King Abdullah University of Science and Technology, Thuwal, 23955-6900, Saudi Arabia
| | - Dale N Richardson
- Instituto Gulbenkian de Ciência, Rua da Quinta Grande 6, 2780-156, Oeiras, Portugal
| | - Hiroaki Fujii
- Molecular Plant Biology, Department of Biochemistry, University of Turku, FI-20014, Turku, Finland
| | - Stefan Arold
- Division of Biological and Environmental Sciences and Engineering, King Abdullah University of Science and Technology, Thuwal, 23955-6900, Saudi Arabia
| | - Pedro L Rodriguez
- Instituto de Biologia Molecular y Celular de Plantas, Consejo Superior de Investigaciones Cientificas-Universidad Politecnica de Valencia, ES-46022, Valencia, Spain
| | - Paula Duque
- Instituto Gulbenkian de Ciência, Rua da Quinta Grande 6, 2780-156, Oeiras, Portugal
| | - Magdy M Mahfouz
- Laboratory for Genome Engineering, Division of Biological Sciences, 4700 King Abdullah University of Science and Technology, Thuwal, 23955-6900, Saudi Arabia
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Srinivasan A, Jiménez-Gómez JM, Fornara F, Soppe WJJ, Brambilla V. Alternative splicing enhances transcriptome complexity in desiccating seeds. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2016; 58:947-958. [PMID: 27121908 DOI: 10.1111/jipb.12482] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/16/2016] [Accepted: 04/20/2016] [Indexed: 05/22/2023]
Abstract
Before being dispersed in the environment, mature seeds need to be dehydrated. The survival of seeds after dispersal depends on their low hydration in combination with high desiccation tolerance. These characteristics are established during seed maturation. Some key seed maturation genes have been reported to be regulated by alternative splicing (AS). However, so far AS was described only for single genes and a comprehensive analysis of AS during seed maturation has been lacking. We investigated gene expression and AS during Arabidopsis thaliana seed development at a global level, before and after desiccation. Bioinformatics tools were developed to identify differentially spliced regions within genes. Our data suggest the importance and shows the peculiar features of AS during seed desiccation. We identified AS in 34% of genes that are expressed at both timepoints before and after desiccation. Most of these AS transcript variants had not been found before in other tissues. Among the AS genes some seed master regulators could be found. Interestingly, 6% of all expressed transcripts were not transcriptionally regulated during desiccation, but only modified by AS. We propose that AS should be more routinely taken into account in the analysis of transcriptomic data to prevent overlooking potentially important regulators.
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Affiliation(s)
- Arunkumar Srinivasan
- Department of Plant Breeding and Genetics, Max Planck Institute for Plant Breeding Research, Cologne, Germany
- Open Analytics, Antwerp, Belgium
| | - José M Jiménez-Gómez
- Department of Plant Breeding and Genetics, Max Planck Institute for Plant Breeding Research, Cologne, Germany
- Institut Jean-Pierre Bourgin, Institut National de la Recherche Agronomique, Versailles, France
| | - Fabio Fornara
- University of Milan, Department of Biosciences, Milano 20133, Italy
| | - Wim J J Soppe
- Department of Plant Breeding and Genetics, Max Planck Institute for Plant Breeding Research, Cologne, Germany
| | - Vittoria Brambilla
- Department of Plant Breeding and Genetics, Max Planck Institute for Plant Breeding Research, Cologne, Germany
- University of Milan, Department of Biosciences, Milano 20133, Italy
- University of Milan, Department of Agricultural and Environmental Sciences, via Celoria 2, 20133 Milano, Italy
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Li S, Yamada M, Han X, Ohler U, Benfey PN. High-Resolution Expression Map of the Arabidopsis Root Reveals Alternative Splicing and lincRNA Regulation. Dev Cell 2016; 39:508-522. [PMID: 27840108 DOI: 10.1016/j.devcel.2016.10.012] [Citation(s) in RCA: 178] [Impact Index Per Article: 22.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2016] [Revised: 08/15/2016] [Accepted: 10/17/2016] [Indexed: 12/31/2022]
Abstract
The extent to which alternative splicing and long intergenic noncoding RNAs (lincRNAs) contribute to the specialized functions of cells within an organ is poorly understood. We generated a comprehensive dataset of gene expression from individual cell types of the Arabidopsis root. Comparisons across cell types revealed that alternative splicing tends to remove parts of coding regions from a longer, major isoform, providing evidence for a progressive mechanism of splicing. Cell-type-specific intron retention suggested a possible origin for this common form of alternative splicing. Coordinated alternative splicing across developmental stages pointed to a role in regulating differentiation. Consistent with this hypothesis, distinct isoforms of a transcription factor were shown to control developmental transitions. lincRNAs were generally lowly expressed at the level of individual cell types, but co-expression clusters provided clues as to their function. Our results highlight insights gained from analysis of expression at the level of individual cell types.
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Affiliation(s)
- Song Li
- Department of Biology and HHMI, Duke University, Durham, NC 27708, USA
| | - Masashi Yamada
- Department of Biology and HHMI, Duke University, Durham, NC 27708, USA
| | - Xinwei Han
- Department of Biology and HHMI, Duke University, Durham, NC 27708, USA
| | - Uwe Ohler
- Department of Biostatistics & Bioinformatics, Duke University, Durham, NC 27710, USA; Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine, 13125 Berlin, Germany.
| | - Philip N Benfey
- Department of Biology and HHMI, Duke University, Durham, NC 27708, USA.
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38
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Jakšić AM, Schlötterer C. The Interplay of Temperature and Genotype on Patterns of Alternative Splicing in Drosophila melanogaster. Genetics 2016; 204:315-25. [PMID: 27440867 PMCID: PMC5012396 DOI: 10.1534/genetics.116.192310] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2016] [Accepted: 07/08/2016] [Indexed: 01/02/2023] Open
Abstract
Alternative splicing is the highly regulated process of variation in the removal of introns from premessenger-RNA transcripts. The consequences of alternative splicing on the phenotype are well documented, but the impact of the environment on alternative splicing is not yet clear. We studied variation in alternative splicing among four different temperatures, 13, 18, 23, and 29°, in two Drosophila melanogaster genotypes. We show plasticity of alternative splicing with up to 10% of the expressed genes being differentially spliced between the most extreme temperatures for a given genotype. Comparing the two genotypes at different temperatures, we found <1% of the genes being differentially spliced at 18°. At extreme temperatures, however, we detected substantial differences in alternative splicing-with almost 10% of the genes having differential splicing between the genotypes: a magnitude similar to between species differences. Genes with differential alternative splicing between genotypes frequently exhibit dominant inheritance. Remarkably, the pattern of surplus of differences in alternative splicing at extreme temperatures resembled the pattern seen for gene expression intensity. Since different sets of genes were involved for the two phenotypes, we propose that purifying selection results in the reduction of differences at benign temperatures. Relaxed purifying selection at temperature extremes, on the other hand, may cause the divergence in gene expression and alternative splicing between the two strains in rarely encountered environments.
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Affiliation(s)
- Ana Marija Jakšić
- Institut für Populationsgenetik, Vetmeduni Vienna, 1210 Vienna, Austria Vienna Graduate School of Population Genetics, Vetmeduni Vienna, 1210 Vienna, Austria
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The OsCYP19-4 Gene Is Expressed as Multiple Alternatively Spliced Transcripts Encoding Isoforms with Distinct Cellular Localizations and PPIase Activities under Cold Stress. Int J Mol Sci 2016; 17:ijms17071154. [PMID: 27447607 PMCID: PMC4964526 DOI: 10.3390/ijms17071154] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2016] [Revised: 07/05/2016] [Accepted: 07/08/2016] [Indexed: 12/03/2022] Open
Abstract
Alternative splicing (AS) is an important molecular mechanism by which single genes can generate multiple mRNA isoforms. We reported previously that, in Oryza sativa, the cyclophilin 19-4 (OsCYP19-4.1) transcript was significantly upregulated in response to cold stress, and that transgenic plants were cold tolerant. Here we show that, under cold stress, OsCYP19-4 produces eight transcript variants by intron retention and exon skipping, resulting in production of four distinct protein isoforms. The OsCYP19-4 AS isoforms exhibited different cellular localizations in the epidermal cells: in contrast to OsCYP19-4.1, the OsCYP19-4.2 and OsCYP19-4.3 proteins were primarily targeted to guard and subsidiary cells, whereas OsCYP19-4.5, which consists largely of an endoplasmic reticulum (ER) targeting signal, was co-localized with the RFP-BiP marker in the ER. In OsCYP19-4.2, the key residues of the PPIase domain are altered; consistent with this, recombinant OsCYP19-4.2 had significantly lower PPIase activity than OsCYP19-4.1 in vitro. Specific protein-protein interactions between OsCYP19-4.2/3 and AtRCN1 were verified in yeast two-hybrid (Y2H) and bimolecular fluoresence complementation (BiFC assays), although the OsCYP19-4 isoforms could not bind each other. Based on these results, we propose that two OsCYP19-4 AS isoforms, OsCYP19-4.2 and OsCYP19-4.3, play roles linking auxin transport and cold stress via interactions with RCN1.
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40
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Moustafa K, Cross JM. Genetic Approaches to Study Plant Responses to Environmental Stresses: An Overview. BIOLOGY 2016; 5:biology5020020. [PMID: 27196939 PMCID: PMC4929534 DOI: 10.3390/biology5020020] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/15/2016] [Revised: 05/02/2016] [Accepted: 05/10/2016] [Indexed: 12/31/2022]
Abstract
The assessment of gene expression levels is an important step toward elucidating gene functions temporally and spatially. Decades ago, typical studies were focusing on a few genes individually, whereas now researchers are able to examine whole genomes at once. The upgrade of throughput levels aided the introduction of systems biology approaches whereby cell functional networks can be scrutinized in their entireties to unravel potential functional interacting components. The birth of systems biology goes hand-in-hand with huge technological advancements and enables a fairly rapid detection of all transcripts in studied biological samples. Even so, earlier technologies that were restricted to probing single genes or a subset of genes still have their place in research laboratories. The objective here is to highlight key approaches used in gene expression analysis in plant responses to environmental stresses, or, more generally, any other condition of interest. Northern blots, RNase protection assays, and qPCR are described for their targeted detection of one or a few transcripts at a once. Differential display and serial analysis of gene expression represent non-targeted methods to evaluate expression changes of a significant number of gene transcripts. Finally, microarrays and RNA-seq (next-generation sequencing) contribute to the ultimate goal of identifying and quantifying all transcripts in a cell under conditions or stages of study. Recent examples of applications as well as principles, advantages, and drawbacks of each method are contrasted. We also suggest replacing the term “Next-Generation Sequencing (NGS)” with another less confusing synonym such as “RNA-seq”, “high throughput sequencing”, or “massively parallel sequencing” to avoid confusion with any future sequencing technologies.
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Affiliation(s)
- Khaled Moustafa
- Conservatoire National des Arts et Métiers, Paris 75003, France.
| | - Joanna M Cross
- Faculty of Agriculture, Inonu University, Malatya 44000, Turkey.
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Zhang C, Yang H, Yang H. Evolutionary Character of Alternative Splicing in Plants. Bioinform Biol Insights 2016; 9:47-52. [PMID: 26819552 PMCID: PMC4721685 DOI: 10.4137/bbi.s33716] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2015] [Revised: 10/19/2015] [Accepted: 10/24/2015] [Indexed: 12/21/2022] Open
Abstract
Alternative splicing (AS) is one of the most important ways to enhance the functional diversity of genes. Huge amounts of data have been produced by microarray, expressed sequence tag, and RNA-seq, and plenty of methods have been developed specifically for this task. The most frequently asked questions in previous research were as follows. What is the content rate of AS genes among the whole gene set? How many AS types are presented in the genome, and which type is dominant? How about the conservation ability of AS among different species? Which kinds of isoforms from some genes have the environmental response to help individual adaptation? Based on this background, we collected analysis results from 17 species to try to map out the landscape of AS studies in plants. We have noted the shortages of previous results, and we appeal to all scientists working in the AS field to make a standard protocol so that analyses between different projects are comparable.
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Affiliation(s)
- Chengjun Zhang
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan, People's Republic of China
| | - Hong Yang
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan, People's Republic of China
| | - Huizhao Yang
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan, People's Republic of China
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Kim JY, Ryu JY, Baek K, Park CM. High temperature attenuates the gravitropism of inflorescence stems by inducing SHOOT GRAVITROPISM 5 alternative splicing in Arabidopsis. THE NEW PHYTOLOGIST 2016; 209:265-279. [PMID: 26256266 DOI: 10.1111/nph.13602] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/10/2015] [Accepted: 07/09/2015] [Indexed: 06/04/2023]
Abstract
In higher plants, gravitropism proceeds through three sequential steps in the responding organs: perception of gravity signals, signal transduction and asymmetric cell elongation. Light and temperature also influence the gravitropic orientation of plant organs. A series of Arabidopsis shoot gravitropism (sgr) mutants has been shown to exhibit disturbed shoot gravitropism. SGR5 is functionally distinct from other SGR members in that it mediates the early events of gravitropic responses in inflorescence stems. Here, we demonstrated that SGR5 alternative splicing produces two protein variants (SGR5α and SGR5β) in modulating the gravitropic response of inflorescence stems at high temperatures. SGR5β inhibits SGR5α function by forming non-DNA-binding heterodimers. Transgenic plants overexpressing SGR5β (35S:SGR5β) exhibit reduced gravitropic growth of inflorescence stems, as observed in the SGR5-deficient sgr5-5 mutant. Interestingly, SGR5 alternative splicing is accelerated at high temperatures, resulting in the high-level accumulation of SGR5β transcripts. When plants were exposed to high temperatures, whereas gravitropic curvature was reduced in Col-0 inflorescence stems, it was uninfluenced in the inflorescence stems of 35S:SGR5β transgenic plants and sgr5-5 mutant. We propose that the thermoresponsive alternative splicing of SGR5 provides an adaptation strategy by which plants protect the shoots from hot air under high temperature stress in natural habitats.
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Affiliation(s)
- Joo-Young Kim
- Department of Chemistry, Seoul National University, Seoul, 151-742, Korea
| | - Jae Yong Ryu
- Department of Chemistry, Seoul National University, Seoul, 151-742, Korea
| | - Kon Baek
- Department of Chemistry, Seoul National University, Seoul, 151-742, Korea
| | - Chung-Mo Park
- Department of Chemistry, Seoul National University, Seoul, 151-742, Korea
- Plant Genomics and Breeding Institute, Seoul National University, Seoul, 151-742, Korea
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43
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Thatcher SR, Danilevskaya ON, Meng X, Beatty M, Zastrow-Hayes G, Harris C, Van Allen B, Habben J, Li B. Genome-Wide Analysis of Alternative Splicing during Development and Drought Stress in Maize. PLANT PHYSIOLOGY 2016; 170:586-99. [PMID: 26582726 PMCID: PMC4704579 DOI: 10.1104/pp.15.01267] [Citation(s) in RCA: 92] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/13/2015] [Accepted: 11/17/2015] [Indexed: 05/18/2023]
Abstract
Alternative splicing plays a crucial role in plant development as well as stress responses. Although alternative splicing has been studied during development and in response to stress, the interplay between these two factors remains an open question. To assess the effects of drought stress on developmentally regulated splicing in maize (Zea mays), 94 RNA-seq libraries from ear, tassel, and leaf of the B73 public inbred line were constructed at four developmental stages under both well-watered and drought conditions. This analysis was supplemented with a publicly available series of 53 libraries from developing seed, embryo, and endosperm. More than 48,000 novel isoforms, often with stage- or condition-specific expression, were uncovered, suggesting that developmentally regulated alternative splicing occurs in thousands of genes. Drought induced large developmental splicing changes in leaf and ear but relatively few in tassel. Most developmental stage-specific splicing changes affected by drought were tissue dependent, whereas stage-independent changes frequently overlapped between leaf and ear. A linear relationship was found between gene expression changes in splicing factors and alternative spicing of other genes during development. Collectively, these results demonstrate that alternative splicing is strongly associated with tissue type, developmental stage, and stress condition.
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Affiliation(s)
- Shawn R Thatcher
- DuPont Pioneer, Wilmington, Delaware 19880 (S.R.T., B.L.); andDuPont Pioneer, Johnston, Iowa 50131 (O.N.D., X.M., M.B., G.Z.-H., C.H., B.V.A., J.H.)
| | - Olga N Danilevskaya
- DuPont Pioneer, Wilmington, Delaware 19880 (S.R.T., B.L.); andDuPont Pioneer, Johnston, Iowa 50131 (O.N.D., X.M., M.B., G.Z.-H., C.H., B.V.A., J.H.)
| | - Xin Meng
- DuPont Pioneer, Wilmington, Delaware 19880 (S.R.T., B.L.); andDuPont Pioneer, Johnston, Iowa 50131 (O.N.D., X.M., M.B., G.Z.-H., C.H., B.V.A., J.H.)
| | - Mary Beatty
- DuPont Pioneer, Wilmington, Delaware 19880 (S.R.T., B.L.); andDuPont Pioneer, Johnston, Iowa 50131 (O.N.D., X.M., M.B., G.Z.-H., C.H., B.V.A., J.H.)
| | - Gina Zastrow-Hayes
- DuPont Pioneer, Wilmington, Delaware 19880 (S.R.T., B.L.); andDuPont Pioneer, Johnston, Iowa 50131 (O.N.D., X.M., M.B., G.Z.-H., C.H., B.V.A., J.H.)
| | - Charlotte Harris
- DuPont Pioneer, Wilmington, Delaware 19880 (S.R.T., B.L.); andDuPont Pioneer, Johnston, Iowa 50131 (O.N.D., X.M., M.B., G.Z.-H., C.H., B.V.A., J.H.)
| | - Brandon Van Allen
- DuPont Pioneer, Wilmington, Delaware 19880 (S.R.T., B.L.); andDuPont Pioneer, Johnston, Iowa 50131 (O.N.D., X.M., M.B., G.Z.-H., C.H., B.V.A., J.H.)
| | - Jeffrey Habben
- DuPont Pioneer, Wilmington, Delaware 19880 (S.R.T., B.L.); andDuPont Pioneer, Johnston, Iowa 50131 (O.N.D., X.M., M.B., G.Z.-H., C.H., B.V.A., J.H.)
| | - Bailin Li
- DuPont Pioneer, Wilmington, Delaware 19880 (S.R.T., B.L.); andDuPont Pioneer, Johnston, Iowa 50131 (O.N.D., X.M., M.B., G.Z.-H., C.H., B.V.A., J.H.)
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44
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Ling Z, Zhou W, Baldwin IT, Xu S. Insect herbivory elicits genome-wide alternative splicing responses in Nicotiana attenuata. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2015; 84:228-43. [PMID: 26306554 DOI: 10.1111/tpj.12997] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/08/2015] [Revised: 08/04/2015] [Accepted: 08/11/2015] [Indexed: 05/06/2023]
Abstract
Changes in gene expression and alternative splicing (AS) are involved in many responses to abiotic and biotic stresses in eukaryotic organisms. In response to attack and oviposition by insect herbivores, plants elicit rapid changes in gene expression which are essential for the activation of plant defenses; however, the herbivory-induced changes in AS remain unstudied. Using mRNA sequencing, we performed a genome-wide analysis on tobacco hornworm (Manduca sexta) feeding-induced AS in both leaves and roots of Nicotiana attenuata. Feeding by M. sexta for 5 h reduced total AS events by 7.3% in leaves but increased them in roots by 8.0% and significantly changed AS patterns in leaves and roots of existing AS genes. Feeding by M. sexta also resulted in increased (in roots) and decreased (in leaves) transcript levels of the serine/arginine-rich (SR) proteins that are involved in the AS machinery of plants and induced changes in SR gene expression that were jasmonic acid (JA)-independent in leaves but JA-dependent in roots. Changes in AS and gene expression elicited by M. sexta feeding were regulated independently in both tissues. This study provides genome-wide evidence that insect herbivory induces changes not only in the levels of gene expression but also in their splicing, which might contribute to defense against and/or tolerance of herbivory.
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Affiliation(s)
- Zhihao Ling
- Department of Molecular Ecology, Max Planck Institute for Chemical Ecology, Hans-Knöll-Straße 8, D-07745, Jena, Germany
| | - Wenwu Zhou
- Department of Molecular Ecology, Max Planck Institute for Chemical Ecology, Hans-Knöll-Straße 8, D-07745, Jena, Germany
| | - Ian T Baldwin
- Department of Molecular Ecology, Max Planck Institute for Chemical Ecology, Hans-Knöll-Straße 8, D-07745, Jena, Germany
| | - Shuqing Xu
- Department of Molecular Ecology, Max Planck Institute for Chemical Ecology, Hans-Knöll-Straße 8, D-07745, Jena, Germany
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45
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Brown JWS, Simpson CG, Marquez Y, Gadd GM, Barta A, Kalyna M. Lost in Translation: Pitfalls in Deciphering Plant Alternative Splicing Transcripts. THE PLANT CELL 2015; 27:2083-7. [PMID: 26286536 PMCID: PMC4568512 DOI: 10.1105/tpc.15.00572] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/25/2015] [Revised: 07/29/2015] [Accepted: 08/09/2015] [Indexed: 05/19/2023]
Abstract
Transcript annotation in plant databases is incomplete and often inaccurate, leading to misinterpretation. As more and more RNA-seq data are generated, plant scientists need to be aware of potential pitfalls and understand the nature and impact of specific alternative splicing transcripts on protein production. A primary area of concern and the topic of this article is the (mis)annotation of open reading frames and premature termination codons. The basic message is that to adequately address expression and functions of transcript isoforms, it is necessary to be able to predict their fate in terms of whether protein isoforms are generated or specific transcripts are unproductive or degraded.
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Affiliation(s)
- John W S Brown
- Plant Sciences Division, School of Life Sciences, University of Dundee, Invergowrie, Dundee DD2 5DA, Scotland, United Kingdom Cell and Molecular Sciences, The James Hutton Institute, Invergowrie, Dundee DD2 5DA, Scotland, United Kingdom
| | - Craig G Simpson
- Cell and Molecular Sciences, The James Hutton Institute, Invergowrie, Dundee DD2 5DA, Scotland, United Kingdom
| | - Yamile Marquez
- Max F. Perutz Laboratories, Medical University of Vienna, 1030 Vienna, Austria Center for Integrative Bioinformatics Vienna, Max F. Perutz Laboratories, Medical University of Vienna, 1030 Vienna, Austria
| | - Geoffrey M Gadd
- Geomicrobiology Group, School of Life Sciences, University of Dundee, Dundee DD1 5EH, Scotland, United Kingdom
| | - Andrea Barta
- Max F. Perutz Laboratories, Medical University of Vienna, 1030 Vienna, Austria
| | - Maria Kalyna
- Department of Applied Genetics and Cell Biology, BOKU-University of Natural Resources and Life Sciences, 1190 Vienna, Austria
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Chen H, Chen X, Chen D, Li J, Zhang Y, Wang A. A comparison of the low temperature transcriptomes of two tomato genotypes that differ in freezing tolerance: Solanum lycopersicum and Solanum habrochaites. BMC PLANT BIOLOGY 2015; 15:132. [PMID: 26048292 PMCID: PMC4458020 DOI: 10.1186/s12870-015-0521-6] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/21/2014] [Accepted: 05/11/2015] [Indexed: 05/18/2023]
Abstract
BACKGROUND Solanum lycopersicum and Solanum habrochaites are closely related plant species; however, their cold tolerance capacities are different. The wild species S. habrochaites is more cold tolerant than the cultivated species S. lycopersicum. RESULTS The transcriptomes of S. lycopersicum and S. habrochaites leaf tissues under cold stress were studied using Illumina high-throughput RNA sequencing. The results showed that more than 200 million reads could be mapped to identify genes, microRNAs (miRNAs), and alternative splicing (AS) events to confirm the transcript abundance under cold stress. The results indicated that 21% and 23% of genes were differentially expressed in the cultivated and wild tomato species, respectively, and a series of changes in S. lycopersicum and S. habrochaites transcriptomes occur when plants are moved from warm to cold conditions. Moreover, the gene expression patterns for S. lycopersicum and S. habrochaites were dissimilar; however, there were some overlapping genes that were regulated by low temperature in both tomato species. An AS analysis identified 75,885 novel splice junctions among 172,910 total splice junctions, which suggested that the relative abundance of alternative intron isoforms in S. lycopersicum and S. habrochaites shifted significantly under cold stress. In addition, we identified 89 miRNA sequences that may regulate relevant target genes. Our data indicated that some miRNAs (e.g., miR159, miR319, and miR6022) play roles in the response to cold stress. CONCLUSIONS Differences in gene expression, AS events, and miRNAs under cold stress may contribute to the observed differences in cold tolerance of these two tomato species.
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Affiliation(s)
- Hongyu Chen
- Heilongjiang Provincial Key University Laboratory of Agricultural Functional Genes, College of Life Science, Northeast Agricultural University, Harbin, 150030, China.
| | - Xiuling Chen
- College of Horticulture, Northeast Agricultural University, Harbin, 150030, China.
| | | | - Jingfu Li
- College of Horticulture, Northeast Agricultural University, Harbin, 150030, China.
| | - Yi Zhang
- ABLife, Inc, Wuhan, 430075, China.
| | - Aoxue Wang
- Heilongjiang Provincial Key University Laboratory of Agricultural Functional Genes, College of Life Science, Northeast Agricultural University, Harbin, 150030, China.
- College of Horticulture, Northeast Agricultural University, Harbin, 150030, China.
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47
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Unmasking alternative splicing inside protein-coding exons defines exitrons and their role in proteome plasticity. Genome Res 2015; 25:995-1007. [PMID: 25934563 PMCID: PMC4484396 DOI: 10.1101/gr.186585.114] [Citation(s) in RCA: 113] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2014] [Accepted: 04/30/2015] [Indexed: 11/25/2022]
Abstract
Alternative splicing (AS) diversifies transcriptomes and proteomes and is widely recognized as a key mechanism for regulating gene expression. Previously, in an analysis of intron retention events in Arabidopsis, we found unusual AS events inside annotated protein-coding exons. Here, we also identify such AS events in human and use these two sets to analyse their features, regulation, functional impact, and evolutionary origin. As these events involve introns with features of both introns and protein-coding exons, we name them exitrons (exonic introns). Though exitrons were detected as a subset of retained introns, they are clearly distinguishable, and their splicing results in transcripts with different fates. About half of the 1002 Arabidopsis and 923 human exitrons have sizes of multiples of 3 nucleotides (nt). Splicing of these exitrons results in internally deleted proteins and affects protein domains, disordered regions, and various post-translational modification sites, thus broadly impacting protein function. Exitron splicing is regulated across tissues, in response to stress and in carcinogenesis. Intriguingly, annotated intronless genes can be also alternatively spliced via exitron usage. We demonstrate that at least some exitrons originate from ancestral coding exons. Based on our findings, we propose a “splicing memory” hypothesis whereby upon intron loss imprints of former exon borders defined by vestigial splicing regulatory elements could drive the evolution of exitron splicing. Altogether, our studies show that exitron splicing is a conserved strategy for increasing proteome plasticity in plants and animals, complementing the repertoire of AS events.
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Browning KS, Bailey-Serres J. Mechanism of cytoplasmic mRNA translation. THE ARABIDOPSIS BOOK 2015; 13:e0176. [PMID: 26019692 PMCID: PMC4441251 DOI: 10.1199/tab.0176] [Citation(s) in RCA: 144] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
Protein synthesis is a fundamental process in gene expression that depends upon the abundance and accessibility of the mRNA transcript as well as the activity of many protein and RNA-protein complexes. Here we focus on the intricate mechanics of mRNA translation in the cytoplasm of higher plants. This chapter includes an inventory of the plant translational apparatus and a detailed review of the translational processes of initiation, elongation, and termination. The majority of mechanistic studies of cytoplasmic translation have been carried out in yeast and mammalian systems. The factors and mechanisms of translation are for the most part conserved across eukaryotes; however, some distinctions are known to exist in plants. A comprehensive understanding of the complex translational apparatus and its regulation in plants is warranted, as the modulation of protein production is critical to development, environmental plasticity and biomass yield in diverse ecosystems and agricultural settings.
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Affiliation(s)
- Karen S. Browning
- Department of Molecular Biosciences and Institute for Cell and Molecular Biology, University of Texas at Austin, Austin TX 78712-0165
- Both authors contributed equally to this work
| | - Julia Bailey-Serres
- Department of Botany and Plant Sciences and Center for Plant Cell Biology, University of California, Riverside, CA, 92521 USA
- Both authors contributed equally to this work
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A protocol for visual analysis of alternative splicing in RNA-Seq data using integrated genome browser. Methods Mol Biol 2014; 1158:123-37. [PMID: 24792048 DOI: 10.1007/978-1-4939-0700-7_8] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/16/2023]
Abstract
Ultrahigh-throughput sequencing of cDNA (RNA-Seq) is an invaluable resource for investigating alternative splicing in an organism. Alternative splicing is a form of posttranscriptional regulation in which primary RNA transcripts from a single gene can be spliced in multiple ways leading to different RNA and protein products. In plants and other species, it has been shown that many genes involved in circadian regulation are alternatively spliced. As new RNA-Seq data sets become available, these data will lead to new insights into links between regulation RNA splicing and the circadian system. Analyzing RNA-Seq data sets requires software tools that can display RNA-Seq read alignments alongside gene models, enabling assessment of how treatments or developmental stages affect splicing patterns and production of novel variants. The Integrated Genome Browser (IGB) software program is a free and flexible desktop tool that enables discovery and quantification of alternative splicing. In this protocol, we use IGB and a cold-stress RNA-Seq data set to examine alternative splicing of Arabidopsis thaliana LHY, a circadian clock regulator. IGB is freely available from http://www.bioviz.org .
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Abstract
It is widely appreciated that short tandem repeat (STR) variation underlies substantial phenotypic variation in organisms. Some propose that the high mutation rates of STRs in functional genomic regions facilitate evolutionary adaptation. Despite their high mutation rate, some STRs show little to no variation in populations. One such STR occurs in the Arabidopsis thaliana gene PFT1 (MED25), where it encodes an interrupted polyglutamine tract. Although the PFT1 STR is large (∼270 bp), and thus expected to be extremely variable, it shows only minuscule variation across A. thaliana strains. We hypothesized that the PFT1 STR is under selective constraint, due to previously undescribed roles in PFT1 function. We investigated this hypothesis using plants expressing transgenic PFT1 constructs with either an endogenous STR or synthetic STRs of varying length. Transgenic plants carrying the endogenous PFT1 STR generally performed best in complementing a pft1 null mutant across adult PFT1-dependent traits. In stark contrast, transgenic plants carrying a PFT1 transgene lacking the STR phenocopied a pft1 loss-of-function mutant for flowering time phenotypes and were generally hypomorphic for other traits, establishing the functional importance of this domain. Transgenic plants carrying various synthetic constructs occupied the phenotypic space between wild-type and pft1 loss-of-function mutants. By varying PFT1 STR length, we discovered that PFT1 can act as either an activator or repressor of flowering in a photoperiod-dependent manner. We conclude that the PFT1 STR is constrained to its approximate wild-type length by its various functional requirements. Our study implies that there is strong selection on STRs not only to generate allelic diversity, but also to maintain certain lengths pursuant to optimal molecular function.
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