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Zhu H, Yang JL, Chen W. Epigenetic insights into an epimutant colorless non-ripening: from fruit ripening to stress responses. FRONTIERS IN PLANT SCIENCE 2024; 15:1440120. [PMID: 39015288 PMCID: PMC11250591 DOI: 10.3389/fpls.2024.1440120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/29/2024] [Accepted: 06/12/2024] [Indexed: 07/18/2024]
Abstract
The epigenetic machinery has received extensive attention due to its involvement in plant growth, development, and adaptation to environmental changes. Recent studies often highlight the epigenetic regulatory network by discussing various epigenetic mutants across various plant species. However, a systemic understanding of essential epigenetic regulatory mechanisms remains limited due to a lack of representative mutants involved in multiple biological processes. Colorless Non-ripening (Cnr), a spontaneous epimutant isolated from a commercial population, was initially characterized for its role in fruit ripening regulation. Cnr fruits exhibit an immature phenotype with yellow skin, attributed to hypermethylation of the SQUAMOSA PROMOTER BINDING PROTEIN-LIKE-CNR (SlSPL-CNR) promoter, resulting in the repression of gene expression. In addition to DNA methylation, this process also involves histone modification and microRNA, integrating multiple epigenetic regulatory factors. Interestingly, knockout mutants of SlSPL-CNR display phenotypical distinctions from Cnr in fruit ripening, indicating complex genetic and epigenetic control over the non-ripening phenotype in Cnr fruits. Accumulating evidence suggests that Cnr epimutation is pleiotropic, participating in various biological processes such as Cd stress, Fe deficiency, vivipary, and cell death. Therefore, the Cnr epimutant serve as an excellent model for unveiling how epigenetic mechanisms are involved in diverse biological processes. This review paper focuses on recent research advances regarding the Cnr epimutant, delving into its complex genetic and epigenetic regulatory mechanisms, with the aim of enhancing our understanding and facilitating the development of high-quality, high-yield crops through epigenetic modification.
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Affiliation(s)
- Huihui Zhu
- College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, China
- Key Laboratory of Vegetable Biology, College of Landscape and Horticulture, Yunnan Agricultural University, Kunming, China
| | - Jian Li Yang
- Key Laboratory of Vegetable Biology, College of Landscape and Horticulture, Yunnan Agricultural University, Kunming, China
| | - Weiwei Chen
- College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, China
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2
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Nivedha M, Harish S, Angappan K, Karthikeyan G, Kumar KK, Murugan M, Infant Richard J. Profiling of Groundnut bud necrosis orthotospovirus-responsive microRNA and their targets in tomato based on deep sequencing. J Virol Methods 2024; 327:114924. [PMID: 38574773 DOI: 10.1016/j.jviromet.2024.114924] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2023] [Revised: 03/26/2024] [Accepted: 04/01/2024] [Indexed: 04/06/2024]
Abstract
Tomato, an extensively cultivated vegetable crop produces miRNAs in response to infection with Groundnut bud necrosis orthotospovirus, a viral pathogen causing significant economic losses. High-throughput miRNA sequencing was performed on tomato leaves inoculated with GBNV and mock-inoculated leaves as controls. Analysis revealed 73 known miRNAs belonging to 24 miRNA families, with variable expression levels. Interestingly, 39 miRNAs were upregulated, and 34 were downregulated in response to GBNV infection. Stem-loop quantitative reverse transcription PCR validated the differential expression of selected miRNAs. Additionally, 30 miRNA encoded proteins were identified to be involved in disease resistance and susceptibility. The miRNA-target interactions were found to play significant roles in cellular and metabolic activities, as well as modulating signaling pathways during the plant-virus interaction. The findings shed light on the intricate regulatory network of miRNAs in tomato response to viral infection and may contribute to developing strategies for improving crop protection against viral diseases.
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Affiliation(s)
- M Nivedha
- Department of Plant Pathology, Tamil Nadu Agricultural University, Coimbatore, Tamil Nadu 641 003, India
| | - S Harish
- Department of Plant Pathology, Tamil Nadu Agricultural University, Coimbatore, Tamil Nadu 641 003, India.
| | - K Angappan
- Department of Plant Pathology, Tamil Nadu Agricultural University, Coimbatore, Tamil Nadu 641 003, India
| | - G Karthikeyan
- Department of Plant Pathology, Tamil Nadu Agricultural University, Coimbatore, Tamil Nadu 641 003, India
| | - K K Kumar
- Department of Plant Biotechnology, Centre for Plant Molecular Biology and Biotechnology, Tamil Nadu Agricultural University, Coimbatore, Tamil Nadu 641 003, India
| | - M Murugan
- Department of Agricultural Entomology, Tamil Nadu Agricultural University, Coimbatore, Tamil Nadu 641 003, India
| | - J Infant Richard
- Department of Plant Molecular Biology and Bioinformatics, Centre for Plant Molecular Biology and Biotechnology, Tamil Nadu Agricultural University, Coimbatore, Tamil Nadu 641 003, India
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3
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Sharma D, Koul A, Bhushan S, Gupta S, Kaul S, Dhar MK. Insights into microRNA-mediated interaction and regulation of metabolites in tomato. PLANT BIOLOGY (STUTTGART, GERMANY) 2023; 25:1142-1153. [PMID: 37681459 DOI: 10.1111/plb.13572] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/24/2023] [Accepted: 07/23/2023] [Indexed: 09/09/2023]
Abstract
microRNAs direct regulation of various metabolic pathways in plants and animals. miRNAs may be useful in developing novel/elite genotypes, with enhanced metabolites and disease resistance. We examined miRNAs in tomato. In tomato, miRNAs in the carotenoid pathway have not been fully elucidated. We examined the potential role of miRNAs in biosynthesis of carotenoids, transcript profiling of miRNAs and their possible targets (genes and transcription factors) at different development stages of tomato using stem-loop PCR and RT-qPCR. We also identified miRNAs targeting key flavonoid genes, such as chalcone isomerase (CHI), and dihydroflavonol-4-reductase (DFR). Distinct expression profiles of miRNAs and their targets were found in fruits of three tomato accessions, suggesting carotenoid regulation by miRNAs at various stages of fruit development. This was also confirmed using HPLC of the carotenoids. The present study may help in understanding possible regulation of carotenoid biosynthesis. The identified miRNAs can be exploited to enhance biosynthesis of different carotenoids in plants.
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Affiliation(s)
- D Sharma
- Genome Research Laboratory, School of Biotechnology, University of Jammu, Jammu, India
| | - A Koul
- Department of Pharmacy and Pharmaceutical Sciences, University of Alberta, Edmonton, AB, Canada
| | - S Bhushan
- Department of Botany, Central University of Jammu, Bagla (Rahya Suchani), Samba, Jammu, India
| | - S Gupta
- Genome Research Laboratory, School of Biotechnology, University of Jammu, Jammu, India
| | - S Kaul
- Genome Research Laboratory, School of Biotechnology, University of Jammu, Jammu, India
| | - M K Dhar
- Genome Research Laboratory, School of Biotechnology, University of Jammu, Jammu, India
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Green D, Singh A, Tippett VL, Tattersall L, Shah KM, Siachisumo C, Ward NJ, Thomas P, Carter S, Jeys L, Sumathi V, McNamara I, Elliott DJ, Gartland A, Dalmay T, Fraser WD. YBX1-interacting small RNAs and RUNX2 can be blocked in primary bone cancer using CADD522. J Bone Oncol 2023; 39:100474. [PMID: 36936386 PMCID: PMC10015236 DOI: 10.1016/j.jbo.2023.100474] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2023] [Revised: 02/28/2023] [Accepted: 02/28/2023] [Indexed: 03/07/2023] Open
Abstract
Primary bone cancer (PBC) comprises several subtypes each underpinned by distinctive genetic drivers. This driver diversity produces novel morphological features and clinical behaviour that serendipitously makes PBC an excellent metastasis model. Here, we report that some transfer RNA-derived small RNAs termed tRNA fragments (tRFs) perform as a constitutive tumour suppressor mechanism by blunting a potential pro-metastatic protein-RNA interaction. This mechanism is reduced in PBC progression with a gradual loss of tRNAGlyTCC cleavage into 5' end tRF-GlyTCC when comparing low-grade, intermediate-grade and high-grade patient tumours. We detected recurrent activation of miR-140 leading to upregulated RUNX2 expression in high-grade patient tumours. Both tRF-GlyTCC and RUNX2 share a sequence motif in their 3' ends that matches the YBX1 recognition site known to stabilise pro-metastatic mRNAs. Investigating some aspects of this interaction network, gain- and loss-of-function experiments using small RNA mimics and antisense LNAs, respectively, showed that ectopic tRF-GlyTCC reduced RUNX2 expression and dispersed 3D micromass architecture in vitro. iCLIP sequencing revealed YBX1 physical binding to the 3' UTR of RUNX2. The interaction between YBX1, tRF-GlyTCC and RUNX2 led to the development of the RUNX2 inhibitor CADD522 as a PBC treatment. CADD522 assessment in vitro revealed significant effects on PBC cell behaviour. In xenograft mouse models, CADD522 as a single agent without surgery significantly reduced tumour volume, increased overall and metastasis-free survival and reduced cancer-induced bone disease. Our results provide insight into PBC molecular abnormalities that have led to the identification of new targets and a new therapeutic.
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Key Words
- CADD522
- CADD522, computer aided drug design molecule 522
- CI, confidence interval
- CNV, copy number variant
- CS, chondrosarcoma
- CTC, circulating tumour cell
- DE, differentially expressed
- ES, Ewing sarcoma
- HD, high definition
- HR, hazard ratio
- OS, osteosarcoma
- RBP, RNA binding protein
- RNU6-1, U6 small nuclear 1
- ROI, region-of-interest
- Rnl, T4 RNA ligase
- SNV, single nucleotide variant
- SV, structural variant
- bone cancer
- iCLIP, individual nucleotide resolution cross-linking and immunoprecipitation
- mRNA, messenger RNA
- miRNA
- miRNA, microRNA
- piRNA, piwi interacting RNA
- sRNA, small RNA
- small RNA
- tRF
- tRF, transfer RNA fragment
- tRNA, transfer RNA
- ysRNA, Y RNA-derived sRNA
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Affiliation(s)
- Darrell Green
- Biomedical Research Centre, Norwich Medical School, University of East Anglia, Norwich, UK
- Corresponding author.
| | - Archana Singh
- School of Biological Sciences, University of East Anglia, Norwich, UK
| | - Victoria L. Tippett
- The Mellanby Centre for Musculoskeletal Research, Department of Oncology and Metabolism, The University of Sheffield, UK
| | - Luke Tattersall
- The Mellanby Centre for Musculoskeletal Research, Department of Oncology and Metabolism, The University of Sheffield, UK
| | - Karan M. Shah
- The Mellanby Centre for Musculoskeletal Research, Department of Oncology and Metabolism, The University of Sheffield, UK
| | | | - Nicole J. Ward
- School of Biological Sciences, University of East Anglia, Norwich, UK
| | - Paul Thomas
- School of Biological Sciences, University of East Anglia, Norwich, UK
- Henry Wellcome Laboratory for Cell Imaging, Faculty of Science, University of East Anglia, Norwich, UK
| | - Simon Carter
- Orthopaedic Oncology, Royal Orthopaedic Hospital, Birmingham, UK
| | - Lee Jeys
- Orthopaedic Oncology, Royal Orthopaedic Hospital, Birmingham, UK
| | - Vaiyapuri Sumathi
- Musculoskeletal Pathology, University Hospitals Birmingham, Royal Orthopaedic Hospital, Birmingham, UK
| | - Iain McNamara
- Orthopaedics & Trauma, Norfolk and Norwich University Hospital, Norwich, UK
| | | | - Alison Gartland
- The Mellanby Centre for Musculoskeletal Research, Department of Oncology and Metabolism, The University of Sheffield, UK
| | - Tamas Dalmay
- School of Biological Sciences, University of East Anglia, Norwich, UK
| | - William D. Fraser
- Biomedical Research Centre, Norwich Medical School, University of East Anglia, Norwich, UK
- Clinical Biochemistry, Diabetes and Endocrinology, Norfolk and Norwich University Hospital, Norwich, UK
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Abstract
Small RNAs (sRNAs) are key regulators of transcriptomes and proteomes of organisms through their sequence-specific interaction with complementary RNA targets. sRNAs can be classified according to their origin and mode of action into different classes such as: microRNAs (miRNAs), small interfering RNAs (siRNAs) and PIWI-interacting RNAs (piRNAs). The abundance and specific spatio-temporal expression of many sRNAs, especially miRNAs, is relevant for their biological function. Northern blotting is a widely used technique to study sRNAs because it is quantitative, relatively inexpensive, and readily available for most laboratories. This chapter describes the protocols for radioactive and non-radioactive sRNA Northern blot analysis, which includes RNA extraction, polyacrylamide gel electrophoresis, membrane transfer, hybridisation and detection of sRNA using oligonucleotide probes. The protocol is described to prepare most of the reagents needed in the lab, but also timesaving commercial reagent alternatives are included. Suggestions and nuances obtained from experience are included as Notes.
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Affiliation(s)
- Claudia Martinho
- Department of Plant Sciences, University of Cambridge, Cambridge, UK
- Department of Algal Development and Evolution, Max Planck Institute for Biology Tübingen, Tübingen, Germany
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Williams EC, Chazarra-Gil R, Shahsavari A, Mohorianu I. The Sum of Two Halves May Be Different from the Whole-Effects of Splitting Sequencing Samples Across Lanes. Genes (Basel) 2022; 13:genes13122265. [PMID: 36553532 PMCID: PMC9777937 DOI: 10.3390/genes13122265] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2022] [Revised: 11/23/2022] [Accepted: 11/25/2022] [Indexed: 12/03/2022] Open
Abstract
The advances in high-throughput sequencing (HTS) have enabled the characterisation of biological processes at an unprecedented level of detail; most hypotheses in molecular biology rely on analyses of HTS data. However, achieving increased robustness and reproducibility of results remains a main challenge. Although variability in results may be introduced at various stages, e.g., alignment, summarisation or detection of differential expression, one source of variability was systematically omitted: the sequencing design, which propagates through analyses and may introduce an additional layer of technical variation. We illustrate qualitative and quantitative differences arising from splitting samples across lanes on bulk and single-cell sequencing. For bulk mRNAseq data, we focus on differential expression and enrichment analyses; for bulk ChIPseq data, we investigate the effect on peak calling and the peaks' properties. At the single-cell level, we concentrate on identifying cell subpopulations. We rely on markers used for assigning cell identities; both smartSeq and 10× data are presented. The observed reduction in the number of unique sequenced fragments limits the level of detail on which the different prediction approaches depend. Furthermore, the sequencing stochasticity adds in a weighting bias corroborated with variable sequencing depths and (yet unexplained) sequencing bias. Subsequently, we observe an overall reduction in sequencing complexity and a distortion in the biological signal across technologies, experimental contexts, organisms and tissues.
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Affiliation(s)
- Eleanor C. Williams
- Wellcome-MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge CB2 0AW, UK
| | - Ruben Chazarra-Gil
- Wellcome-MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge CB2 0AW, UK
- Life Sciences-Transcriptomics and Functional Genomics Lab, Barcelona Supercomputing Center (BSC-CNS), 08034 Barcelona, Spain
| | - Arash Shahsavari
- Wellcome-MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge CB2 0AW, UK
| | - Irina Mohorianu
- Wellcome-MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge CB2 0AW, UK
- Correspondence:
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7
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Tomato MicroRNAs and Their Functions. Int J Mol Sci 2022; 23:ijms231911979. [PMID: 36233279 PMCID: PMC9569937 DOI: 10.3390/ijms231911979] [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: 08/14/2022] [Revised: 09/28/2022] [Accepted: 10/03/2022] [Indexed: 11/05/2022] Open
Abstract
MicroRNAs (miRNAs) define an essential class of non-coding small RNAs that function as posttranscriptional modulators of gene expression. They are coded by MIR genes, several hundreds of which exist in the genomes of Arabidopsis and rice model plants. The functional analysis of Arabidopsis and rice miRNAs indicate that their miRNAs regulate a wide range of processes including development, reproduction, metabolism, and stress. Tomato serves as a major model crop for the study of fleshy fruit development and ripening but until recently, information on the identity of its MIR genes and their coded miRNAs was limited and occasionally contradictory. As a result, the majority of tomato miRNAs remained uncharacterized. Recently, a comprehensive annotation of tomato MIR genes has been carried out by several labs and us. In this review, we curate and organize the resulting partially overlapping MIR annotations into an exhaustive and non-redundant atlas of tomato MIR genes. There are 538 candidate and validated MIR genes in the atlas, of which, 169, 18, and 351 code for highly conserved, Solanaceae-specific, and tomato-specific miRNAs, respectively. Furthermore, a critical review of functional studies on tomato miRNAs is presented, highlighting validated and possible functions, creating a useful resource for future tomato miRNA research.
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8
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He M, Kong X, Jiang Y, Qu H, Zhu H. MicroRNAs: emerging regulators in horticultural crops. TRENDS IN PLANT SCIENCE 2022; 27:936-951. [PMID: 35466027 DOI: 10.1016/j.tplants.2022.03.011] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/10/2021] [Revised: 02/24/2022] [Accepted: 03/17/2022] [Indexed: 05/24/2023]
Abstract
Horticulture is one of the oldest agricultural practices with great popularity throughout the world. Horticultural crops include fruits, vegetables, ornamental plants, as well as medicinal and beverage plants. They are cultivated for food, specific nutrition, and medical use, or for aesthetic pleasure. MicroRNAs (miRNAs), which constitute a major class of endogenous small RNAs in plants, affect a multitude of developmental and physiological processes by imparting sequence specificity to gene regulation. Over the past decade, tens of thousands of miRNAs have been identified in more than 100 horticultural crops and their critical roles in regulating quality development of diverse horticultural crops have been demonstrated. Here, we review how miRNAs have emerged as important regulators and promising tools for horticultural crop improvement.
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Affiliation(s)
- Meiying He
- Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xiangjin Kong
- Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yueming Jiang
- Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Hongxia Qu
- Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China; University of Chinese Academy of Sciences, Beijing 100049, China.
| | - Hong Zhu
- Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China.
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9
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Bravo-Vázquez LA, Srivastava A, Bandyopadhyay A, Paul S. The elusive roles of chloroplast microRNAs: an unexplored facet of the plant transcriptome. PLANT MOLECULAR BIOLOGY 2022; 109:667-671. [PMID: 35614291 DOI: 10.1007/s11103-022-01279-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/07/2022] [Accepted: 04/24/2022] [Indexed: 06/15/2023]
Affiliation(s)
- Luis Alberto Bravo-Vázquez
- Tecnologico de Monterrey, School of Engineering and Sciences, Campus Queretaro, Av. Epigmenio Gonzalez, No. 500 Fracc., 76130, San Pablo, Queretaro, Mexico
| | - Aashish Srivastava
- Section of Bioinformatics, Clinical Laboratory, Haukeland University Hospital, 5021, Bergen, Norway
- Department of Clinical Science, University of Bergen, 5021, Bergen, Norway
| | - Anindya Bandyopadhyay
- International Rice Research Institute, 4031, Manila, Philippines.
- Reliance Industries Ltd., 400701, Navi Mumbai, India.
| | - Sujay Paul
- Tecnologico de Monterrey, School of Engineering and Sciences, Campus Queretaro, Av. Epigmenio Gonzalez, No. 500 Fracc., 76130, San Pablo, Queretaro, Mexico.
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10
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Lin D, Zhu X, Qi B, Gao Z, Tian P, Li Z, Lin Z, Zhang Y, Huang T. SlMIR164A regulates fruit ripening and quality by controlling SlNAM2 and SlNAM3 in tomato. PLANT BIOTECHNOLOGY JOURNAL 2022; 20:1456-1469. [PMID: 35403821 PMCID: PMC9342619 DOI: 10.1111/pbi.13824] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/29/2022] [Revised: 03/25/2022] [Accepted: 04/01/2022] [Indexed: 06/01/2023]
Abstract
MiRNAs are important posttranscriptional regulators of plant development. Many miRNAs, such as the conserved miR164 species, are encoded by families of MIRNA genes, but the specific roles of individual MIRNA genes are largely undefined. Here, we characterize the functions and regulatory mechanisms of SlMIR164A, one of the primary genes of Sly-miR164, in tomato. We show that SlMIR164A is preferentially expressed at late stages of fruit development and plays a vital role in controlling fruit ripening and quality. Loss of function of SlMIR164A by CRISPR/Cas9-mediated mutagenesis results in accelerated fruit ripening and enhanced chloroplast development, which leads to altered sugar and organic acid contents and affects the nutritional quality of fruits. We also show that SlMIR164A modulates fruit ripening and quality through specific target genes, SlNAM2 and SlNAM3, which control key regulators of chloroplast function and fruit ripening processes. MIR164 genes have been shown to play conserved roles in regulating organ ageing, such as leaf senescence and fruit ripening, in a variety of plants, but whether and how their family members in tomato exert the same function remain to be elucidated. Our results reveal a previously undiscovered role of SlMIR164A in ripening control, which will further our understanding of the actions of MIR164 family, as well as the mechanisms of fruit ripening and quality control in tomato. Moreover, as loss of SlMIR164A exhibits minor impacts on organ morphology, our results can be leveraged in tomato breeding for specific manipulation of fruit ripening and quality to facilitate tomato improvement in agriculture.
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Affiliation(s)
- Dongbo Lin
- Guangdong Provincial Key Laboratory for Plant EpigeneticsCollege of Life Sciences and OceanographyShenzhen UniversityShenzhenGuangdongChina
- Key Laboratory of Optoelectronic Devices and Systems of Ministry of Education and GuangdongCollege of Physics and Optoelectronic EngineeringShenzhen UniversityShenzhenGuangdongChina
| | - Xiaoen Zhu
- Guangdong Provincial Key Laboratory for Plant EpigeneticsCollege of Life Sciences and OceanographyShenzhen UniversityShenzhenGuangdongChina
| | - Binglin Qi
- Guangdong Provincial Key Laboratory for Plant EpigeneticsCollege of Life Sciences and OceanographyShenzhen UniversityShenzhenGuangdongChina
| | - Zhong Gao
- Guangdong Provincial Key Laboratory for Plant EpigeneticsCollege of Life Sciences and OceanographyShenzhen UniversityShenzhenGuangdongChina
| | - Peng Tian
- Guangdong Provincial Key Laboratory for Plant EpigeneticsCollege of Life Sciences and OceanographyShenzhen UniversityShenzhenGuangdongChina
| | - Ziwei Li
- Guangdong Provincial Key Laboratory for Plant EpigeneticsCollege of Life Sciences and OceanographyShenzhen UniversityShenzhenGuangdongChina
| | - Zeteng Lin
- Guangdong Provincial Key Laboratory for Plant EpigeneticsCollege of Life Sciences and OceanographyShenzhen UniversityShenzhenGuangdongChina
| | - Yongxia Zhang
- Guangdong Provincial Key Laboratory for Plant EpigeneticsCollege of Life Sciences and OceanographyShenzhen UniversityShenzhenGuangdongChina
| | - Tengbo Huang
- Guangdong Provincial Key Laboratory for Plant EpigeneticsCollege of Life Sciences and OceanographyShenzhen UniversityShenzhenGuangdongChina
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11
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Baldrich P, Bélanger S, Kong S, Pokhrel S, Tamim S, Teng C, Schiebout C, Gurazada SGR, Gupta P, Patel P, Razifard H, Nakano M, Dusia A, Meyers BC, Frank MH. The evolutionary history of small RNAs in Solanaceae. PLANT PHYSIOLOGY 2022; 189:644-665. [PMID: 35642548 PMCID: PMC9157080 DOI: 10.1093/plphys/kiac089] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/07/2022] [Accepted: 02/07/2022] [Indexed: 06/01/2023]
Abstract
The Solanaceae or "nightshade" family is an economically important group with remarkable diversity. To gain a better understanding of how the unique biology of the Solanaceae relates to the family's small RNA (sRNA) genomic landscape, we downloaded over 255 publicly available sRNA data sets that comprise over 2.6 billion reads of sequence data. We applied a suite of computational tools to predict and annotate two major sRNA classes: (1) microRNAs (miRNAs), typically 20- to 22-nucleotide (nt) RNAs generated from a hairpin precursor and functioning in gene silencing and (2) short interfering RNAs (siRNAs), including 24-nt heterochromatic siRNAs typically functioning to repress repetitive regions of the genome via RNA-directed DNA methylation, as well as secondary phased siRNAs and trans-acting siRNAs generated via miRNA-directed cleavage of a polymerase II-derived RNA precursor. Our analyses described thousands of sRNA loci, including poorly understood clusters of 22-nt siRNAs that accumulate during viral infection. The birth, death, expansion, and contraction of these sRNA loci are dynamic evolutionary processes that characterize the Solanaceae family. These analyses indicate that individuals within the same genus share similar sRNA landscapes, whereas comparisons between distinct genera within the Solanaceae reveal relatively few commonalities.
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Affiliation(s)
- Patricia Baldrich
- Donald Danforth Plant Science Center, St. Louis, Missouri 63132, USA
| | | | - Shuyao Kong
- School of Integrative Plant Science, Cornell University, Ithaca, New York 14853, USA
| | - Suresh Pokhrel
- Donald Danforth Plant Science Center, St. Louis, Missouri 63132, USA
- School of Integrative Plant Science, Cornell University, Ithaca, New York 14853, USA
- Division of Plant Science and Technology, University of Missouri, Columbia, Missouri 65211, USA
| | - Saleh Tamim
- Center for Bioinformatics and Computational Biology, University of Delaware, Newark, Delaware 19711, USA
| | - Chong Teng
- Donald Danforth Plant Science Center, St. Louis, Missouri 63132, USA
| | | | - Sai Guna Ranjan Gurazada
- Center for Bioinformatics and Computational Biology, University of Delaware, Newark, Delaware 19711, USA
- Corteva Agriscience, Wilmington, Delaware 19805, USA
| | - Pallavi Gupta
- Donald Danforth Plant Science Center, St. Louis, Missouri 63132, USA
- Institute for Data Science & Informatics, University of Missouri, Columbia, Missouri 65211, USA
| | - Parth Patel
- Center for Bioinformatics and Computational Biology, University of Delaware, Newark, Delaware 19711, USA
| | - Hamid Razifard
- School of Integrative Plant Science, Cornell University, Ithaca, New York 14853, USA
| | - Mayumi Nakano
- Donald Danforth Plant Science Center, St. Louis, Missouri 63132, USA
| | - Ayush Dusia
- Center for Bioinformatics and Computational Biology, University of Delaware, Newark, Delaware 19711, USA
| | - Blake C Meyers
- Donald Danforth Plant Science Center, St. Louis, Missouri 63132, USA
- Division of Plant Science and Technology, University of Missouri, Columbia, Missouri 65211, USA
| | - Margaret H Frank
- Donald Danforth Plant Science Center, St. Louis, Missouri 63132, USA
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12
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Zhao P, Wang F, Deng Y, Zhong F, Tian P, Lin D, Deng J, Zhang Y, Huang T. Sly-miR159 regulates fruit morphology by modulating GA biosynthesis in tomato. PLANT BIOTECHNOLOGY JOURNAL 2022; 20:833-845. [PMID: 34882929 PMCID: PMC9055814 DOI: 10.1111/pbi.13762] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/23/2021] [Accepted: 11/28/2021] [Indexed: 05/29/2023]
Abstract
Fruit morphology is an important agronomical trait of many crops. Here, we identify Sly-miR159 as an important regulator of fruit morphology in tomato, a model species of fleshy-fruit development. We show that Sly-miR159 functions through its target SlGAMYB2 to control fruit growth. Suppression of Sly-miR159 and overexpression of SlGAMYB2 result in larger fruits with a reduced length/width ratio, while loss of function of SlGAMYB2 leads to the formation of smaller and more elongated fruits. Gibberellin (GA) is a major phytohormone that regulates fruit development in tomato. We show the Sly-miR159-SlGAMYB2 pathway controls fruit morphology by modulating GA biosynthesis. In particular, we demonstrate that Sly-miR159 promotes GA biosynthesis largely through the direct repression of the GA biosynthetic gene SlGA3ox2 by SlGAMYB2. Together, our findings reveal the action of Sly-miR159 on GA biosynthesis as a previously unidentified mechanism that controls fruit morphology in tomato. Modulating this pathway may have potential applications in tomato breeding for manipulating fruit growth and facilitating the process of fruit improvement.
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Affiliation(s)
- Panpan Zhao
- Guangdong Provincial Key Laboratory for Plant EpigeneticsCollege of Life Sciences and OceanographyShenzhen UniversityShenzhenGuangdongChina
- Key Laboratory of Optoelectronic Devices and Systems of Ministry of Education and GuangdongCollege of Optoelectronic EngineeringShenzhen UniversityShenzhenGuangdongChina
| | - Fengpan Wang
- Guangdong Provincial Key Laboratory for Plant EpigeneticsCollege of Life Sciences and OceanographyShenzhen UniversityShenzhenGuangdongChina
- Key Laboratory of Optoelectronic Devices and Systems of Ministry of Education and GuangdongCollege of Optoelectronic EngineeringShenzhen UniversityShenzhenGuangdongChina
| | - Yinjiao Deng
- Guangdong Provincial Key Laboratory for Plant EpigeneticsCollege of Life Sciences and OceanographyShenzhen UniversityShenzhenGuangdongChina
| | - Fanjia Zhong
- Guangdong Provincial Key Laboratory for Plant EpigeneticsCollege of Life Sciences and OceanographyShenzhen UniversityShenzhenGuangdongChina
| | - Peng Tian
- Guangdong Provincial Key Laboratory for Plant EpigeneticsCollege of Life Sciences and OceanographyShenzhen UniversityShenzhenGuangdongChina
- Key Laboratory of Optoelectronic Devices and Systems of Ministry of Education and GuangdongCollege of Optoelectronic EngineeringShenzhen UniversityShenzhenGuangdongChina
| | - Dongbo Lin
- Guangdong Provincial Key Laboratory for Plant EpigeneticsCollege of Life Sciences and OceanographyShenzhen UniversityShenzhenGuangdongChina
- Key Laboratory of Optoelectronic Devices and Systems of Ministry of Education and GuangdongCollege of Optoelectronic EngineeringShenzhen UniversityShenzhenGuangdongChina
| | - Juhui Deng
- Guangdong Provincial Key Laboratory for Plant EpigeneticsCollege of Life Sciences and OceanographyShenzhen UniversityShenzhenGuangdongChina
| | - Yongxia Zhang
- Guangdong Provincial Key Laboratory for Plant EpigeneticsCollege of Life Sciences and OceanographyShenzhen UniversityShenzhenGuangdongChina
| | - Tengbo Huang
- Guangdong Provincial Key Laboratory for Plant EpigeneticsCollege of Life Sciences and OceanographyShenzhen UniversityShenzhenGuangdongChina
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13
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Gupta SK, Vishwakarma A, Kenea HD, Galsurker O, Cohen H, Aharoni A, Arazi T. CRISPR/Cas9 mutants of tomato MICRORNA164 genes uncover their functional specialization in development. PLANT PHYSIOLOGY 2021; 187:1636-1652. [PMID: 34618074 PMCID: PMC8566253 DOI: 10.1093/plphys/kiab376] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/25/2021] [Accepted: 07/15/2021] [Indexed: 05/27/2023]
Abstract
Plant MICRORNA164 (miR164) plays diverse regulatory functions by post-transcriptional repression of certain NAM/ATAF/CUC-domain transcription factors. However, the involvement of miR164 in fleshy fruit development and ripening remains poorly understood. Here, de novo prediction of tomato (Solanum lycopersicum) MIR164 genes identified four genes (SlMIR164a-d), of which SlMIR164d has an atypically long pre-miRNA. The roles of the fruit expressed SlMIR164a, b, and d were studied by analysis of their Clustered Regularly Interspaced Short Palindromic Repeats mutants. The slmir164bCR mutant plants exhibited shoot and flower abnormalities characteristic of ectopic boundary specification, whereas the shoot and flower development of slmir164aCR and slmir164dCR mutants were indistinguishable from wild-type. Strikingly, the knockout of SlMIR164a practically eliminated sly-miR164 from the developing and ripening fruit pericarp. The sly-miR164-deficient slmir164aCR fruits were smaller than the wild-type, due to reduced pericarp cell division and expansion, and displayed intense red color and matte, instead of glossy appearance, upon ripening. We found that the fruit skin phenotypes were associated with morphologically abnormal outer epidermis and thicker cuticle. Quantitation of sly-miR164 target transcripts in slmir164aCR ripening fruits demonstrated the upregulation of SlNAM3 and SlNAM2. Specific expression of their miR164-resistant versions in the pericarp resulted in the formation of extremely small fruits with abnormal epidermis, highlighting the importance of their negative regulation by sly-miR164a. Taken together, our results demonstrate that SlMIR164a and SlMIR164b play specialized roles in development: SlMIR164b is required for shoot and flower boundary specification, and SlMIR164a is required for fruit growth including the expansion of its outer epidermis, which determines the properties of the fruit skin.
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Affiliation(s)
- Suresh Kumar Gupta
- Institute of Plant Sciences, ARO, Volcani Center, Rishon LeZion 7505101, Israel
| | | | - Hawi Deressa Kenea
- Institute of Plant Sciences, ARO, Volcani Center, Rishon LeZion 7505101, Israel
- Department of Plant Science, The Robert H. Smith Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, Rehovot 7610001, Israel
| | - Ortal Galsurker
- Institute of Plant Sciences, ARO, Volcani Center, Rishon LeZion 7505101, Israel
| | - Hagai Cohen
- Institute of Plant Sciences, ARO, Volcani Center, Rishon LeZion 7505101, Israel
| | - Asaph Aharoni
- Department of Plant and Environmental Sciences, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Tzahi Arazi
- Institute of Plant Sciences, ARO, Volcani Center, Rishon LeZion 7505101, Israel
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14
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Wu F, Xu J, Gao T, Huang D, Jin W. Molecular mechanism of modulating miR482b level in tomato with botrytis cinerea infection. BMC PLANT BIOLOGY 2021; 21:496. [PMID: 34706648 PMCID: PMC8555085 DOI: 10.1186/s12870-021-03203-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/02/2021] [Accepted: 09/01/2021] [Indexed: 06/13/2023]
Abstract
BACKGROUND Plant miRNAs are involved in the response to biotic and abiotic stresses by altering their expression levels, and they play an important role in the regulation of plant resistance to stress. However, the molecular mechanism that regulates the expression levels of miRNAs in plants with biotic and abiotic stress still needs to be explored. Previously, we found that the expression of the miR482 family was changed in tomato infected by Botrytis cinerea. In this study, we investigated and uncovered the mechanism underlying the response of miR482 to B. cinerea infection in tomato. RESULTS First, RT-qPCR was employed to detect the expression patterns of miR482b in tomato infected by B. cinerea, and results showed that miR482b primary transcripts (pri-miR482b) were up-regulated in B. cinerea-infected leaves, but the mature miR482b was down-regulated. Subsequently, we used rapid amplification cDNA end method to amplify the full-length of pri-miR482b. Result showed that the pri-miR482b had two isoforms, with the longer one (consisting 300 bp) having an extra fragment of 53 bp in the 3'-end compared with the shorter one. In vitro Dicer assay indicated that the longer isoform pri-miR482b-x1 had higher efficiency in the post-transcriptional splicing of miRNA than the shorter isoform pri-miR482b-x2. In addition, the transcription level of mature miR482b was much higher in transgenic Arabidopsis overexpressing pri-miR482b-x1 than that in OE pri-miR482b-x2 Arabidopsis. These results confirmed that this extra 53 bp in pri-miR482b-x1 might play a key role in the miR482b biogenesis of post-transcription processing. CONCLUSIONS Extra 53 bp in pri-miR482b-x1 enhanced miR482b biogenesis, which elevated the transcription level of miR482b. This study clarified the response of miR482 to B. cinerea infection in tomato, thereby helping us further understand the molecular mechanisms that regulate the expression levels of other miRNAs.
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Affiliation(s)
- Fangli Wu
- Key Laboratory of Plant Secondary Metabolism and Regulation of Zhejiang Province, College of Life Sciences and medicine, Zhejiang Sci-Tech University, 310018, Hangzhou, China
| | - Jinfeng Xu
- Key Laboratory of Plant Secondary Metabolism and Regulation of Zhejiang Province, College of Life Sciences and medicine, Zhejiang Sci-Tech University, 310018, Hangzhou, China
| | - Tiantian Gao
- Key Laboratory of Plant Secondary Metabolism and Regulation of Zhejiang Province, College of Life Sciences and medicine, Zhejiang Sci-Tech University, 310018, Hangzhou, China
| | - Diao Huang
- Key Laboratory of Plant Secondary Metabolism and Regulation of Zhejiang Province, College of Life Sciences and medicine, Zhejiang Sci-Tech University, 310018, Hangzhou, China
| | - Weibo Jin
- Key Laboratory of Plant Secondary Metabolism and Regulation of Zhejiang Province, College of Life Sciences and medicine, Zhejiang Sci-Tech University, 310018, Hangzhou, China.
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15
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Pan H, Lyu S, Chen Y, Xu S, Ye J, Chen G, Wu S, Li X, Chen J, Pan D. MicroRNAs and Transcripts Associated with an Early Ripening Mutant of Pomelo ( Citrus grandis Osbeck). Int J Mol Sci 2021; 22:9348. [PMID: 34502256 PMCID: PMC8431688 DOI: 10.3390/ijms22179348] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Revised: 08/21/2021] [Accepted: 08/24/2021] [Indexed: 11/16/2022] Open
Abstract
'Liuyuezaoyou' is an early-ripening cultivar selected from a bud mutation of Citrus grandis Osbeck 'Guanximiyou'. They were designated here as MT and WT, respectively. The fruit of MT matures about 45 days earlier than WT, which was accompanied by significant changes in key phytohormones, sugar compounds and organic acids. Recent studies have showed that microRNAs (miRNAs) play an important role in regulation of fruit ripening process. The aim of this study was to compare MT fruits with WT ones to uncover if miRNAs were implicated in the ripening of C. grandis. Fruits of both WT and MT at four developmental stages were analyzed using high-throughput sequencing and RT-PCR. Several independent miRNA libraries were constructed and sequenced. A total of 747 known miRNAs were identified and 99 novel miRNAs were predicted across all libraries. The novel miRNAs were found to have hairpin structures and possess star sequences. These results showed that transcriptome and miRNAs are substantially involved in a complex and comprehensive network in regulation of fruit ripening of this species. Further analysis of the network model revealed intricate interactions of miRNAs with mRNAs during the fleshy fruit ripening process. Several identified miRNAs have potential targets. These include auxin-responsive protein IAA9, sucrose synthase 3, V-type proton ATPase, NCED1 (ABA biosynthesis) and PL1/5 (pectate lyase genes), as well as NAC100 putative coordinated regulation networks, whose interactions with respective miRNAs may contribute significantly to fruit ripening of C. grandis.
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Affiliation(s)
- Heli Pan
- College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (H.P.); (S.L.); (Y.C.); (S.X.); (G.C.); (S.W.); (X.L.)
| | - Shiheng Lyu
- College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (H.P.); (S.L.); (Y.C.); (S.X.); (G.C.); (S.W.); (X.L.)
- Department of Environmental Horticulture and Mid-Florida Research and Education Center, Institute of Food and Agricultural Sciences, University of Florida, Apopka, FL 32703, USA
- State Key Laboratory of Subtropical Silviculture, Zhejiang Agricultural and Forestry University, Hangzhou 311300, China
| | - Yanqiong Chen
- College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (H.P.); (S.L.); (Y.C.); (S.X.); (G.C.); (S.W.); (X.L.)
- Institute of Oceanography, Minjiang University, Fuzhou 350108, China
| | - Shirong Xu
- College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (H.P.); (S.L.); (Y.C.); (S.X.); (G.C.); (S.W.); (X.L.)
| | - Jianwen Ye
- Agricultural and Rural Bureau of Pinghe County, Zhangzhou 363700, China;
| | - Guixin Chen
- College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (H.P.); (S.L.); (Y.C.); (S.X.); (G.C.); (S.W.); (X.L.)
| | - Shaohua Wu
- College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (H.P.); (S.L.); (Y.C.); (S.X.); (G.C.); (S.W.); (X.L.)
| | - Xiaoting Li
- College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (H.P.); (S.L.); (Y.C.); (S.X.); (G.C.); (S.W.); (X.L.)
| | - Jianjun Chen
- Department of Environmental Horticulture and Mid-Florida Research and Education Center, Institute of Food and Agricultural Sciences, University of Florida, Apopka, FL 32703, USA
| | - Dongming Pan
- College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (H.P.); (S.L.); (Y.C.); (S.X.); (G.C.); (S.W.); (X.L.)
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16
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Moutsopoulos I, Maischak L, Lauzikaite E, Vasquez Urbina S, Williams E, Drost HG, Mohorianu I. noisyR: enhancing biological signal in sequencing datasets by characterizing random technical noise. Nucleic Acids Res 2021; 49:e83. [PMID: 34076236 PMCID: PMC8373073 DOI: 10.1093/nar/gkab433] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2021] [Revised: 04/16/2021] [Accepted: 05/06/2021] [Indexed: 01/22/2023] Open
Abstract
High-throughput sequencing enables an unprecedented resolution in transcript quantification, at the cost of magnifying the impact of technical noise. The consistent reduction of random background noise to capture functionally meaningful biological signals is still challenging. Intrinsic sequencing variability introducing low-level expression variations can obscure patterns in downstream analyses. We introduce noisyR, a comprehensive noise filter to assess the variation in signal distribution and achieve an optimal information-consistency across replicates and samples; this selection also facilitates meaningful pattern recognition outside the background-noise range. noisyR is applicable to count matrices and sequencing data; it outputs sample-specific signal/noise thresholds and filtered expression matrices. We exemplify the effects of minimizing technical noise on several datasets, across various sequencing assays: coding, non-coding RNAs and interactions, at bulk and single-cell level. An immediate consequence of filtering out noise is the convergence of predictions (differential-expression calls, enrichment analyses and inference of gene regulatory networks) across different approaches.
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Affiliation(s)
- Ilias Moutsopoulos
- Wellcome-MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge CB2 0AW, UK
| | - Lukas Maischak
- Computational Biology Group, Department of Molecular Biology, Max Planck Institute for Developmental Biology, Max-Planck Ring 1, 72076 Tübingen, Germany
| | - Elze Lauzikaite
- Wellcome-MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge CB2 0AW, UK
| | - Sergio A Vasquez Urbina
- Computational Biology Group, Department of Molecular Biology, Max Planck Institute for Developmental Biology, Max-Planck Ring 1, 72076 Tübingen, Germany
| | - Eleanor C Williams
- Wellcome-MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge CB2 0AW, UK
| | - Hajk-Georg Drost
- Computational Biology Group, Department of Molecular Biology, Max Planck Institute for Developmental Biology, Max-Planck Ring 1, 72076 Tübingen, Germany
| | - Irina I Mohorianu
- Wellcome-MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge CB2 0AW, UK
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17
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Anand A, Pandi G. Noncoding RNA: An Insight into Chloroplast and Mitochondrial Gene Expressions. Life (Basel) 2021; 11:life11010049. [PMID: 33450961 PMCID: PMC7828403 DOI: 10.3390/life11010049] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2020] [Revised: 12/28/2020] [Accepted: 01/05/2021] [Indexed: 12/22/2022] Open
Abstract
Regulation of gene expression in any biological system is a complex process with many checkpoints at the transcriptional, post-transcriptional and translational levels. The control mechanism is mediated by various protein factors, secondary metabolites and a newly included regulatory member, i.e., noncoding RNAs (ncRNAs). It is known that ncRNAs modulate the mRNA or protein profiles of the cell depending on the degree of complementary and context of the microenvironment. In plants, ncRNAs are essential for growth and development in normal conditions by controlling various gene expressions and have emerged as a key player to guard plants during adverse conditions. In order to have smooth functioning of the plants under any environmental pressure, two very important DNA-harboring semi-autonomous organelles, namely, chloroplasts and mitochondria, are considered as main players. These organelles conduct the most crucial metabolic pathways that are required to maintain cell homeostasis. Thus, it is imperative to explore and envisage the molecular machineries responsible for gene regulation within the organelles and their coordination with nuclear transcripts. Therefore, the present review mainly focuses on ncRNAs origination and their gene regulation in chloroplasts and plant mitochondria.
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Affiliation(s)
- Asha Anand
- Correspondence: (A.A.); (G.P.); Tel.: +91-452-245-8230 (G.P.)
| | - Gopal Pandi
- Correspondence: (A.A.); (G.P.); Tel.: +91-452-245-8230 (G.P.)
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18
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Gaafar YZA, Ziebell H. Novel targets for engineering Physostegia chlorotic mottle and tomato brown rugose fruit virus-resistant tomatoes: in silico prediction of tomato microRNA targets. PeerJ 2020; 8:e10096. [PMID: 33194382 PMCID: PMC7597636 DOI: 10.7717/peerj.10096] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2020] [Accepted: 09/14/2020] [Indexed: 11/20/2022] Open
Abstract
Background Physostegia chlorotic mottle virus (PhCMoV; genus: Alphanucleorhabdovirus, family: Rhabdoviridae) and tomato brown rugose fruit virus (ToBRFV; genus: Tobamovirus, family: Virgaviridae) are newly emerging plant viruses that have a dramatic effect on tomato production. Among various known virus-control strategies, RNAi-mediated defence has shown the potential to protect plants against various pathogens including viral infections. Micro(mi)RNAs play a major role in RNAi-mediated defence. Methods Using in silico analyses, we investigated the possibility of tomato-encoded miRNAs (TomiRNA) to target PhCMoV and ToBRFV genomes using five different algorithms, i.e., miRanda, RNAhybrid, RNA22, Tapirhybrid and psRNATarget. Results The results revealed that 14 loci on PhCMoV and 10 loci on ToBRFV can be targeted by the TomiRNAs based on the prediction of at least three algorithms. Interestingly, one TomiRNA, miR6026, can target open reading frames from both viruses, i.e., the phosphoprotein encoding gene of PhCMoV, and the two replicase components of ToBRFV. There are currently no commercially available PhCMoV- or ToBRFV-resistant tomato varieties, therefore the predicted data provide useful information for the development of PhCMoV- and ToBFRV-resistant tomato plants.
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Affiliation(s)
- Yahya Zakaria Abdou Gaafar
- Institute for Epidemiology and Pathogen Diagnostics, Julius Kühn Institute (JKI) -Federal Research Centre for Cultivated Plants, Braunschweig, Lower Saxony, Germany
| | - Heiko Ziebell
- Institute for Epidemiology and Pathogen Diagnostics, Julius Kühn Institute (JKI) -Federal Research Centre for Cultivated Plants, Braunschweig, Lower Saxony, Germany
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19
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Green D, Eyre H, Singh A, Taylor JT, Chu J, Jeys L, Sumathi V, Coonar A, Rassl D, Babur M, Forster D, Alzabin S, Ponthan F, McMahon A, Bigger B, Reekie T, Kassiou M, Williams K, Dalmay T, Fraser WD, Finegan KG. Targeting the MAPK7/MMP9 axis for metastasis in primary bone cancer. Oncogene 2020; 39:5553-5569. [PMID: 32655131 PMCID: PMC7426263 DOI: 10.1038/s41388-020-1379-0] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2020] [Revised: 05/24/2020] [Accepted: 06/23/2020] [Indexed: 02/07/2023]
Abstract
Metastasis is the leading cause of cancer-related death. This multistage process involves contribution from both tumour cells and the tumour stroma to release metastatic cells into the circulation. Circulating tumour cells (CTCs) survive circulatory cytotoxicity, extravasate and colonise secondary sites effecting metastatic outcome. Reprogramming the transcriptomic landscape is a metastatic hallmark, but detecting underlying master regulators that drive pathological gene expression is a key challenge, especially in childhood cancer. Here we used whole tumour plus single-cell RNA-sequencing in primary bone cancer and CTCs to perform weighted gene co-expression network analysis to systematically detect coordinated changes in metastatic transcript expression. This approach with comparisons applied to data collected from cell line models, clinical samples and xenograft mouse models revealed mitogen-activated protein kinase 7/matrix metallopeptidase 9 (MAPK7/MMP9) signalling as a driver for primary bone cancer metastasis. RNA interference knockdown of MAPK7 reduces proliferation, colony formation, migration, tumour growth, macrophage residency/polarisation and lung metastasis. Parallel to these observations were reduction of activated interleukins IL1B, IL6, IL8 plus mesenchymal markers VIM and VEGF in response to MAPK7 loss. Our results implicate a newly discovered, multidimensional MAPK7/MMP9 signalling hub in primary bone cancer metastasis that is clinically actionable.
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Affiliation(s)
- Darrell Green
- Norwich Medical School, University of East Anglia, Norwich, UK
| | - Heather Eyre
- Faculty of Biology Medicine and Health, University of Manchester, Manchester, UK
| | | | - Jessica T Taylor
- Faculty of Biology Medicine and Health, University of Manchester, Manchester, UK
| | - Jason Chu
- Faculty of Biology Medicine and Health, University of Manchester, Manchester, UK
| | - Lee Jeys
- Orthopaedic Oncology, The Royal Orthopaedic Hospital, Birmingham, UK
| | - Vaiyapuri Sumathi
- Musculoskeletal Pathology, The Royal Orthopaedic Hospital, Birmingham, UK
| | - Aman Coonar
- Thoracic Surgery, The Royal Papworth Hospital, Cambridge, UK
| | - Doris Rassl
- Pathology, The Royal Papworth Hospital, Cambridge, UK
| | - Muhammad Babur
- Faculty of Biology Medicine and Health, University of Manchester, Manchester, UK
| | - Duncan Forster
- Wolfson Molecular Imaging Centre, University of Manchester, Manchester, UK
| | | | | | - Adam McMahon
- Wolfson Molecular Imaging Centre, University of Manchester, Manchester, UK
| | - Brian Bigger
- Faculty of Biology Medicine and Health, University of Manchester, Manchester, UK
| | - Tristan Reekie
- School of Chemistry, University of Sydney, Sydney, Australia
| | - Michael Kassiou
- School of Chemistry, University of Sydney, Sydney, Australia
| | - Kaye Williams
- Faculty of Biology Medicine and Health, University of Manchester, Manchester, UK
| | - Tamas Dalmay
- School of Biological Sciences, University of East Anglia, Norwich, UK
| | - William D Fraser
- Norwich Medical School, University of East Anglia, Norwich, UK.
- Clinical Biochemistry, Norfolk and Norwich University Hospital, Norwich, UK.
- Diabetes and Endocrinology, Norfolk and Norwich University Hospital, Norwich, UK.
| | - Katherine G Finegan
- Faculty of Biology Medicine and Health, University of Manchester, Manchester, UK.
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20
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Zuo J, Grierson D, Courtney LT, Wang Y, Gao L, Zhao X, Zhu B, Luo Y, Wang Q, Giovannoni JJ. Relationships between genome methylation, levels of non-coding RNAs, mRNAs and metabolites in ripening tomato fruit. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2020; 103:980-994. [PMID: 32314448 DOI: 10.1111/tpj.14778] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/27/2018] [Revised: 03/12/2020] [Accepted: 03/23/2020] [Indexed: 05/28/2023]
Abstract
Ripening of tomato fruit is a complex tightly orchestrated developmental process that involves multiple physiological and metabolic changes that render fruit attractive, palatable and nutritious. Ripening requires initiation, activation and coordination of key pathways at the transcriptional and post-transcriptional levels that lead to ethylene synthesis and downstream ripening events determining quality. We studied wild-type, Gr and r mutant fruits at the coding and non-coding transcriptomic, metabolomic and genome methylation levels. Numerous differentially expressed non-coding RNAs were identified and quantified and potential competing endogenous RNA regulation models were constructed. Multiple changes in gene methylation were linked to the ethylene pathway and ripening processes. A combined analysis of changes in genome methylation, long non-coding RNAs, circular RNAs, micro-RNAs and fruit metabolites revealed many differentially expressed genes (DEGs) with differentially methylated regions encoding transcription factors and key enzymes related to ethylene or carotenoid pathways potentially targeted by differentially expressed non-coding RNAs. These included ACO2 (targeted by MSTRG.59396.1 and miR396b), CTR1 (targeted by MSTRG.43594.1 and miR171b), ERF2 (targeted by MSTRG.183681.1), ERF5 (targeted by miR9470-3p), PSY1 (targeted by MSTRG.95226.7), ZISO (targeted by 12:66127788|66128276) and NCED (targeted by MSTRG.181568.2). Understanding the functioning of this intricate genetic regulatory network provides new insights into the underlying integration and relationships between the multiple events that collectively determine the ripe phenotype.
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Affiliation(s)
- Jinhua Zuo
- Key Laboratory of Vegetable Postharvest Processing, Ministry of Agriculture and Rural Affairs, Beijing Key Laboratory of Fruits and Vegetable Storage and Processing, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China) of Ministry of Agriculture, Key Laboratory of Urban Agriculture (North) of Ministry of Agriculture, Beijing Vegetable Research Center, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
- United States Department of Agriculture - Agricultural Research Service and Boyce Thompson Institute for Plant Research, Cornell University Campus, Ithaca, NY, 14853, USA
| | - Donald Grierson
- School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough, Leicestershire, LE12 5RD, UK
| | - Lance T Courtney
- United States Department of Agriculture - Agricultural Research Service and Boyce Thompson Institute for Plant Research, Cornell University Campus, Ithaca, NY, 14853, USA
| | - Yunxiang Wang
- Beijing Academy of Forestry and Pomology Sciences, Beijing Academy of Agriculture and Forestry Sciences, Beijing, 100093, China
| | - Lipu Gao
- Key Laboratory of Vegetable Postharvest Processing, Ministry of Agriculture and Rural Affairs, Beijing Key Laboratory of Fruits and Vegetable Storage and Processing, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China) of Ministry of Agriculture, Key Laboratory of Urban Agriculture (North) of Ministry of Agriculture, Beijing Vegetable Research Center, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
| | - Xiaoyan Zhao
- Key Laboratory of Vegetable Postharvest Processing, Ministry of Agriculture and Rural Affairs, Beijing Key Laboratory of Fruits and Vegetable Storage and Processing, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China) of Ministry of Agriculture, Key Laboratory of Urban Agriculture (North) of Ministry of Agriculture, Beijing Vegetable Research Center, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
| | - Benzhong Zhu
- Laboratory of Postharvest Molecular Biology of Fruits and vegetables, Department of Food Biotechnology, College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, 100083, China
| | - Yunbo Luo
- Laboratory of Postharvest Molecular Biology of Fruits and vegetables, Department of Food Biotechnology, College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, 100083, China
| | - Qing Wang
- Key Laboratory of Vegetable Postharvest Processing, Ministry of Agriculture and Rural Affairs, Beijing Key Laboratory of Fruits and Vegetable Storage and Processing, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China) of Ministry of Agriculture, Key Laboratory of Urban Agriculture (North) of Ministry of Agriculture, Beijing Vegetable Research Center, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
| | - James J Giovannoni
- United States Department of Agriculture - Agricultural Research Service and Boyce Thompson Institute for Plant Research, Cornell University Campus, Ithaca, NY, 14853, USA
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21
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Prakash V, Singh A, Singh AK, Dalmay T, Chakraborty S. Tobacco RNA-dependent RNA polymerase 1 affects the expression of defence-related genes in Nicotiana benthamiana upon Tomato leaf curl Gujarat virus infection. PLANTA 2020; 252:11. [PMID: 32613448 DOI: 10.1007/s00425-020-03417-y] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/03/2020] [Accepted: 06/26/2020] [Indexed: 05/25/2023]
Abstract
MAIN CONCLUSION RNA-dependent RNA polymerase 1 of Nicotiana tabacum modulates ToLCGV pathogenesis by influencing a number of defence-related genes in N. benthamiana plants. Key means of plants protecting themselves from the invading viruses is through RNA silencing. RNA-dependent RNA polymerase-1 (RDR1) is one of the crucial proteins of the RNA silencing pathway, which is induced after infection by viruses. RDR1 functions in the generation of small interfering RNAs (siRNAs) against the viral genome, thus it is antiviral in nature. Here, we used the transgenic Nicotiana benthamiana plant expressing N. tabacum NtRDR1 and observed reduced susceptibility towards Tomato leaf curl Gujarat virus (ToLCGV) infection compared to the wild-type N. benthamiana plants. To understand the reason for such reduced susceptibility, we prepared high-definition small RNA (sRNA) cDNA libraries from ToLCGV-infected wild-type N. benthamiana and NtRDR1 expressing N. benthamiana lines and carried out next-generation sequencing (NGS). We found that upon ToLCGV infection the majority of siRNAs generated from the host genome were of the 24 nucleotide (nt) class, while viral siRNAs (vsiRNAs) were of the 21-22-nt class, indicating that transcriptional gene silencing (TGS) is the major pathway for silencing of host genes while viral genes are silenced, predominantly, by post transcriptional gene silencing (PTGS) pathways. We estimated the changes in the expression of various defence-related genes, such as Constitutively Photomorphogenic-9 (COP9) signalosome (CSN) complex subunit-7, Pentatricopeptide repeat containing protein (PPRP), Laccase-3, Glutathione peroxidase-1 (GPX-1), Universal stress protein (USP) A-like protein, Heat shock transcription factor B4 (HSTF-B4), Auxin response factor-18 (ARF18), WRKY-6 and Short chain dehydrogenase reductase-3a. The differential expression of these genes might be linked with the enhanced tolerance of NtRDR1 N. benthamiana transgenic plants to ToLCGV. Our study suggests that reduced expression of subunit-7 of CSN complex and WRKY6, and increased expression of USPA-like protein might be linked with the reduced susceptibility of NtRDR1-transgenic N. benthamiana plants to ToLCGV.
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Affiliation(s)
- Ved Prakash
- Molecular Virology Laboratory, School of Life Sciences, Jawaharlal Nehru University, New Delhi, India
- School of Biological Sciences, University of East Anglia, Norwich, UK
| | - Archana Singh
- School of Biological Sciences, University of East Anglia, Norwich, UK
- Earlham Institute, Norwich Research Park, Norwich, NR4 7UH, UK
| | - Ashish Kumar Singh
- Molecular Virology Laboratory, School of Life Sciences, Jawaharlal Nehru University, New Delhi, India
| | - Tamas Dalmay
- School of Biological Sciences, University of East Anglia, Norwich, UK
| | - Supriya Chakraborty
- Molecular Virology Laboratory, School of Life Sciences, Jawaharlal Nehru University, New Delhi, India.
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22
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Ma L, Mu J, Grierson D, Wang Y, Gao L, Zhao X, Zhu B, Luo Y, Shi K, Wang Q, Zuo J. Noncoding RNAs: functional regulatory factors in tomato fruit ripening. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2020; 133:1753-1762. [PMID: 32211918 DOI: 10.1007/s00122-020-03582-4] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/10/2019] [Accepted: 03/12/2020] [Indexed: 06/10/2023]
Abstract
Tomato has emerged as the model system for investigations into the regulation of fleshy-fruit ripening and senescence, and the ripening process involving the coordinated regulation at the gene/chromatin/epigenetic, transcriptional, post-transcriptional and protein levels. Noncoding RNAs play important roles in fruit ripening as important transcriptional and post-transcriptional regulatory factors. In this review, we systematically summarize the recent advances in the regulation of tomato fruit ripening involved in ethylene biosynthesis and signal transduction, fruit pigment accumulation, fruit flavor and aroma, fruit texture by noncoding RNAs and their coordinate regulatory network model were set up and also suggest future directions for the functional regulations of noncoding RNAs on tomato fruit ripening.
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Affiliation(s)
- Lili Ma
- Key Laboratory of Vegetable Postharvest Processing, Ministry of Agriculture, Beijing Key Laboratory of Fruits and Vegetable Storage and Processing, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China) of Ministry of Agriculture, Key Laboratory of Urban Agriculture (North) of Ministry of Agriculture, Beijing Vegetable Research Center, Beijing Academy of Agriculture and Forestry Sciences, Beijing, 100097, China
- College of Food Science and Technology, Hebei Agricultural University, Baoding, 071001, China
| | - Jianlou Mu
- College of Food Science and Technology, Hebei Agricultural University, Baoding, 071001, China
| | - Donald Grierson
- School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough, Leicestershire, LE12 5RD, UK
| | - Yunxiang Wang
- Beijing Academy of Forestry and Pomology Sciences, Beijing Academy of Agriculture and Forestry Sciences, Beijing, 100093, China
| | - Lipu Gao
- Key Laboratory of Vegetable Postharvest Processing, Ministry of Agriculture, Beijing Key Laboratory of Fruits and Vegetable Storage and Processing, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China) of Ministry of Agriculture, Key Laboratory of Urban Agriculture (North) of Ministry of Agriculture, Beijing Vegetable Research Center, Beijing Academy of Agriculture and Forestry Sciences, Beijing, 100097, China
| | - Xiaoyan Zhao
- Key Laboratory of Vegetable Postharvest Processing, Ministry of Agriculture, Beijing Key Laboratory of Fruits and Vegetable Storage and Processing, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China) of Ministry of Agriculture, Key Laboratory of Urban Agriculture (North) of Ministry of Agriculture, Beijing Vegetable Research Center, Beijing Academy of Agriculture and Forestry Sciences, Beijing, 100097, China
| | - Benzhong Zhu
- Laboratory of Postharvest Molecular Biology of Fruits and Vegetables, Department of Food Biotechnology, College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, 100083, China
| | - Yunbo Luo
- Laboratory of Postharvest Molecular Biology of Fruits and Vegetables, Department of Food Biotechnology, College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, 100083, China
| | - Kai Shi
- Department of Horticulture, Zhejiang University, Hangzhou, 310058, China.
| | - Qing Wang
- Key Laboratory of Vegetable Postharvest Processing, Ministry of Agriculture, Beijing Key Laboratory of Fruits and Vegetable Storage and Processing, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China) of Ministry of Agriculture, Key Laboratory of Urban Agriculture (North) of Ministry of Agriculture, Beijing Vegetable Research Center, Beijing Academy of Agriculture and Forestry Sciences, Beijing, 100097, China.
| | - Jinhua Zuo
- Key Laboratory of Vegetable Postharvest Processing, Ministry of Agriculture, Beijing Key Laboratory of Fruits and Vegetable Storage and Processing, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China) of Ministry of Agriculture, Key Laboratory of Urban Agriculture (North) of Ministry of Agriculture, Beijing Vegetable Research Center, Beijing Academy of Agriculture and Forestry Sciences, Beijing, 100097, China.
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23
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Sun S, Wang X, Wang K, Cui X. Dissection of complex traits of tomato in the post-genome era. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2020; 133:1763-1776. [PMID: 31745578 DOI: 10.1007/s00122-019-03478-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/19/2019] [Accepted: 11/09/2019] [Indexed: 06/10/2023]
Abstract
We present the main advances of dissection of complex traits in tomato by omics, the genes identified to control complex traits and the application of CRISPR/Cas9 in tomato breeding. Complex traits are believed to be under the control of multiple genes, each with different effects and interaction with environmental factors. Advance development of sequencing and molecular technologies has enabled the recognition of the genomic structure of most organisms and the identification of a nearly limitless number of markers that have made it to accelerate the speed of QTL identification and gene cloning. Meanwhile, multiomics have been used to identify the genetic variations among different tomato species, determine the expression profiles of genes in different tissues and at distinct developmental stages, and detect metabolites in different pathways and processes. The combination of these data facilitates to reveal mechanism underlying complex traits. Moreover, mutants generated by mutagens and genome editing provide relatively rich genetic variation for deciphering the complex traits and exploiting them in tomato breeding. In this article, we present the main advances of complex trait dissection in tomato by omics since the release of the tomato genome sequence in 2012. We provide further insight into some tomato complex traits because of the causal genetic variations discovered so far and explore the utilization of CRISPR/Cas9 for the modification of tomato complex traits.
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Affiliation(s)
- Shuai Sun
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
- Sino-Dutch Joint Laboratory of Horticultural Genomics, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Xiaotian Wang
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
- Sino-Dutch Joint Laboratory of Horticultural Genomics, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Ketao Wang
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
- Sino-Dutch Joint Laboratory of Horticultural Genomics, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Xia Cui
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, 100081, China.
- Sino-Dutch Joint Laboratory of Horticultural Genomics, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, 100081, China.
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24
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Baykal U. Development of a sensitive primer extension method for direct detection and quantification of miRNAs from plants. PLoS One 2020; 15:e0230251. [PMID: 32163493 PMCID: PMC7067424 DOI: 10.1371/journal.pone.0230251] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2019] [Accepted: 02/25/2020] [Indexed: 11/18/2022] Open
Abstract
MicroRNAs (miRNAs) are short non-coding RNA molecules that regulate target gene expression in various organisms. Functional studies are therefore required to determine their temporal and spatial expression patterns. Primer extension has been used as a sensitive and reliable approach to identify miRNAs (∼21–22 nt) in the mammalian system and can be used in other systems such as plants. However, a well-defined method is required for ease of application and reproducibility. Here, a radioactive primer extension method was developed for the quantitative detection of miRNAs found in total RNA samples from plants. As a proof of concept, miR173 and miR828 were detected by primer extension in total RNA samples isolated from Arabidopsis. The assay involved the extension reaction of the miRNA guide strand with a radiolabeled specific primer. Using a manual DNA sequencer, primers extended with reverse transcriptase were separated on a denaturing polyacrylamide gel. The gel was then dried and exposed to a PhosphorImager screen for size-dependent product identification up to a single base difference. Quantification was done based on the intensity of radioactive signals by normalizing the cDNA products to an internal control. The primer extension was proven to be efficient to detect and quantify miRNAs in plant total RNA samples without subsequent enrichment of low-molecular-weight RNA species. This method, optimized for Arabidopsis, can be applied to a wide variety of organisms for the detection and quantification of miRNAs as well as siRNAs.
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Affiliation(s)
- Ulku Baykal
- Department of Genetics and Bioengineering, Giresun University, Güre, Giresun, Turkey
- * E-mail:
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25
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Schaefer LK, Parlange F, Buchmann G, Jung E, Wehrli A, Herren G, Müller MC, Stehlin J, Schmid R, Wicker T, Keller B, Bourras S. Cross-Kingdom RNAi of Pathogen Effectors Leads to Quantitative Adult Plant Resistance in Wheat. FRONTIERS IN PLANT SCIENCE 2020; 11:253. [PMID: 32211008 PMCID: PMC7076181 DOI: 10.3389/fpls.2020.00253] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/15/2019] [Accepted: 02/18/2020] [Indexed: 05/30/2023]
Abstract
Cross-kingdom RNA interference (RNAi) is a biological process allowing plants to transfer small regulatory RNAs to invading pathogens to trigger the silencing of target virulence genes. Transient assays in cereal powdery mildews suggest that silencing of one or two effectors could lead to near loss of virulence, but evidence from stable RNAi lines is lacking. We established transient host-induced gene silencing (HIGS) in wheat, and demonstrate that targeting an essential housekeeping gene in the wheat powdery mildew pathogen (Blumeria graminis f. sp. tritici) results in significant reduction of virulence at an early stage of infection. We generated stable transgenic RNAi wheat lines encoding a HIGS construct simultaneously silencing three B.g. tritici effectors including SvrPm3 a1/f1 , a virulence factor involved in the suppression of the Pm3 powdery mildew resistance gene. We show that all targeted effectors are effectively downregulated by HIGS, resulting in reduced fungal virulence on adult wheat plants. Our findings demonstrate that stable HIGS of effector genes can lead to quantitative gain of resistance without major pleiotropic effects in wheat.
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Affiliation(s)
| | - Francis Parlange
- Department of Plant and Microbial Biology, University of Zurich, Zurich, Switzerland
| | - Gabriele Buchmann
- Department of Plant and Microbial Biology, University of Zurich, Zurich, Switzerland
| | - Esther Jung
- Department of Plant and Microbial Biology, University of Zurich, Zurich, Switzerland
| | - Andreas Wehrli
- Department of Plant and Microbial Biology, University of Zurich, Zurich, Switzerland
| | - Gerhard Herren
- Department of Plant and Microbial Biology, University of Zurich, Zurich, Switzerland
| | - Marion Claudia Müller
- Department of Plant and Microbial Biology, University of Zurich, Zurich, Switzerland
| | - Jonas Stehlin
- Department of Plant and Microbial Biology, University of Zurich, Zurich, Switzerland
| | - Roman Schmid
- Department of Plant and Microbial Biology, University of Zurich, Zurich, Switzerland
| | - Thomas Wicker
- Department of Plant and Microbial Biology, University of Zurich, Zurich, Switzerland
| | - Beat Keller
- Department of Plant and Microbial Biology, University of Zurich, Zurich, Switzerland
| | - Salim Bourras
- Department of Plant and Microbial Biology, University of Zurich, Zurich, Switzerland
- Department of Forest Mycology and Plant Pathology, Division of Plant Pathology, Swedish University of Agricultural Sciences, Uppsala, Sweden
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26
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Osorio S, Carneiro RT, Lytovchenko A, McQuinn R, Sørensen I, Vallarino JG, Giovannoni JJ, Fernie AR, Rose JKC. Genetic and metabolic effects of ripening mutations and vine detachment on tomato fruit quality. PLANT BIOTECHNOLOGY JOURNAL 2020; 18:106-118. [PMID: 31131540 PMCID: PMC6920187 DOI: 10.1111/pbi.13176] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/17/2018] [Revised: 02/26/2019] [Accepted: 05/20/2019] [Indexed: 05/18/2023]
Abstract
Tomato (Solanum lycopersicum) fruit ripening is regulated co-operatively by the action of ethylene and a hierarchy of transcription factors, including RIPENING INHIBITOR (RIN) and NON-RIPENING (NOR). Mutations in these two genes have been adopted commercially to delay ripening, and accompanying textural deterioration, as a means to prolong shelf life. However, these mutations also affect desirable traits associated with colour and nutritional value, although the extent of this trade-off has not been assessed in detail. Here, we evaluated changes in tomato fruit pericarp primary metabolite and carotenoid pigment profiles, as well as the dynamics of specific associated transcripts, in the rin and nor mutants during late development and postharvest storage, as well of those of the partially ripening delayed fruit ripening (dfd) tomato genotype. These profiles were compared with those of the wild-type tomato cultivars Ailsa Craig (AC) and M82. We also evaluated the metabolic composition of M82 fruit ripened on or off the vine over a similar period. In general, the dfd mutation resulted in prolonged firmness and maintenance of quality traits without compromising key metabolites (sucrose, glucose/fructose and glucose) and sectors of intermediary metabolism, including tricarboxylic acid cycle intermediates. Our analysis also provided insights into the regulation of carotenoid formation and highlighted the importance of the polyamine, putrescine, in extending fruit shelf life. Finally, the metabolic composition analysis of M82 fruit ripened on or off the vine provided insights into the import into fruit of compounds, such as sucrose, during ripening.
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Affiliation(s)
- Sonia Osorio
- Max‐Planck‐Institut für Molekulare PflanzenphysiologiePotsdam‐GolmGermany
- Department of Molecular Biology and BiochemistryInstituto de Hortofruticultura Subtropical y Mediterránea “La Mayora”University of Malaga‐Consejo Superior de Investigaciones CientíficasMálagaSpain
| | - Raphael T. Carneiro
- Plant Biology SectionSchool of Integrative Plant ScienceCornell UniversityIthacaNYUSA
| | - Anna Lytovchenko
- Max‐Planck‐Institut für Molekulare PflanzenphysiologiePotsdam‐GolmGermany
| | - Ryan McQuinn
- Plant Biology SectionSchool of Integrative Plant ScienceCornell UniversityIthacaNYUSA
- Boyce Thompson Institute for Plant Research and USDA‐ARSRobert W. Holley CenterIthacaNYUSA
| | - Iben Sørensen
- Plant Biology SectionSchool of Integrative Plant ScienceCornell UniversityIthacaNYUSA
| | - José G. Vallarino
- Max‐Planck‐Institut für Molekulare PflanzenphysiologiePotsdam‐GolmGermany
- Department of Molecular Biology and BiochemistryInstituto de Hortofruticultura Subtropical y Mediterránea “La Mayora”University of Malaga‐Consejo Superior de Investigaciones CientíficasMálagaSpain
| | - James J. Giovannoni
- Plant Biology SectionSchool of Integrative Plant ScienceCornell UniversityIthacaNYUSA
- Boyce Thompson Institute for Plant Research and USDA‐ARSRobert W. Holley CenterIthacaNYUSA
| | - Alisdair R. Fernie
- Max‐Planck‐Institut für Molekulare PflanzenphysiologiePotsdam‐GolmGermany
| | - Jocelyn K. C. Rose
- Plant Biology SectionSchool of Integrative Plant ScienceCornell UniversityIthacaNYUSA
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27
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Identification of miRNAs and Their Target Genes Involved in Cucumber Fruit Expansion Using Small RNA and Degradome Sequencing. Biomolecules 2019; 9:biom9090483. [PMID: 31547414 PMCID: PMC6769560 DOI: 10.3390/biom9090483] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2019] [Revised: 09/09/2019] [Accepted: 09/11/2019] [Indexed: 11/17/2022] Open
Abstract
Fruit expansion is an essential and very complex biological process. Regulatory roles of microRNAs (miRNAs) and miRNA-mRNA modules in the cucumber fruit expansion are not yet to be investigated. In this work, 1253 known and 1269 novel miRNAs were identified from nine cucumber fruit small RNA (sRNA) libraries through high-throughput sequencing. A total of 105 highly differentially expressed miRNAs were recognized in the fruit on five days post anthesis with pollination (EXP_5d) sRNA library. Further, expression patterns of 11 differentially expressed miRNAs were validated by quantitative real-time PCR (qRT-PCR). The expression patterns were similar to sRNAs sequencing data. Transcripts of 1155 sequences were predicted as target genes of differentially expressed miRNAs by degradome sequencing. Gene Ontology (GO) enrichment showed that these target genes were involved in 24 biological processes, 15 cell components and nine molecular functions. Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis demonstrated that these target genes were significantly enriched in 19 pathways and the enriched KEGG pathways were associated with environmental adaptation, signal transduction and translation. Based on the functional prediction of miRNAs and target genes, our findings suggest that miRNAs have a potential regulatory role in cucumber fruit expansion by targeting their target genes, which provide important data for understanding the miRNA-mediated regulatory networks controlling fruit expansion in cucumber. Specific miRNAs could be selected for further functional research and molecular breeding in cucumber.
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28
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Carbone F, Bruno L, Perrotta G, Bitonti MB, Muzzalupo I, Chiappetta A. Identification of miRNAs involved in fruit ripening by deep sequencing of Olea europaea L. transcriptome. PLoS One 2019; 14:e0221460. [PMID: 31437230 PMCID: PMC6705801 DOI: 10.1371/journal.pone.0221460] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2019] [Accepted: 08/08/2019] [Indexed: 12/05/2022] Open
Abstract
BACKGROUND The ripening process of olive fruits is associated with chemical and/or enzymatic specific transformations, making them particularly attractive to animals and humans. In olive drupes, including 'Cassanese' ones, ripening is usually accompanied by progressive chromatic change, resulting in a final red-brown colourization of both epidermis and mesocarp. This event has an exception in the 'Leucocarpa', in which we observed the destabilization in the equilibrium between the chlorophyll metabolism and that of the other pigments, particularly the anthocyanins, whose switch-off during maturation promotes the white colouration of the fruits. Recently, transcription profiling of 'Leucocarpa' and 'Cassanese' olives along ripening, performed through an Illumina RNA-seq approach, has provided useful insights on genes functions involved in fruit maturation such as those related to the biosynthesis of flavonoids and anthocyanins. METHODOLOGY To assess expression alterations of genes involved in flavonoids and anthocyanins biosynthetic pathways during ripening, possibly caused by small nuclear RNA (snRNA) in olive drupes, snRNA libraries from 'Leucocarpa' and 'Cassanese' were constructed with RNAs extracted at 100 and 130 Days After Flowering (DAF) and sequenced by an Illumina approach. 130 conserved microRNAs (miRNA) in the Viridiplantae belonging to 14 miRNA families were identified. Regarding the 130 conserved miRNAs, approximately the 48% were identified in all libraries, 5 and 18 miRNAs were shared between the "Cassanese" (C100, C130) and "Leucocarpa" (L100, L130) libraries, respectively. CONCLUSION For the remaining reads not-matching with known miRNAs in the Viridiplantae, we combined secondary structure and minimum free energy to discover novel olive miRNAs. Based on these analyses, 492 sequences were considered as putative novel miRNAs. The putative target genes of identified miRNA were computationally predicted by alignment with the olive drupe transcripts obtained from the same samples. A total of 218 transcripts were predicted as targets of 130 known and 492 putative novel miRNAs. Interestingly, some identified target genes are involved in negative regulation of anthocyanin metabolic process. Quantification of the expression pattern of three miRNA and their target transcripts by qRT-PCR assay confirmed the results of Illumina sequencing.
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Affiliation(s)
- Fabrizio Carbone
- Department of Biology, Ecology and Earth Science, University of Calabria, Arcavacata Rende (CS) IT
| | - Leonardo Bruno
- Research Centre for Olive, Citrus and Tree Fruit—Council for Agricultural Research and Economics, Rende (CS) IT
| | | | - Maria B. Bitonti
- Research Centre for Olive, Citrus and Tree Fruit—Council for Agricultural Research and Economics, Rende (CS) IT
| | - Innocenzo Muzzalupo
- Department of Biology, Ecology and Earth Science, University of Calabria, Arcavacata Rende (CS) IT
| | - Adriana Chiappetta
- Research Centre for Olive, Citrus and Tree Fruit—Council for Agricultural Research and Economics, Rende (CS) IT
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29
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Hong YH, Meng J, He XL, Zhang YY, Luan YS. Overexpression of MiR482c in Tomato Induces Enhanced Susceptibility to Late Blight. Cells 2019; 8:E822. [PMID: 31382588 PMCID: PMC6721620 DOI: 10.3390/cells8080822] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2019] [Revised: 07/30/2019] [Accepted: 08/01/2019] [Indexed: 01/18/2023] Open
Abstract
Tomato is the highest-value fruit/vegetable crop worldwide. However, the quality and yield of tomatoes are severely affected by late blight. MicroRNA482s (miR482s) are involved in the plant's immune system. In this study, miR482c was transiently and stably overexpressed in tomatoes in transgenic plants to explore its mechanism in tomato resistance against late blight. Transgenic tomato plants with transiently overexpressed miR482c displayed a larger lesion area than the control plants upon infection. Furthermore, compared with wild-type (WT) tomato plants, the transgenic tomato plants stably overexpressing miR482c displayed a decreased expression of target genes accompanied by lower peroxidase (POD), superoxide dismutase (SOD), and phenylalanine ammonia-lyase (PAL) activity activities and higher malondialdehyde (MDA) content, thereby leading to a decline in reactive oxygen species (ROS) scavenging ability and aggravating the damage of lipid peroxidation product accumulation on the cell membrane, eventually enhancing plant susceptibility. This finding indicates that miR482c may act as a negative regulator in tomato resistance by regulating nucleotide binding sites and leucine-rich repeat (NBS-LRR) expression levels and ROS levels.
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Affiliation(s)
- Yu-Hui Hong
- School of Bioengineering, Dalian University of Technology, Dalian 116024, China
| | - Jun Meng
- School of Computer Science and Technology, Dalian University of Technology, Dalian 116024, China
| | - Xiao-Li He
- School of Bioengineering, Dalian University of Technology, Dalian 116024, China
| | - Yuan-Yuan Zhang
- School of Bioengineering, Dalian University of Technology, Dalian 116024, China
| | - Yu-Shi Luan
- School of Bioengineering, Dalian University of Technology, Dalian 116024, China.
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30
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Nash W, Mohorianu I, Chapman T. Mate choice and gene expression signatures associated with nutritional adaptation in the medfly (Ceratitis capitata). Sci Rep 2019; 9:6704. [PMID: 31040302 PMCID: PMC6491435 DOI: 10.1038/s41598-019-42610-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2018] [Accepted: 02/25/2019] [Indexed: 11/09/2022] Open
Abstract
Evolutionary responses to nutrition are key to understanding host shifts and the resulting potential for reproductive isolation. Experimental evolution has previously been used to describe the responses of the medfly (Ceratitis capitata) to larval diets with different nutritional properties. Within 30 generations this led to divergence in larval development time, egg to adult survival and adaptation in adult body size. Here we used mRNA-seq to identify differences in gene expression patterns in these same populations, using males from the 60th generation of nutritional selection. We validated differential expression by using qRT-PCR and found that genes linked to metabolism, oxidative phosphorylation and proteolysis were significantly over-represented among the differentially expressed genes. The results provide the first genome-wide survey of the putative mechanisms underpinning evolved responses to nutritional adaptation. In addition, we tested the hypothesis that nutritional adaptation can alter mating patterns. We found evidence for assortative mating by diet at generation 60, but not 90. Hence, the pattern was variable across generations and there was no evidence overall for any isolating mating divergence between the lines. Overall, the results provide insight into the mechanisms underpinning dietary adaptation and extend our knowledge of which traits represent core responses to nutritional selection.
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Affiliation(s)
- Will Nash
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich, NR4 7TJ, UK.,Earlham Institute, Norwich Research Park, Norwich, NR4 7UZ, UK
| | - Irina Mohorianu
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich, NR4 7TJ, UK. .,School of Computing Sciences, University of East Anglia, Norwich Research Park, Norwich, NR4 7TJ, UK.
| | - Tracey Chapman
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich, NR4 7TJ, UK.
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Seo E, Kim T, Park JH, Yeom SI, Kim S, Seo MK, Shin C, Choi D. Genome-wide comparative analysis in Solanaceous species reveals evolution of microRNAs targeting defense genes in Capsicum spp. DNA Res 2019; 25:561-575. [PMID: 30060137 PMCID: PMC6289781 DOI: 10.1093/dnares/dsy025] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2018] [Accepted: 07/12/2018] [Indexed: 01/06/2023] Open
Abstract
MicroRNAs (miRNAs) play roles in various biological processes in plants including growth, development, and disease resistance. Previous studies revealed that some plant miRNAs produce secondary small interfering RNAs (siRNAs) such as phased, secondary siRNAs (phasiRNAs), and they regulate a cascade of gene expression. We performed a genome-wide comparative analysis of miRNAs in Solanaceous species (pepper, tomato, and potato), from an evolutionary perspective. Microsynteny of miRNAs was analysed based on the genomic loci and their flanking genes and most of the well-conserved miRNA genes maintained microsynteny in Solanaceae. We identified target genes of the miRNAs via degradome analysis and found that several miRNAs target many genes encoding nucleotide-binding leucine-rich repeat (NLR) or receptor-like proteins (RLPs), which are known to be major players in defense responses. In addition, disease-resistance-associated miRNAs trigger phasiRNA production in pepper, indicating amplification of the regulation of disease-resistance gene families. Among these, miR-n033a-3p, whose target NLRs have been duplicated in pepper, targets more NLRs belonging to specific subgroup in pepper than those in potato. miRNAs targeting resistance genes might have evolved to regulate numerous targets in Solanaceae, following expansion of target resistance genes. This study provides an insight into evolutionary relationship between miRNAs and their target defense genes in plants.
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Affiliation(s)
- Eunyoung Seo
- Department of Plant Science, Seoul National University, Seoul, Republic of Korea.,Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul, Republic of Korea.,Plant Genomics and Breeding Institute, Seoul National University, Seoul, Republic of Korea
| | - Taewook Kim
- Department of Agricultural Biotechnology, Seoul National University, Seoul, Republic of Korea
| | - June Hyun Park
- Department of Agricultural Biotechnology, Seoul National University, Seoul, Republic of Korea
| | - Seon-In Yeom
- Division of Applied Life Science (BK21 Plus Program), Department of Agricultural Plant Science, Institute of Agriculture & Life Science, Gyeongsang National University, Jinju, Republic of Korea
| | - Seungill Kim
- Plant Genomics and Breeding Institute, Seoul National University, Seoul, Republic of Korea
| | - Min-Ki Seo
- Plant Genomics and Breeding Institute, Seoul National University, Seoul, Republic of Korea
| | - Chanseok Shin
- Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul, Republic of Korea.,Plant Genomics and Breeding Institute, Seoul National University, Seoul, Republic of Korea.,Department of Agricultural Biotechnology, Seoul National University, Seoul, Republic of Korea
| | - Doil Choi
- Department of Plant Science, Seoul National University, Seoul, Republic of Korea.,Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul, Republic of Korea.,Plant Genomics and Breeding Institute, Seoul National University, Seoul, Republic of Korea
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An integrated analysis of mRNA and sRNA transcriptional profiles in tomato root: Insights on tomato wilt disease. PLoS One 2018; 13:e0206765. [PMID: 30395631 PMCID: PMC6218063 DOI: 10.1371/journal.pone.0206765] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2018] [Accepted: 10/18/2018] [Indexed: 11/19/2022] Open
Abstract
Tomato wilt disease caused by Fusarium oxysporum f. sp. lycopersici (FOL) is a worldwide destructive disease of tomato. As exploring gene expression and function approaches constitute an initial point for investigating pathogen-host interaction, we performed RNA-seq and sRNA-seq analysis to investigate the transcriptome of tomato root under FOL infection. Differentially expressed (DE) protein-coding gene and miRNA gene profiles upon inoculation with FOL were presented at twenty-four hours post-inoculation in four treatments. A total of more than 182.6 million and 132.2 million high quality clean reads were obtained by RNA-seq and sRNA-seq, respectively. A large overlap was found in DE mRNAs between susceptible cultivar Moneymaker and resistant cultivar Motelle. Gene Ontology terms were mainly classified into catalytic activity, metabolic process and binding. Combining with qRT-PCR and Northern blot, we validated the transcriptional profile of five genes and five miRNAs conferred to FOL infection. Our work allowed comprehensive understanding of different transcriptional reaction of genes/miRNAs between the susceptible and resistant cultivars tomato to the FOL challenge, which could offer us with a future direction to generate models of mediated resistance responses.
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Identification of browning-related microRNAs and their targets reveals complex miRNA-mediated browning regulatory networks in Luffa cylindrica. Sci Rep 2018; 8:16242. [PMID: 30389964 PMCID: PMC6214963 DOI: 10.1038/s41598-018-33896-9] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2018] [Accepted: 10/07/2018] [Indexed: 11/09/2022] Open
Abstract
As a non-coding and endogenous small RNA, MicroRNA (miRNA) takes a vital regulatory role in plant growth and development. Long-term storage and processing of many fruits and vegetables, including Luffa, are subject to influences from browning, a common post-harvest problem that adversely affects flavor, aroma, and nutritional value. The browning regulatory networks mediated by miRNA, however, remain largely unexplored. For a systematic identification of browning-responsive miRNAs and the targets, we built two RNA libraries from Luffa pulps of near-isogenic line, with resistant and sensitive browning characteristics respectively, and then sequenced them using Solexa high-throughput technology. We consequently identified 179 known miRNAs that represent 17 non-conserved miRNA families and 24 conserved families, as well as 84 potential novel miRNAs, among which 16 miRNAs (eight known and eight novel miRNAs) were found to exhibit significant differential expressions and were thus identified as browning-related miRNAs. We then studied those browning-responsive miRNAs and the corresponding targets with RT-qPCR and finally validated their expression patterns. The results revealed that the expression patterns are specific to plant development stages and the miRNAs are identified with 39 target transcripts, which involve in plant development, defense response, transcriptional regulation, and signal transduction. After characterizing these miRNAs and their targets, we propose a browning regulatory network model of miRNA-mediatation in this paper. The findings of the work are helpful for the understanding of miRNA-mediated regulatory mechanisms of browning in Luffa, and will facilitate genetic improvement of pulp characteristics in Luffa.
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Dan M, Huang M, Liao F, Qin R, Liang X, Zhang E, Huang M, Huang Z, He Q. Identification of Ethylene Responsive miRNAs and Their Targets from Newly Harvested Banana Fruits Using High-Throughput Sequencing. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2018; 66:10628-10639. [PMID: 30192539 DOI: 10.1021/acs.jafc.8b01844] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
The roles of microRNAs (miRNAs) related to ethylene response in banana fruits remain unknown because many miRNAs are differentially expressed as the fruit ripens, making the identification of ethylene-responsive miRNAs difficult. Using newly harvested banana fruits (within 5 h after harvest) as material, we found that these fruit did not ripen when treated with 5 μL/L of ethylene for 12 h at 22 °C. Two miRNA libraries were generated from newly harvested banana fruits with and without ethylene treatment and sequenced. In total, 128 known miRNAs belonging to 42 miRNA families were obtained, and 12 novel miRNAs were identified. Among them, 22 were differentially expressed in response to ethylene treatment, among which 6 known miRNAs and their putative targets were validated using qRT-PCR. These putative targets encoded proteins including GATA, ARF, DLC, and AGO, etc. KEGG and GO analyses showed that miRNAs differentially expressed in response to ethylene mainly function in the molecular and biological processes.
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Affiliation(s)
- Ming Dan
- Institute of Agro-food Science & Technology , Guangxi Academy of Agricultural Sciences , 174 East Daxue Road , Nanning 530007 , China
| | - Meihua Huang
- Institute of Agro-food Science & Technology , Guangxi Academy of Agricultural Sciences , 174 East Daxue Road , Nanning 530007 , China
- Guangxi Crop Genetic Improvement Laboratory , Nanning 530007 , China
| | - Fen Liao
- Institute of Agro-food Science & Technology , Guangxi Academy of Agricultural Sciences , 174 East Daxue Road , Nanning 530007 , China
| | - Renyuan Qin
- Institute of Agro-food Science & Technology , Guangxi Academy of Agricultural Sciences , 174 East Daxue Road , Nanning 530007 , China
| | - Xiaojun Liang
- Institute of Agro-food Science & Technology , Guangxi Academy of Agricultural Sciences , 174 East Daxue Road , Nanning 530007 , China
| | - Ezhen Zhang
- Institute of Agro-food Science & Technology , Guangxi Academy of Agricultural Sciences , 174 East Daxue Road , Nanning 530007 , China
| | - Maokang Huang
- Institute of Agro-food Science & Technology , Guangxi Academy of Agricultural Sciences , 174 East Daxue Road , Nanning 530007 , China
| | | | - Quanguang He
- Institute of Agro-food Science & Technology , Guangxi Academy of Agricultural Sciences , 174 East Daxue Road , Nanning 530007 , China
- Guangxi Key Laboratory of Fruits and Vegetables Storage-Processing Technology , Nanning 530007 , China
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35
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Taller D, Bálint J, Gyula P, Nagy T, Barta E, Baksa I, Szittya G, Taller J, Havelda Z. Expansion of Capsicum annuum fruit is linked to dynamic tissue-specific differential expression of miRNA and siRNA profiles. PLoS One 2018; 13:e0200207. [PMID: 30044813 PMCID: PMC6059424 DOI: 10.1371/journal.pone.0200207] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2018] [Accepted: 06/21/2018] [Indexed: 11/19/2022] Open
Abstract
Small regulatory RNAs, such as microRNAs (miRNAs) and small interfering RNAs (siRNAs) have emerged as important transcriptional and post-transcriptional regulators controlling a wide variety of physiological processes including fruit development. Data are, however, limited for their potential roles in developmental processes determining economically important traits of crops. The current study aimed to discover and characterize differentially expressed miRNAs and siRNAs in sweet pepper (Capsicum annuum) during fruit expansion. High-throughput sequencing was employed to determine the small regulatory RNA expression profiles in various fruit tissues, such as placenta, seed, and flesh at 28 and 40 days after anthesis. Comparative differential expression analyses of conserved, already described and our newly predicted pepper-specific miRNAs revealed that fruit expansion is accompanied by an increasing level of miRNA-mediated regulation of gene expression. Accordingly, ARGONAUTE1 protein, the primary executor of miRNA-mediated regulation, continuously accumulated to an extremely high level in the flesh. We also identified numerous pepper-specific, heterochromatin-associated 24-nt siRNAs (hetsiRNAs) which were extremely abundant in the seeds, as well as 21-nt and 24-nt phased siRNAs (phasiRNAs) that were expressed mainly in the placenta and the seeds. This work provides comprehensive tissue-specific miRNA and siRNA expression landscape for a developing pepper fruit. We identified several novel, abundantly expressing tissue- and pepper-specific small regulatory RNA species. Our data show that fruit expansion is associated with extensive changes in sRNA abundance, raising the possibility that manipulation of sRNA pathways may be employed to improve the quality and quantity of the pepper fruit.
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Affiliation(s)
- Dénes Taller
- National Agricultural Research and Innovation Centre, Agricultural Biotechnology Institute, Gödöllő, Hungary
| | - Jeannette Bálint
- National Agricultural Research and Innovation Centre, Agricultural Biotechnology Institute, Gödöllő, Hungary
| | - Péter Gyula
- National Agricultural Research and Innovation Centre, Agricultural Biotechnology Institute, Gödöllő, Hungary
| | - Tibor Nagy
- National Agricultural Research and Innovation Centre, Agricultural Biotechnology Institute, Gödöllő, Hungary
| | - Endre Barta
- National Agricultural Research and Innovation Centre, Agricultural Biotechnology Institute, Gödöllő, Hungary
| | - Ivett Baksa
- National Agricultural Research and Innovation Centre, Agricultural Biotechnology Institute, Gödöllő, Hungary
| | - György Szittya
- National Agricultural Research and Innovation Centre, Agricultural Biotechnology Institute, Gödöllő, Hungary
| | - János Taller
- Department of Plant Science and Biotechnology, Georgikon Faculty, University of Pannonia, Keszthely, Hungary
| | - Zoltán Havelda
- National Agricultural Research and Innovation Centre, Agricultural Biotechnology Institute, Gödöllő, Hungary
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36
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Fowler EK, Mohorianu I, Smith DT, Dalmay T, Chapman T. Small RNA populations revealed by blocking rRNA fragments in Drosophila melanogaster reproductive tissues. PLoS One 2018; 13:e0191966. [PMID: 29474379 PMCID: PMC5825024 DOI: 10.1371/journal.pone.0191966] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2017] [Accepted: 01/15/2018] [Indexed: 12/31/2022] Open
Abstract
RNA interference (RNAi) is a complex and highly conserved regulatory mechanism mediated via small RNAs (sRNAs). Recent technical advances in high throughput sequencing have enabled an increasingly detailed analysis of sRNA abundances and profiles in specific body parts and tissues. This enables investigations of the localized roles of microRNAs (miRNAs) and small interfering RNAs (siRNAs). However, variation in the proportions of non-coding RNAs in the samples being compared can hinder these analyses. Specific tissues may vary significantly in the proportions of fragments of longer non-coding RNAs (such as ribosomal RNA or transfer RNA) present, potentially reflecting tissue-specific differences in biological functions. For example, in Drosophila, some tissues contain a highly abundant 30nt rRNA fragment (the 2S rRNA) as well as abundant 5’ and 3’ terminal rRNA fragments. These can pose difficulties for the construction of sRNA libraries as they can swamp the sequencing space and obscure sRNA abundances. Here we addressed this problem and present a modified “rRNA blocking” protocol for the construction of high-definition (HD) adapter sRNA libraries, in D. melanogaster reproductive tissues. The results showed that 2S rRNAs targeted by blocking oligos were reduced from >80% to < 0.01% total reads. In addition, the use of multiple rRNA blocking oligos to bind the most abundant rRNA fragments allowed us to reveal the underlying sRNA populations at increased resolution. Side-by-side comparisons of sequencing libraries of blocked and non-blocked samples revealed that rRNA blocking did not change the miRNA populations present, but instead enhanced their abundances. We suggest that this rRNA blocking procedure offers the potential to improve the in-depth analysis of differentially expressed sRNAs within and across different tissues.
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Affiliation(s)
- Emily K. Fowler
- School of Biological Sciences, University of East Anglia, Norwich Research Park, United Kingdom
| | - Irina Mohorianu
- School of Biological Sciences, University of East Anglia, Norwich Research Park, United Kingdom
- School of Computing Sciences, University of East Anglia, Norwich Research Park, United Kingdom
| | - Damian T. Smith
- School of Biological Sciences, University of East Anglia, Norwich Research Park, United Kingdom
| | - Tamas Dalmay
- School of Biological Sciences, University of East Anglia, Norwich Research Park, United Kingdom
| | - Tracey Chapman
- School of Biological Sciences, University of East Anglia, Norwich Research Park, United Kingdom
- * E-mail:
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37
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Ward NJ, Green D, Higgins J, Dalmay T, Münsterberg A, Moxon S, Wheeler GN. microRNAs associated with early neural crest development in Xenopus laevis. BMC Genomics 2018; 19:59. [PMID: 29347911 PMCID: PMC5774138 DOI: 10.1186/s12864-018-4436-0] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2017] [Accepted: 01/04/2018] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND The neural crest (NC) is a class of transitory stem cell-like cells unique to vertebrate embryos. NC cells arise within the dorsal neural tube where they undergo an epithelial to mesenchymal transition in order to migrate and differentiate throughout the developing embryo. The derivative cell types give rise to multiple tissues, including the craniofacial skeleton, peripheral nervous system and skin pigment cells. Several well-studied gene regulatory networks underpin NC development, which when disrupted can lead to various neurocristopathies such as craniofrontonasal dysplasia, DiGeorge syndrome and some forms of cancer. Small RNAs, such as microRNAs (miRNAs) are non-coding RNA molecules important in post-transcriptional gene silencing and critical for cellular regulation of gene expression. RESULTS To uncover novel small RNAs in NC development we used high definition adapters and next generation sequencing of libraries derived from ectodermal explants of Xenopus laevis embryos induced to form neural and NC tissue. Ectodermal and blastula animal pole (blastula) stage tissues were also sequenced. We show that miR-427 is highly abundant in all four tissue types though in an isoform specific manner and we define a set of 11 miRNAs that are enriched in the NC. In addition, we show miR-301a and miR-338 are highly expressed in both the NC and blastula suggesting a role for these miRNAs in maintaining the stem cell-like phenotype of NC cells. CONCLUSION We have characterised the miRNAs expressed in Xenopus embryonic explants treated to form ectoderm, neural or NC tissue. This has identified novel tissue specific miRNAs and highlighted differential expression of miR-427 isoforms.
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Affiliation(s)
- Nicole J. Ward
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich, NR4 7TJ UK
| | - Darrell Green
- Norwich Medical School, University of East Anglia, Norwich Research Park, Norwich, NR4 7TJ UK
| | - Janet Higgins
- Regulatory Genomics, Earlham Institute, Norwich Research Park, Norwich, NR4 7UZ UK
| | - Tamas Dalmay
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich, NR4 7TJ UK
| | - Andrea Münsterberg
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich, NR4 7TJ UK
| | - Simon Moxon
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich, NR4 7TJ UK
| | - Grant N. Wheeler
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich, NR4 7TJ UK
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38
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Bradley D, Xu P, Mohorianu II, Whibley A, Field D, Tavares H, Couchman M, Copsey L, Carpenter R, Li M, Li Q, Xue Y, Dalmay T, Coen E. Evolution of flower color pattern through selection on regulatory small RNAs. Science 2017; 358:925-928. [DOI: 10.1126/science.aao3526] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2017] [Accepted: 10/06/2017] [Indexed: 12/19/2022]
Abstract
Small RNAs (sRNAs) regulate genes in plants and animals. Here, we show that population-wide differences in color patterns in snapdragon flowers are caused by an inverted duplication that generates sRNAs. The complexity and size of the transcripts indicate that the duplication represents an intermediate on the pathway to microRNA evolution. The sRNAs repress a pigment biosynthesis gene, creating a yellow highlight at the site of pollinator entry. The inverted duplication exhibits steep clines in allele frequency in a natural hybrid zone, showing that the allele is under selection. Thus, regulatory interactions of evolutionarily recent sRNAs can be acted upon by selection and contribute to the evolution of phenotypic diversity.
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Affiliation(s)
- Desmond Bradley
- Department of Cell and Developmental Biology, John Innes Centre, Colney Lane, Norwich NR4 7UH, UK
| | - Ping Xu
- School of Biological Sciences, University of East Anglia, Norwich, NR4 7TJ, UK
| | - Irina-Ioana Mohorianu
- School of Biological Sciences, University of East Anglia, Norwich, NR4 7TJ, UK
- School of Computing Sciences, University of East Anglia, Norwich NR4 7TJ, UK
| | - Annabel Whibley
- Department of Cell and Developmental Biology, John Innes Centre, Colney Lane, Norwich NR4 7UH, UK
| | - David Field
- Department of Botany and Biodiversity Research, University of Vienna, Faculty of Life Sciences, Rennweg 14, A-1030 Vienna, Austria
- Institute of Science and Technology Austria, Klosterneuburg, Austria
| | - Hugo Tavares
- Department of Cell and Developmental Biology, John Innes Centre, Colney Lane, Norwich NR4 7UH, UK
| | - Matthew Couchman
- Department of Cell and Developmental Biology, John Innes Centre, Colney Lane, Norwich NR4 7UH, UK
| | - Lucy Copsey
- Department of Cell and Developmental Biology, John Innes Centre, Colney Lane, Norwich NR4 7UH, UK
| | - Rosemary Carpenter
- Department of Cell and Developmental Biology, John Innes Centre, Colney Lane, Norwich NR4 7UH, UK
| | - Miaomiao Li
- State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, and National Center for Plant Gene Research, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100190, China
| | - Qun Li
- State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, and National Center for Plant Gene Research, Beijing 100101, China
| | - Yongbiao Xue
- State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, and National Center for Plant Gene Research, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100190, China
- Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China
| | - Tamas Dalmay
- School of Biological Sciences, University of East Anglia, Norwich, NR4 7TJ, UK
| | - Enrico Coen
- Department of Cell and Developmental Biology, John Innes Centre, Colney Lane, Norwich NR4 7UH, UK
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Green D, Mohorianu I, Piec I, Turner J, Beadsmoore C, Toms A, Ball R, Nolan J, McNamara I, Dalmay T, Fraser WD. MicroRNA expression in a phosphaturic mesenchymal tumour. Bone Rep 2017; 7:63-69. [PMID: 28932769 PMCID: PMC5596358 DOI: 10.1016/j.bonr.2017.09.001] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/02/2017] [Revised: 08/31/2017] [Accepted: 09/04/2017] [Indexed: 12/12/2022] Open
Abstract
Phosphaturic mesenchymal tumours are a heterogeneous set of bone and soft tissue neoplasms that can cause a number of paraneoplastic syndromes such as tumour induced osteomalacia. The term phosphaturic comes from the common finding that these tumours secrete high levels of fibroblast growth factor 23 which causes renal phosphate wasting leading to hypophosphatemia. Phosphaturic mesenchymal tumours are rare and diagnosis is difficult. A very active 68 year old male presented with bone pain and muscle weakness. He was hypophosphataemic and total alkaline phosphatase was markedly elevated. The patient was placed on vitamin D supplementation but his condition progressed. In the fifth year of presentation the patient required the use of a wheelchair and described “explosive” bone pain on physical contact. Serum 1,25 dihydroxyvitamin D was low and serum fibroblast growth factor 23 was significantly elevated, raising suspicion of a phosphaturic mesenchymal tumour. A lesion was detected in his left femoral head and the patient underwent a total hip replacement. The patient displayed a rapid improvement to his condition and during a three year follow up period he returned to an active lifestyle. As molecular testing may help provide a robust diagnosis and is particularly useful in rare diseases we took a next generation sequencing approach to identify a differential expression of small RNAs in the resected tumour. Small RNAs are non-coding RNA molecules that play a key role in regulation of gene expression and can be used as specific biomarkers. We found an upregulation of miR-197. We also found a downregulation of miR-20b, miR-144 and miR-335 which is a small RNA profile typical of osteosarcoma. MiR-21, the most frequently upregulated microRNA in cancer, was downregulated. We conclude that the specific small RNA profile is typical of osteosarcoma except for the downregulation of oncogenic miR-21. Transcriptional plasticity of miR-197, which is computationally predicted to target fibroblast growth factor 23 messenger RNA, may be upregulated in a cellular effort to correct the ectopic expression of the protein.
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Affiliation(s)
- Darrell Green
- Norwich Medical School, University of East Anglia, Norwich Research Park, Norwich NR4 7TJ, United Kingdom
| | - Irina Mohorianu
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich NR4 7TJ, United Kingdom
| | - Isabelle Piec
- Norwich Medical School, University of East Anglia, Norwich Research Park, Norwich NR4 7TJ, United Kingdom
| | - Jeremy Turner
- Department of Diabetes and Endocrinology, Norfolk and Norwich University Hospital, Norwich Research Park, NR4 7UY, United Kingdom
| | - Clare Beadsmoore
- Norwich Radiology Academy, Norfolk and Norwich University Hospital, Norwich Research Park, NR4 7UB, United Kingdom
| | - Andoni Toms
- Norwich Radiology Academy, Norfolk and Norwich University Hospital, Norwich Research Park, NR4 7UB, United Kingdom
| | - Richard Ball
- Norfolk and Waveney Cellular Pathology Service, Norfolk and Norwich University Hospital, Norwich Research Park, NR4 7UB, United Kingdom
| | - John Nolan
- Department of Orthopaedics and Trauma, Norfolk and Norwich University Hospital, Norwich Research Park, NR4 7UY, United Kingdom
| | - Iain McNamara
- Department of Orthopaedics and Trauma, Norfolk and Norwich University Hospital, Norwich Research Park, NR4 7UY, United Kingdom
| | - Tamas Dalmay
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich NR4 7TJ, United Kingdom
| | - William D Fraser
- Norwich Medical School, University of East Anglia, Norwich Research Park, Norwich NR4 7TJ, United Kingdom.,Department of Diabetes and Endocrinology, Norfolk and Norwich University Hospital, Norwich Research Park, NR4 7UY, United Kingdom.,Department of Clinical Biochemistry, Norfolk and Norwich University Hospital, Norwich Research Park, NR4 7UY, United Kingdom
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40
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Paicu C, Mohorianu I, Stocks M, Xu P, Coince A, Billmeier M, Dalmay T, Moulton V, Moxon S. miRCat2: accurate prediction of plant and animal microRNAs from next-generation sequencing datasets. Bioinformatics 2017; 33:2446-2454. [PMID: 28407097 PMCID: PMC5870699 DOI: 10.1093/bioinformatics/btx210] [Citation(s) in RCA: 43] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2017] [Revised: 03/28/2017] [Accepted: 04/10/2017] [Indexed: 01/05/2023] Open
Abstract
MOTIVATION MicroRNAs are a class of ∼21-22 nt small RNAs which are excised from a stable hairpin-like secondary structure. They have important gene regulatory functions and are involved in many pathways including developmental timing, organogenesis and development in eukaryotes. There are several computational tools for miRNA detection from next-generation sequencing datasets. However, many of these tools suffer from high false positive and false negative rates. Here we present a novel miRNA prediction algorithm, miRCat2. miRCat2 incorporates a new entropy-based approach to detect miRNA loci, which is designed to cope with the high sequencing depth of current next-generation sequencing datasets. It has a user-friendly interface and produces graphical representations of the hairpin structure and plots depicting the alignment of sequences on the secondary structure. RESULTS We test miRCat2 on a number of animal and plant datasets and present a comparative analysis with miRCat, miRDeep2, miRPlant and miReap. We also use mutants in the miRNA biogenesis pathway to evaluate the predictions of these tools. Results indicate that miRCat2 has an improved accuracy compared with other methods tested. Moreover, miRCat2 predicts several new miRNAs that are differentially expressed in wild-type versus mutants in the miRNA biogenesis pathway. AVAILABILITY AND IMPLEMENTATION miRCat2 is part of the UEA small RNA Workbench and is freely available from http://srna-workbench.cmp.uea.ac.uk/. CONTACT v.moulton@uea.ac.uk or s.moxon@uea.ac.uk. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Claudia Paicu
- The Earlham Institute, Norwich Research Park, Norwich, UK
- School of Computing Sciences, University of East Anglia, Norwich Research Park, Norwich, UK
| | - Irina Mohorianu
- School of Computing Sciences, University of East Anglia, Norwich Research Park, Norwich, UK
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich, UK
| | - Matthew Stocks
- School of Computing Sciences, University of East Anglia, Norwich Research Park, Norwich, UK
| | - Ping Xu
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich, UK
| | - Aurore Coince
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich, UK
| | - Martina Billmeier
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich, UK
| | - Tamas Dalmay
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich, UK
| | - Vincent Moulton
- School of Computing Sciences, University of East Anglia, Norwich Research Park, Norwich, UK
| | - Simon Moxon
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich, UK
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41
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Mohorianu I, Bretman A, Smith DT, Fowler EK, Dalmay T, Chapman T. Comparison of alternative approaches for analysing multi-level RNA-seq data. PLoS One 2017; 12:e0182694. [PMID: 28792517 PMCID: PMC5549751 DOI: 10.1371/journal.pone.0182694] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2017] [Accepted: 07/21/2017] [Indexed: 11/19/2022] Open
Abstract
RNA sequencing (RNA-seq) is widely used for RNA quantification in the environmental, biological and medical sciences. It enables the description of genome-wide patterns of expression and the identification of regulatory interactions and networks. The aim of RNA-seq data analyses is to achieve rigorous quantification of genes/transcripts to allow a reliable prediction of differential expression (DE), despite variation in levels of noise and inherent biases in sequencing data. This can be especially challenging for datasets in which gene expression differences are subtle, as in the behavioural transcriptomics test dataset from D. melanogaster that we used here. We investigated the power of existing approaches for quality checking mRNA-seq data and explored additional, quantitative quality checks. To accommodate nested, multi-level experimental designs, we incorporated sample layout into our analyses. We employed a subsampling without replacement-based normalization and an identification of DE that accounted for the hierarchy and amplitude of effect sizes within samples, then evaluated the resulting differential expression call in comparison to existing approaches. In a final step to test for broader applicability, we applied our approaches to a published set of H. sapiens mRNA-seq samples, The dataset-tailored methods improved sample comparability and delivered a robust prediction of subtle gene expression changes. The proposed approaches have the potential to improve key steps in the analysis of RNA-seq data by incorporating the structure and characteristics of biological experiments.
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Affiliation(s)
- Irina Mohorianu
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich, United Kingdom
- School of Computing Sciences, University of East Anglia, Norwich Research Park, Norwich, United Kingdom
| | - Amanda Bretman
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich, United Kingdom
- School of Biology, University of Leeds, Leeds, LS2 9JT, United Kingdom
| | - Damian T. Smith
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich, United Kingdom
| | - Emily K. Fowler
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich, United Kingdom
| | - Tamas Dalmay
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich, United Kingdom
| | - Tracey Chapman
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich, United Kingdom
- * E-mail:
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Zhang H, Yin L, Wang H, Wang G, Ma X, Li M, Wu H, Fu Q, Zhang Y, Yi H. Genome-wide identification of Hami melon miRNAs with putative roles during fruit development. PLoS One 2017; 12:e0180600. [PMID: 28742088 PMCID: PMC5524408 DOI: 10.1371/journal.pone.0180600] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2017] [Accepted: 06/16/2017] [Indexed: 11/19/2022] Open
Abstract
MicroRNAs represent a family of small endogenous, non-coding RNAs that play critical regulatory roles in plant growth, development, and environmental stress responses. Hami melon is famous for its attractive flavor and excellent nutritional value, however, the mechanisms underlying the fruit development and ripening remains largely unknown. Here, we performed small RNA sequencing to investigate the roles of miRNAs during Hami melon fruit development. Two batches of flesh samples were collected at four fruit development stages. Small RNA sequencing yielded a total of 54,553,424 raw reads from eight libraries. 113 conserved miRNAs belonging to 30 miRNA families and nine novel miRNAs comprising nine miRNA families were identified. The expression of 42 conserved miRNAs and three Hami melon-specific miRNAs significantly changed during fruit development. Furthermore, 484 and 124 melon genes were predicted as putative targets of 29 conserved and nine Hami melon-specific miRNA families, respectively. GO enrichment analysis were performed on target genes, "transcription, DNA-dependent", "rRNA processing", "oxidation reduction", "signal transduction", "regulation of transcription, DNA-dependent", and "metabolic process" were the over-represented biological process terms. Cleavage sites of six target genes were validated using 5' RACE. Our results present a comprehensive set of identification and characterization of Hami melon fruit miRNAs and their potential targets, which provide valuable basis towards understanding the regulatory mechanisms in programmed process of normal Hami fruit development and ripening. Specific miRNAs could be selected for further research and applications in breeding practices.
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Affiliation(s)
- Hong Zhang
- Hami Melon Research Center, Xinjiang Academy of Agricultural Sciences, Urumqi, Xinjiang, China
| | - Lan Yin
- ABLife, Inc., Wuhan, Hubei, China
| | - Huaisong Wang
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Guangzhi Wang
- Hami Melon Research Center, Xinjiang Academy of Agricultural Sciences, Urumqi, Xinjiang, China
| | - Xinli Ma
- Hami Melon Research Center, Xinjiang Academy of Agricultural Sciences, Urumqi, Xinjiang, China
| | - Meihua Li
- Hami Melon Research Center, Xinjiang Academy of Agricultural Sciences, Urumqi, Xinjiang, China
| | - Haibo Wu
- Hami Melon Research Center, Xinjiang Academy of Agricultural Sciences, Urumqi, Xinjiang, China
| | - Qiushi Fu
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Yi Zhang
- ABLife, Inc., Wuhan, Hubei, China
| | - Hongping Yi
- Hami Melon Research Center, Xinjiang Academy of Agricultural Sciences, Urumqi, Xinjiang, China
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Beckers M, Mohorianu I, Stocks M, Applegate C, Dalmay T, Moulton V. Comprehensive processing of high-throughput small RNA sequencing data including quality checking, normalization, and differential expression analysis using the UEA sRNA Workbench. RNA (NEW YORK, N.Y.) 2017; 23:823-835. [PMID: 28289155 PMCID: PMC5435855 DOI: 10.1261/rna.059360.116] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/23/2016] [Accepted: 02/28/2017] [Indexed: 06/06/2023]
Abstract
Recently, high-throughput sequencing (HTS) has revealed compelling details about the small RNA (sRNA) population in eukaryotes. These 20 to 25 nt noncoding RNAs can influence gene expression by acting as guides for the sequence-specific regulatory mechanism known as RNA silencing. The increase in sequencing depth and number of samples per project enables a better understanding of the role sRNAs play by facilitating the study of expression patterns. However, the intricacy of the biological hypotheses coupled with a lack of appropriate tools often leads to inadequate mining of the available data and thus, an incomplete description of the biological mechanisms involved. To enable a comprehensive study of differential expression in sRNA data sets, we present a new interactive pipeline that guides researchers through the various stages of data preprocessing and analysis. This includes various tools, some of which we specifically developed for sRNA analysis, for quality checking and normalization of sRNA samples as well as tools for the detection of differentially expressed sRNAs and identification of the resulting expression patterns. The pipeline is available within the UEA sRNA Workbench, a user-friendly software package for the processing of sRNA data sets. We demonstrate the use of the pipeline on a H. sapiens data set; additional examples on a B. terrestris data set and on an A. thaliana data set are described in the Supplemental Information A comparison with existing approaches is also included, which exemplifies some of the issues that need to be addressed for sRNA analysis and how the new pipeline may be used to do this.
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Affiliation(s)
- Matthew Beckers
- School of Computing Sciences, University of East Anglia, Norwich, NR4 7TJ, United Kingdom
| | - Irina Mohorianu
- School of Computing Sciences, University of East Anglia, Norwich, NR4 7TJ, United Kingdom
- School of Biological Sciences, University of East Anglia, Norwich, NR4 7TJ, United Kingdom
| | - Matthew Stocks
- School of Computing Sciences, University of East Anglia, Norwich, NR4 7TJ, United Kingdom
| | - Christopher Applegate
- School of Computing Sciences, University of East Anglia, Norwich, NR4 7TJ, United Kingdom
| | - Tamas Dalmay
- School of Biological Sciences, University of East Anglia, Norwich, NR4 7TJ, United Kingdom
| | - Vincent Moulton
- School of Computing Sciences, University of East Anglia, Norwich, NR4 7TJ, United Kingdom
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Zuo J, Wang Q, Han C, Ju Z, Cao D, Zhu B, Luo Y, Gao L. SRNAome and degradome sequencing analysis reveals specific regulation of sRNA in response to chilling injury in tomato fruit. PHYSIOLOGIA PLANTARUM 2017; 160:142-154. [PMID: 27595790 DOI: 10.1111/ppl.12509] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/12/2016] [Revised: 05/12/2016] [Accepted: 07/18/2016] [Indexed: 05/15/2023]
Abstract
Plant genomes encode diverse small RNA classes that function in distinct gene-silencing pathways. To elucidate the intricate regulation of microRNAs (miRNAs) and endogenous small-interfering RNAs (siRNAs) in response to chilling injury in tomato fruit, the deep sequencing and bioinformatic methods were combined to decipher the small RNAs landscape in the control and chilling-injured groups. Except for the known miRNAs and ta-siRNAs, 85 novel miRNAs and 5 ta-siRNAs members belonging to 3 TAS families (TAS5, TAS9 and TAS10) were identified, 34 putative phased small RNAs and 740 cis/trans-natural antisense small-interfering RNAs (nat-siRNAs) were also found in our results which enriched the tomato small RNAs repository. A large number of genes targeted by those miRNAs and siRNAs were predicted to be involved in the chilling injury responsive process and five of them were verified via degradome sequencing. Based on the above results, a regulatory model that comprehensively reveals the relationships between the small RNAs and their targets was set up. This work provides a foundation for further study of the regulation of miRNAs and siRNAs in the plant in response to chilling injury.
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Affiliation(s)
- Jinhua Zuo
- National Engineering Research Center for Vegetables, Beijing Academy of Agriculture and Forestry Sciences, Beijing Key Laboratory of Fruits and Vegetable Storage and Processing, Beijing, 100097, China
| | - Qing Wang
- National Engineering Research Center for Vegetables, Beijing Academy of Agriculture and Forestry Sciences, Beijing Key Laboratory of Fruits and Vegetable Storage and Processing, Beijing, 100097, China
| | - Cong Han
- Laboratory of Postharvest Physiology and Technology of Fruits and Vegetables, Department of Food Science, College of Food Science and Technology, Nanjing Agricultural University, Nanjing, 210095, China
| | - Zheng Ju
- Laboratory of Postharvest Molecular Biology of Fruits and Vegetables, Department of Food Biotechnology, College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, 100083, China
| | - Dongyan Cao
- Laboratory of Postharvest Molecular Biology of Fruits and Vegetables, Department of Food Biotechnology, College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, 100083, China
| | - Benzhong Zhu
- Laboratory of Postharvest Molecular Biology of Fruits and Vegetables, Department of Food Biotechnology, College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, 100083, China
| | - Yunbo Luo
- Laboratory of Postharvest Molecular Biology of Fruits and Vegetables, Department of Food Biotechnology, College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, 100083, China
| | - Lipu Gao
- National Engineering Research Center for Vegetables, Beijing Academy of Agriculture and Forestry Sciences, Beijing Key Laboratory of Fruits and Vegetable Storage and Processing, Beijing, 100097, China
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Özkan S, Mohorianu I, Xu P, Dalmay T, Coutts RHA. Profile and functional analysis of small RNAs derived from Aspergillus fumigatus infected with double-stranded RNA mycoviruses. BMC Genomics 2017; 18:416. [PMID: 28558690 PMCID: PMC5450132 DOI: 10.1186/s12864-017-3773-8] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2016] [Accepted: 05/08/2017] [Indexed: 12/18/2022] Open
Abstract
Background Mycoviruses are viruses that naturally infect and replicate in fungi. Aspergillus fumigatus, an opportunistic pathogen causing fungal lung diseases in humans and animals, was recently shown to harbour several different types of mycoviruses. A well-characterised defence against virus infection is RNA silencing. The A. fumigatus genome encodes essential components of the RNA silencing machinery, including Dicer, Argonaute and RNA-dependent RNA polymerase (RdRP) homologues. Active silencing of double-stranded (ds)RNA and the generation of small RNAs (sRNAs) has been shown for several mycoviruses and it is anticipated that a similar mechanism will be activated in A. fumigatus isolates infected with mycoviruses. Results To investigate the existence and nature of A. fumigatus sRNAs, sRNA-seq libraries of virus-free and virus-infected isolates were created using Scriptminer adapters and compared. Three dsRNA viruses were investigated: Aspergillus fumigatus partitivirus-1 (AfuPV-1, PV), Aspergillus fumigatus chrysovirus (AfuCV, CV) and Aspergillus fumigatus tetramycovirus-1 (AfuTmV-1, NK) which were selected because they induce phenotypic changes such as coloration and sectoring. The dsRNAs of all three viruses, which included two conventionally encapsidated ones PV and CV and one unencapsidated example NK, were silenced and yielded characteristic vsiRNAs together with co-incidental silencing of host fungal genes which shared sequence homology with the viral genomes. Conclusions Virus-derived sRNAs were detected and characterised in the presence of virus infection. Differentially expressed A. fumigatus microRNA-like (miRNA-like) sRNAs and small interfering RNAs (siRNAs) were detected and validated. Host sRNA loci which were differentially expressed as a result of virus infection were also identified. To our knowledge, this is the first study reporting the sRNA profiles of A. fumigatus isolates. Electronic supplementary material The online version of this article (doi:10.1186/s12864-017-3773-8) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Selin Özkan
- Department of Life Sciences, Faculty of Natural Sciences, Imperial College London, London, UK. .,Current Address: Vocational School of Health Services, Ahi Evran University, Kırşehir, Turkey.
| | - Irina Mohorianu
- School of Biological Sciences, University of East Anglia, Norwich, UK.,School of Computing Sciences, University of East Anglia, Norwich, UK
| | - Ping Xu
- School of Biological Sciences, University of East Anglia, Norwich, UK
| | - Tamas Dalmay
- School of Biological Sciences, University of East Anglia, Norwich, UK
| | - Robert H A Coutts
- Department of Life Sciences, Faculty of Natural Sciences, Imperial College London, London, UK.,Current Address: Geography, Environment and Agriculture Division, Department of Biological and Environmental Sciences, School of Life and Medical Sciences, University of Hertfordshire, Hatfield, UK
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Green D, Mohorianu I, McNamara I, Dalmay T, Fraser WD. miR-16 is highly expressed in Paget's associated osteosarcoma. Endocr Relat Cancer 2017; 24:L27-L31. [PMID: 28377382 DOI: 10.1530/erc-16-0487] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/03/2017] [Accepted: 03/07/2017] [Indexed: 11/08/2022]
Affiliation(s)
- Darrell Green
- Norwich Medical SchoolUniversity of East Anglia, Norwich Research Park, Norwich, UK
| | - Irina Mohorianu
- School of Biological SciencesUniversity of East Anglia, Norwich Research Park, Norwich, UK
| | - Iain McNamara
- Department of Orthopaedics and TraumaNorfolk and Norwich University Hospital, Norwich Research Park, Norwich, UK
| | - Tamas Dalmay
- School of Biological SciencesUniversity of East Anglia, Norwich Research Park, Norwich, UK
| | - William D Fraser
- Norwich Medical SchoolUniversity of East Anglia, Norwich Research Park, Norwich, UK
- Department of Diabetes and EndocrinologyNorfolk and Norwich University Hospital, Norwich Research Park, Norwich, UK
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47
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Collins DH, Mohorianu I, Beckers M, Moulton V, Dalmay T, Bourke AFG. MicroRNAs Associated with Caste Determination and Differentiation in a Primitively Eusocial Insect. Sci Rep 2017; 7:45674. [PMID: 28361900 PMCID: PMC5374498 DOI: 10.1038/srep45674] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2016] [Accepted: 03/02/2017] [Indexed: 01/08/2023] Open
Abstract
In eusocial Hymenoptera (ants, bees and wasps), queen and worker adult castes typically arise via environmental influences. A fundamental challenge is to understand how a single genome can thereby produce alternative phenotypes. A powerful approach is to compare the molecular basis of caste determination and differentiation along the evolutionary trajectory between primitively and advanced eusocial species, which have, respectively, relatively undifferentiated and strongly differentiated adult castes. In the advanced eusocial honeybee, Apis mellifera, studies suggest that microRNAs (miRNAs) play an important role in the molecular basis of caste determination and differentiation. To investigate how miRNAs affect caste in eusocial evolution, we used deep sequencing and Northern blots to isolate caste-associated miRNAs in the primitively eusocial bumblebee Bombus terrestris. We found that the miRNAs Bte-miR-6001-5p and -3p are more highly expressed in queen- than in worker-destined late-instar larvae. These are the first caste-associated miRNAs from outside advanced eusocial Hymenoptera, so providing evidence for caste-associated miRNAs occurring relatively early in eusocial evolution. Moreover, we found little evidence that miRNAs previously shown to be associated with caste in A. mellifera were differentially expressed across caste pathways in B. terrestris, suggesting that, in eusocial evolution, the caste-associated role of individual miRNAs is not conserved.
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Affiliation(s)
- David H Collins
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich NR4 7TJ, UK
| | - Irina Mohorianu
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich NR4 7TJ, UK.,School of Computing Sciences, University of East Anglia, Norwich Research Park, Norwich NR4 7TJ, UK
| | - Matthew Beckers
- School of Computing Sciences, University of East Anglia, Norwich Research Park, Norwich NR4 7TJ, UK
| | - Vincent Moulton
- School of Computing Sciences, University of East Anglia, Norwich Research Park, Norwich NR4 7TJ, UK
| | - Tamas Dalmay
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich NR4 7TJ, UK
| | - Andrew F G Bourke
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich NR4 7TJ, UK
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48
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Omidvar V, Mohorianu I, Dalmay T, Zheng Y, Fei Z, Pucci A, Mazzucato A, Večeřová V, Sedlářova M, Fellner M. Transcriptional regulation of male-sterility in 7B-1 male-sterile tomato mutant. PLoS One 2017; 12:e0170715. [PMID: 28178307 PMCID: PMC5298235 DOI: 10.1371/journal.pone.0170715] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2016] [Accepted: 01/09/2017] [Indexed: 11/18/2022] Open
Abstract
The 7B-1 tomato (Solanum lycopersicum L. cv Rutgers) is a male-sterile mutant with enhanced tolerance to abiotic stress, which makes it a potential candidate for hybrid seed breeding and stress engineering. To underline the molecular mechanism regulating the male-sterility in 7B-1, transcriptomic profiles of the 7B-1 male-sterile and wild type (WT) anthers were studied using mRNA sequencing (RNA-Seq). In total, 768 differentially expressed genes (DEGs) were identified, including 132 up-regulated and 636 down-regulated transcripts. Gene ontology (GO) enrichment analysis of DEGs suggested a general impact of the 7B-1 mutation on metabolic processes, such as proteolysis and carbohydrate catabolic process. Sixteen candidates with key roles in regulation of anther development were subjected to further analysis using qRT-PCR and in situ hybridization. Cytological studies showed several defects associated with anther development in the 7B-1 mutant, including unsynchronized anther maturation, dysfunctional meiosis, arrested microspores, defect in callose degradation and abnormal tapetum development. TUNEL assay showed a defect in programmed cell death (PCD) of tapetal cells in 7B-1 anthers. The present study provides insights into the transcriptome of the 7B-1 mutant. We identified several genes with altered expression level in 7B-1 (including beta-1,3 glucanase, GA2oxs, cystatin, cysteine protease, pectinesterase, TA29, and actin) that could potentially regulate anther developmental processes, such as meiosis, tapetum development, and cell-wall formation/degradation.
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Affiliation(s)
- Vahid Omidvar
- Laboratory of Growth Regulators, Centre of the Region Haná for Biotechnological and Agricultural Research, Palacký University and Institute of Experimental Botany AS CR, Šlechtitelů 27, Olomouc-Holice, Czech Republic
| | - Irina Mohorianu
- School of Computing Sciences, University of East Anglia, Norwich, United Kingdom
- School of Biological Sciences, University of East Anglia, Norwich, United Kingdom
| | - Tamas Dalmay
- School of Biological Sciences, University of East Anglia, Norwich, United Kingdom
| | - Yi Zheng
- Boyce Thompson Institute, Cornell University, Ithaca, NY, United States of America
| | - Zhangjun Fei
- Boyce Thompson Institute, Cornell University, Ithaca, NY, United States of America
| | - Anna Pucci
- Department of Agricultural and Forestry Sciences, University of Tuscia, Viterbo, Italy
| | - Andrea Mazzucato
- Department of Agricultural and Forestry Sciences, University of Tuscia, Viterbo, Italy
| | - Vendula Večeřová
- Department of Botany, Faculty of Science, Palacký University in Olomouc, Šlechtitelů 27, Olomouc-Holice, Czech Republic
| | - Michaela Sedlářova
- Department of Botany, Faculty of Science, Palacký University in Olomouc, Šlechtitelů 27, Olomouc-Holice, Czech Republic
| | - Martin Fellner
- Laboratory of Growth Regulators, Centre of the Region Haná for Biotechnological and Agricultural Research, Palacký University and Institute of Experimental Botany AS CR, Šlechtitelů 27, Olomouc-Holice, Czech Republic
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Wang Y, Wang Q, Gao L, Zhu B, Ju Z, Luo Y, Zuo J. Parsing the Regulatory Network between Small RNAs and Target Genes in Ethylene Pathway in Tomato. FRONTIERS IN PLANT SCIENCE 2017; 8:527. [PMID: 28443119 PMCID: PMC5387102 DOI: 10.3389/fpls.2017.00527] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/11/2016] [Accepted: 03/24/2017] [Indexed: 05/11/2023]
Abstract
Small RNAs are a class of short non-coding endogenous RNAs that play essential roles in many biological processes. Recent studies have reported that microRNAs (miRNAs) are also involved in ethylene signaling in plants. LeERF1 is one of the ethylene response factors (ERFs) in tomato that locates in the downstream of ethylene signal transduction pathway. To elucidate the intricate regulatory roles of small RNAs in ethylene signaling pathway in tomato, the deep sequencing and bioinformatics methods were combined to decipher the small RNAs landscape in wild and sense-/antisense-LeERF1 transgenic tomato fruits. Except for the known miRNAs, 36 putative novel miRNAs, 6 trans-acting short interfering RNAs (ta-siRNAs), and 958 natural antisense small interfering RNAs (nat-siRNAs) were also found in our results, which enriched the tomato small RNAs repository. Among these small RNAs, 9 miRNAs, and 12 nat-siRNAs were differentially expressed between the wild and transgenic tomato fruits significantly. A large amount of target genes of the small RNAs were identified and some of them were involved in ethylene pathway, including AP2 TFs, auxin response factors, F-box proteins, ERF TFs, APETALA2-like protein, and MADS-box TFs. Degradome sequencing further confirmed the targets of miRNAs and six novel targets were also discovered. Furthermore, a regulatory model which reveals the regulation relationships between the small RNAs and their targets involved in ethylene signaling was set up. This work provides basic information for further investigation of the function of small RNAs in ethylene pathway and fruit ripening.
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Affiliation(s)
- Yunxiang Wang
- Key Laboratory of the Vegetable Postharvest Treatment of Ministry of Agriculture, Beijing Vegetable Research Center, Beijing Academy of Agriculture and Forestry SciencesBeijing, China
- Beijing Key Laboratory of Fruits and Vegetable Storage and Processing, Beijing Vegetable Research Center, Beijing Academy of Agriculture and Forestry SciencesBeijing, China
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China) of Ministry of Agriculture, Beijing Vegetable Research Center, Beijing Academy of Agriculture and Forestry SciencesBeijing, China
- Key Laboratory of Urban Agriculture (North) of Ministry of Agriculture, Beijing Vegetable Research Center, Beijing Academy of Agriculture and Forestry SciencesBeijing, China
| | - Qing Wang
- Key Laboratory of the Vegetable Postharvest Treatment of Ministry of Agriculture, Beijing Vegetable Research Center, Beijing Academy of Agriculture and Forestry SciencesBeijing, China
- Beijing Key Laboratory of Fruits and Vegetable Storage and Processing, Beijing Vegetable Research Center, Beijing Academy of Agriculture and Forestry SciencesBeijing, China
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China) of Ministry of Agriculture, Beijing Vegetable Research Center, Beijing Academy of Agriculture and Forestry SciencesBeijing, China
- Key Laboratory of Urban Agriculture (North) of Ministry of Agriculture, Beijing Vegetable Research Center, Beijing Academy of Agriculture and Forestry SciencesBeijing, China
| | - Lipu Gao
- Key Laboratory of the Vegetable Postharvest Treatment of Ministry of Agriculture, Beijing Vegetable Research Center, Beijing Academy of Agriculture and Forestry SciencesBeijing, China
- Beijing Key Laboratory of Fruits and Vegetable Storage and Processing, Beijing Vegetable Research Center, Beijing Academy of Agriculture and Forestry SciencesBeijing, China
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China) of Ministry of Agriculture, Beijing Vegetable Research Center, Beijing Academy of Agriculture and Forestry SciencesBeijing, China
- Key Laboratory of Urban Agriculture (North) of Ministry of Agriculture, Beijing Vegetable Research Center, Beijing Academy of Agriculture and Forestry SciencesBeijing, China
| | - Benzhong Zhu
- Laboratory of Postharvest Molecular Biology of Fruits and Vegetables, Department of Food Biotechnology, College of Food Science and Nutritional Engineering, China Agricultural UniversityBeijing, China
| | - Zheng Ju
- Laboratory of Postharvest Molecular Biology of Fruits and Vegetables, Department of Food Biotechnology, College of Food Science and Nutritional Engineering, China Agricultural UniversityBeijing, China
| | - Yunbo Luo
- Laboratory of Postharvest Molecular Biology of Fruits and Vegetables, Department of Food Biotechnology, College of Food Science and Nutritional Engineering, China Agricultural UniversityBeijing, China
| | - Jinhua Zuo
- Key Laboratory of the Vegetable Postharvest Treatment of Ministry of Agriculture, Beijing Vegetable Research Center, Beijing Academy of Agriculture and Forestry SciencesBeijing, China
- Beijing Key Laboratory of Fruits and Vegetable Storage and Processing, Beijing Vegetable Research Center, Beijing Academy of Agriculture and Forestry SciencesBeijing, China
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China) of Ministry of Agriculture, Beijing Vegetable Research Center, Beijing Academy of Agriculture and Forestry SciencesBeijing, China
- Key Laboratory of Urban Agriculture (North) of Ministry of Agriculture, Beijing Vegetable Research Center, Beijing Academy of Agriculture and Forestry SciencesBeijing, China
- *Correspondence: Jinhua Zuo
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50
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Mohorianu I, Stocks MB, Applegate CS, Folkes L, Moulton V. The UEA Small RNA Workbench: A Suite of Computational Tools for Small RNA Analysis. Methods Mol Biol 2017; 1580:193-224. [PMID: 28439835 DOI: 10.1007/978-1-4939-6866-4_14] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
RNA silencing (RNA interference, RNAi) is a complex, highly conserved mechanism mediated by short, typically 20-24 nt in length, noncoding RNAs known as small RNAs (sRNAs). They act as guides for the sequence-specific transcriptional and posttranscriptional regulation of target mRNAs and play a key role in the fine-tuning of biological processes such as growth, response to stresses, or defense mechanism.High-throughput sequencing (HTS) technologies are employed to capture the expression levels of sRNA populations. The processing of the resulting big data sets facilitated the computational analysis of the sRNA patterns of variation within biological samples such as time point experiments, tissue series or various treatments. Rapid technological advances enable larger experiments, often with biological replicates leading to a vast amount of raw data. As a result, in this fast-evolving field, the existing methods for sequence characterization and prediction of interaction (regulatory) networks periodically require adapting or in extreme cases, a complete redesign to cope with the data deluge. In addition, the presence of numerous tools focused only on particular steps of HTS analysis hinders the systematic parsing of the results and their interpretation.The UEA small RNA Workbench (v1-4), described in this chapter, provides a user-friendly, modular, interactive analysis in the form of a suite of computational tools designed to process and mine sRNA datasets for interesting characteristics that can be linked back to the observed phenotypes. First, we show how to preprocess the raw sequencing output and prepare it for downstream analysis. Then we review some quality checks that can be used as a first indication of sources of variability between samples. Next we show how the Workbench can provide a comparison of the effects of different normalization approaches on the distributions of expression, enhanced methods for the identification of differentially expressed transcripts and a summary of their corresponding patterns. Finally we describe individual analysis tools such as PAREsnip, for the analysis of PARE (degradome) data or CoLIde for the identification of sRNA loci based on their expression patterns and the visualization of the results using the software. We illustrate the features of the UEA sRNA Workbench on Arabidopsis thaliana and Homo sapiens datasets.
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Affiliation(s)
- Irina Mohorianu
- School of Biological Sciences, University of East Anglia, Norwich, UK.,School of Computing Sciences, University of East Anglia, Norwich, UK
| | | | | | | | - Vincent Moulton
- School of Computing Sciences, University of East Anglia, Norwich, UK.
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