1
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Samelak-Czajka A, Wojciechowski P, Marszalek-Zenczak M, Figlerowicz M, Zmienko A. Differences in the intraspecies copy number variation of Arabidopsis thaliana conserved and nonconserved miRNA genes. Funct Integr Genomics 2023; 23:120. [PMID: 37036577 PMCID: PMC10085913 DOI: 10.1007/s10142-023-01043-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2023] [Revised: 03/23/2023] [Accepted: 03/25/2023] [Indexed: 04/11/2023]
Abstract
MicroRNAs (miRNAs) regulate gene expression by RNA interference mechanism. In plants, miRNA genes (MIRs) which are grouped into conserved families, i.e. they are present among the different plant taxa, are involved in the regulation of many developmental and physiological processes. The roles of the nonconserved MIRs-which are MIRs restricted to one plant family, genus, or even species-are less recognized; however, many of them participate in the responses to biotic and abiotic stresses. Both over- and underproduction of miRNAs may influence various biological processes. Consequently, maintaining intracellular miRNA homeostasis seems to be crucial for the organism. Deletions and duplications in the genomic sequence may alter gene dosage and/or activity. We evaluated the extent of copy number variations (CNVs) among Arabidopsis thaliana (Arabidopsis) MIRs in over 1000 natural accessions, using population-based analysis of the short-read sequencing data. We showed that the conserved MIRs were unlikely to display CNVs and their deletions were extremely rare, whereas nonconserved MIRs presented moderate variation. Transposon-derived MIRs displayed exceptionally high diversity. Conversely, MIRs involved in the epigenetic control of transposons reactivated during development were mostly invariable. MIR overlap with the protein-coding genes also limited their variability. At the expression level, a higher rate of nonvariable, nonconserved miRNAs was detectable in Col-0 leaves, inflorescence, and siliques compared to nonconserved variable miRNAs, although the expression of both groups was much lower than that of the conserved MIRs. Our data indicate that CNV rate of Arabidopsis MIRs is related with their age, function, and genomic localization.
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Affiliation(s)
- Anna Samelak-Czajka
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, 61-704, Poznan, Poland
| | - Pawel Wojciechowski
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, 61-704, Poznan, Poland
- Institute of Computing Science, Faculty of Computing and Telecommunications, Poznan University of Technology, 60-965, Poznan, Poland
| | | | - Marek Figlerowicz
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, 61-704, Poznan, Poland.
| | - Agnieszka Zmienko
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, 61-704, Poznan, Poland.
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2
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Mustafin RN, Khusnutdinova E. Perspective for Studying the Relationship of miRNAs with Transposable Elements. Curr Issues Mol Biol 2023; 45:3122-3145. [PMID: 37185728 PMCID: PMC10136691 DOI: 10.3390/cimb45040204] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2023] [Revised: 03/07/2023] [Accepted: 04/03/2023] [Indexed: 05/17/2023] Open
Abstract
Transposable elements are important sources of miRNA, long non-coding RNAs genes, and their targets in the composition of protein-coding genes in plants and animals. Therefore, the detection of expression levels of specific non-coding RNAs in various tissues and cells in normal and pathological conditions may indicate a programmed pattern of transposable elements' activation. This reflects the species-specific composition and distribution of transposable elements in genomes, which underlie gene regulation in every cell division, including during aging. TEs' expression is also regulated by epigenetic factors (DNA methylation, histone modifications), SIRT6, cytidine deaminases APOBEC3, APOBEC1, and other catalytic proteins, such as ERCC, TREX1, RB1, HELLS, and MEGP2. In evolution, protein-coding genes and their regulatory elements are derived from transposons. As part of non-coding regions and introns of genes, they are sensors for transcriptional and post-transcriptional control of expression, using miRNAs and long non-coding RNAs, that arose from transposable elements in evolution. Methods (Orbld, ncRNAclassifier) and databases have been created for determining the occurrence of miRNAs from transposable elements in plants (PlanTE-MIR DB, PlaNC-TE), which can be used to design epigenetic gene networks in ontogenesis. Based on the data accumulated in the scientific literature, the presence of 467 transposon-derived miRNA genes in the human genome has been reliably established. It was proposed to create an updated and controlled online bioinformatics database of miRNAs derived from transposable elements in healthy individuals, as well as expression changes of these miRNAs during aging and various diseases, such as cancer and difficult-to-treat diseases. The use of the information obtained can open new horizons in the management of tissue and organ differentiation to aging slow down. In addition, the created database could become the basis for clarifying the mechanisms of pathogenesis of various diseases (imbalance in the activity of transposable elements, reflected in changes in the expression of miRNAs) and designing their targeted therapy using specific miRNAs as targets. This article provides examples of the detection of transposable elements-derived miRNAs involved in the development of specific malignant neoplasms, aging, and idiopathic pulmonary fibrosis.
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Affiliation(s)
- Rustam Nailevich Mustafin
- Department of Medical Genetics and Fundamental Medicine, Bashkir State Medical University, 450008 Ufa, Russia
| | - Elza Khusnutdinova
- Ufa Federal Research Centre, Institute of Biochemistry and Genetics, Russian Academy of Sciences, 450054 Ufa, Russia
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3
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Pegler JL, Oultram JMJ, Mann CWG, Carroll BJ, Grof CPL, Eamens AL. Miniature Inverted-Repeat Transposable Elements: Small DNA Transposons That Have Contributed to Plant MICRORNA Gene Evolution. PLANTS (BASEL, SWITZERLAND) 2023; 12:1101. [PMID: 36903960 PMCID: PMC10004981 DOI: 10.3390/plants12051101] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/06/2023] [Revised: 02/23/2023] [Accepted: 02/24/2023] [Indexed: 06/18/2023]
Abstract
Angiosperms form the largest phylum within the Plantae kingdom and show remarkable genetic variation due to the considerable difference in the nuclear genome size of each species. Transposable elements (TEs), mobile DNA sequences that can amplify and change their chromosome position, account for much of the difference in nuclear genome size between individual angiosperm species. Considering the dramatic consequences of TE movement, including the complete loss of gene function, it is unsurprising that the angiosperms have developed elegant molecular strategies to control TE amplification and movement. Specifically, the RNA-directed DNA methylation (RdDM) pathway, directed by the repeat-associated small-interfering RNA (rasiRNA) class of small regulatory RNA, forms the primary line of defense to control TE activity in the angiosperms. However, the miniature inverted-repeat transposable element (MITE) species of TE has at times avoided the repressive effects imposed by the rasiRNA-directed RdDM pathway. MITE proliferation in angiosperm nuclear genomes is due to their preference to transpose within gene-rich regions, a pattern of transposition that has enabled MITEs to gain further transcriptional activity. The sequence-based properties of a MITE results in the synthesis of a noncoding RNA (ncRNA), which, after transcription, folds to form a structure that closely resembles those of the precursor transcripts of the microRNA (miRNA) class of small regulatory RNA. This shared folding structure results in a MITE-derived miRNA being processed from the MITE-transcribed ncRNA, and post-maturation, the MITE-derived miRNA can be used by the core protein machinery of the miRNA pathway to regulate the expression of protein-coding genes that harbor homologous MITE insertions. Here, we outline the considerable contribution that the MITE species of TE have made to expanding the miRNA repertoire of the angiosperms.
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Affiliation(s)
- Joseph L. Pegler
- Centre for Plant Science, School of Environmental and Life Sciences, College of Engineering, Science and Environment, University of Newcastle, Callaghan, NSW 2308, Australia
| | - Jackson M. J. Oultram
- Centre for Plant Science, School of Environmental and Life Sciences, College of Engineering, Science and Environment, University of Newcastle, Callaghan, NSW 2308, Australia
| | - Christopher W. G. Mann
- School of Chemistry and Molecular Biosciences, The University of Queensland, St. Lucia, QLD 4072, Australia
| | - Bernard J. Carroll
- School of Chemistry and Molecular Biosciences, The University of Queensland, St. Lucia, QLD 4072, Australia
| | - Christopher P. L. Grof
- Centre for Plant Science, School of Environmental and Life Sciences, College of Engineering, Science and Environment, University of Newcastle, Callaghan, NSW 2308, Australia
| | - Andrew L. Eamens
- School of Health, University of the Sunshine Coast, Maroochydore, QLD 4558, Australia
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4
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Begum Y. Regulatory role of microRNAs (miRNAs) in the recent development of abiotic stress tolerance of plants. Gene 2022; 821:146283. [PMID: 35143944 DOI: 10.1016/j.gene.2022.146283] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2021] [Revised: 01/12/2022] [Accepted: 02/03/2022] [Indexed: 12/21/2022]
Abstract
MicroRNAs (miRNAs) are a distinct groups of single-stranded non-coding, tiny regulatory RNAs approximately 20-24 nucleotides in length. miRNAs negatively influence gene expression at the post-transcriptional level and have evolved considerably in the development of abiotic stress tolerance in a number of model plants and economically important crop species. The present review aims to deliver the information on miRNA-mediated regulation of the expression of major genes or Transcription Factors (TFs), as well as genetic and regulatory pathways. Also, the information on adaptive mechanisms involved in plant abiotic stress responses, prediction, and validation of targets, computational tools, and databases available for plant miRNAs, specifically focus on their exploration for engineering abiotic stress tolerance in plants. The regulatory function of miRNAs in plant growth, development, and abiotic stresses consider in this review, which uses high-throughput sequencing (HTS) technologies to generate large-scale libraries of small RNAs (sRNAs) for conventional screening of known and novel abiotic stress-responsive miRNAs adds complexity to regulatory networks in plants. The discoveries of miRNA-mediated tolerance to multiple abiotic stresses, including salinity, drought, cold, heat stress, nutritional deficiency, UV-radiation, oxidative stress, hypoxia, and heavy metal toxicity, are highlighted and discussed in this review.
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Affiliation(s)
- Yasmin Begum
- Department of Biophysics, Molecular Biology and Bioinformatics, University of Calcutta, 92, APC Road, Kolkata 700009, West Bengal, India; Center of Excellence in Systems Biology and Biomedical Engineering (TEQIP Phase-III), University of Calcutta, JD-2, Sector III, Salt Lake, Kolkata 700106, West Bengal, India.
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5
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Oliveira LS, Patera AC, Domingues DS, Sanches DS, Lopes FM, Bugatti PH, Saito PTM, Maracaja-Coutinho V, Durham AM, Paschoal AR. Computational Analysis of Transposable Elements and CircRNAs in Plants. METHODS IN MOLECULAR BIOLOGY (CLIFTON, N.J.) 2022; 2362:147-172. [PMID: 34195962 DOI: 10.1007/978-1-0716-1645-1_9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
This chapter provides two main contributions: (1) a description of computational tools and databases used to identify and analyze transposable elements (TEs) and circRNAs in plants; and (2) data analysis on public TE and circRNA data. Our goal is to highlight the primary information available in the literature on circular noncoding RNAs and transposable elements in plants. The exploratory analysis performed on publicly available circRNA and TEs data help discuss four sequence features. Finally, we investigate the association on circRNAs:TE in plants in the model organism Arabidopsis thaliana.
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Affiliation(s)
- Liliane Santana Oliveira
- Department of Computer Science, Federal University of Technology-Paraná (UTFPR), Cornélio Procópio, PR, Brazil. .,Embrapa Soja, Londrina, Paraná, Brazil.
| | - Andressa Caroline Patera
- Department of Computer Science, Federal University of Technology-Paraná (UTFPR), Cornélio Procópio, PR, Brazil
| | - Douglas Silva Domingues
- Department of Computer Science, Federal University of Technology-Paraná (UTFPR), Cornélio Procópio, PR, Brazil.,Group of Genomics and Transcriptomes in Plants, Instituto de Biociências de Rio Claro, Universidade Estadual Paulista (UNESP), Rio Claro, SP, Brazil
| | - Danilo Sipoli Sanches
- Department of Computer Science, Federal University of Technology-Paraná (UTFPR), Cornélio Procópio, PR, Brazil
| | - Fabricio Martins Lopes
- Department of Computer Science, Federal University of Technology-Paraná (UTFPR), Cornélio Procópio, PR, Brazil
| | - Pedro Henrique Bugatti
- Department of Computer Science, Federal University of Technology-Paraná (UTFPR), Cornélio Procópio, PR, Brazil
| | - Priscila Tiemi Maeda Saito
- Department of Computer Science, Federal University of Technology-Paraná (UTFPR), Cornélio Procópio, PR, Brazil
| | - Vinicius Maracaja-Coutinho
- Centro de Modelamiento Molecular, Biofísica y Bioinformática-CM2B2, Facultad de Ciencias Quimicas y Farmaceuticas, Universidad de Chile, Santiago, Chile
| | - Alan Mitchell Durham
- Department of Computer Science, Instituto de Matemática e Estatística, Universidade de São Paulo (USP), Cidade Universitária, SP, Brazil
| | - Alexandre Rossi Paschoal
- Department of Computer Science, Federal University of Technology-Paraná (UTFPR), Cornélio Procópio, PR, Brazil.
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6
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Zeng C, Takeda A, Sekine K, Osato N, Fukunaga T, Hamada M. Bioinformatics Approaches for Determining the Functional Impact of Repetitive Elements on Non-coding RNAs. Methods Mol Biol 2022; 2509:315-340. [PMID: 35796972 DOI: 10.1007/978-1-0716-2380-0_19] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
With a large number of annotated non-coding RNAs (ncRNAs), repetitive sequences are found to constitute functional components (termed as repetitive elements) in ncRNAs that perform specific biological functions. Bioinformatics analysis is a powerful tool for improving our understanding of the role of repetitive elements in ncRNAs. This chapter summarizes recent findings that reveal the role of repetitive elements in ncRNAs. Furthermore, relevant bioinformatics approaches are systematically reviewed, which promises to provide valuable resources for studying the functional impact of repetitive elements on ncRNAs.
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Affiliation(s)
- Chao Zeng
- Faculty of Science and Engineering, Waseda University, Tokyo, Japan.
- AIST-Waseda University Computational Bio Big-Data Open Innovation Laboratory (CBBD-OIL), Tokyo, Japan.
| | - Atsushi Takeda
- Faculty of Science and Engineering, Waseda University, Tokyo, Japan
| | - Kotaro Sekine
- Faculty of Science and Engineering, Waseda University, Tokyo, Japan
| | - Naoki Osato
- Faculty of Science and Engineering, Waseda University, Tokyo, Japan
| | - Tsukasa Fukunaga
- Waseda Institute for Advanced Study, Waseda University, Tokyo, Japan
| | - Michiaki Hamada
- Faculty of Science and Engineering, Waseda University, Tokyo, Japan.
- AIST-Waseda University Computational Bio Big-Data Open Innovation Laboratory (CBBD-OIL), Tokyo, Japan.
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7
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Abstract
In this era of big data, sets of methodologies and strategies are designed to extract knowledge from huge volumes of data. However, the cost of where and how to get this information accurately and quickly is extremely important, given the diversity of genomes and the different ways of representing that information. Among the huge set of information and relationships that the genome carries, there are sequences called miRNAs (microRNAs). These sequences were described in the 1990s and are mainly involved in mechanisms of regulation and gene expression. Having this in mind, this chapter focuses on exploring the available literature and providing useful and practical guidance on the miRNA database and tools topic. For that, we organized and present this text in two ways: (a) the update reviews and articles, which best summarize and discuss the theme; and (b) our update investigation on miRNA literature and portals about databases and tools. Finally, we present the main challenge and a possible solution to improve resources and tools.
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Affiliation(s)
- Tharcísio Soares de Amorim
- Department of Computer Science and Bioinformatics and Pattern Recognition Group, Universidade Tecnológica Federal do Paraná (UTFPR), Cornélio Procópio, Brazil
| | - Daniel Longhi Fernandes Pedro
- Department of Computer Science and Bioinformatics and Pattern Recognition Group, Universidade Tecnológica Federal do Paraná (UTFPR), Cornélio Procópio, Brazil
| | - Alexandre Rossi Paschoal
- Department of Computer Science and Bioinformatics and Pattern Recognition Group, Universidade Tecnológica Federal do Paraná (UTFPR), Cornélio Procópio, Brazil.
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8
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Patil S, Joshi S, Jamla M, Zhou X, Taherzadeh MJ, Suprasanna P, Kumar V. MicroRNA-mediated bioengineering for climate-resilience in crops. Bioengineered 2021; 12:10430-10456. [PMID: 34747296 PMCID: PMC8815627 DOI: 10.1080/21655979.2021.1997244] [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: 09/11/2021] [Revised: 10/19/2021] [Accepted: 10/21/2021] [Indexed: 12/24/2022] Open
Abstract
Global projections on the climate change and the dynamic environmental perturbations indicate severe impacts on food security in general, and crop yield, vigor and the quality of produce in particular. Sessile plants respond to environmental challenges such as salt, drought, temperature, heavy metals at transcriptional and/or post-transcriptional levels through the stress-regulated network of pathways including transcription factors, proteins and the small non-coding endogenous RNAs. Amongs these, the miRNAs have gained unprecedented attention in recent years as key regulators for modulating gene expression in plants under stress. Hence, tailoring of miRNAs and their target pathways presents a promising strategy for developing multiple stress-tolerant crops. Plant stress tolerance has been successfully achieved through the over expression of microRNAs such as Os-miR408, Hv-miR82 for drought tolerance; OsmiR535A and artificial DST miRNA for salinity tolerance; and OsmiR535 and miR156 for combined drought and salt stress. Examples of miR408 overexpression also showed improved efficiency of irradiation utilization and carbon dioxide fixation in crop plants. Through this review, we present the current understanding about plant miRNAs, their roles in plant growth and stress-responses, the modern toolbox for identification, characterization and validation of miRNAs and their target genes including in silico tools, machine learning and artificial intelligence. Various approaches for up-regulation or knock-out of miRNAs have been discussed. The main emphasis has been given to the exploration of miRNAs for development of bioengineered climate-smart crops that can withstand changing climates and stressful environments, including combination of stresses, with very less or no yield penalties.
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Affiliation(s)
- Suraj Patil
- Department of Biotechnology, Modern College of Arts, Science and Commerce, Savitribai Phule Pune University, Pune, India
| | - Shrushti Joshi
- Department of Biotechnology, Modern College of Arts, Science and Commerce, Savitribai Phule Pune University, Pune, India
| | - Monica Jamla
- Department of Biotechnology, Modern College of Arts, Science and Commerce, Savitribai Phule Pune University, Pune, India
| | - Xianrong Zhou
- School of Life Science and Biotechnology, Yangtze Normal University, Ch-ongqing, China
| | | | - Penna Suprasanna
- Bhabha Atomic Research Centre, Homi Bhabha National Institute, Mumbai, India
| | - Vinay Kumar
- Department of Biotechnology, Modern College of Arts, Science and Commerce, Savitribai Phule Pune University, Pune, India
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9
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Mokhtar MM, Alsamman AM, Abd-Elhalim HM, El Allali A. CicerSpTEdb: A web-based database for high-resolution genome-wide identification of transposable elements in Cicer species. PLoS One 2021; 16:e0259540. [PMID: 34762703 PMCID: PMC8584679 DOI: 10.1371/journal.pone.0259540] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2021] [Accepted: 10/20/2021] [Indexed: 11/19/2022] Open
Abstract
Recently, Cicer species have experienced increased research interest due to their economic importance, especially in genetics, genomics, and crop improvement. The Cicer arietinum, Cicer reticulatum, and Cicer echinospermum genomes have been sequenced and provide valuable resources for trait improvement. Since the publication of the chickpea draft genome, progress has been made in genome assembly, functional annotation, and identification of polymorphic markers. However, work is still needed to identify transposable elements (TEs) and make them available for researchers. In this paper, we present CicerSpTEdb, a comprehensive TE database for Cicer species that aims to improve our understanding of the organization and structural variations of the chickpea genome. Using structure and homology-based methods, 3942 C. echinospermum, 3579 C. reticulatum, and 2240 C. arietinum TEs were identified. Comparisons between Cicer species indicate that C. echinospermum has the highest number of LTR-RT and hAT TEs. C. reticulatum has more Mutator, PIF Harbinger, Tc1 Mariner, and CACTA TEs, while C. arietinum has the highest number of Helitron. CicerSpTEdb enables users to search and visualize TEs by location and download their results. The database will provide a powerful resource that can assist in developing TE target markers for molecular breeding and answer related biological questions. Database URL: http://cicersptedb.easyomics.org/index.php.
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Affiliation(s)
- Morad M. Mokhtar
- African Genome Center, Mohammed VI Polytechnic University, Ben Guerir, Morocco
- * E-mail: (AEA); (MMM)
| | | | - Haytham M. Abd-Elhalim
- Agricultural Genetic Engineering Research Institute, Agricultural Research Center, Giza, Egypt
| | - Achraf El Allali
- African Genome Center, Mohammed VI Polytechnic University, Ben Guerir, Morocco
- * E-mail: (AEA); (MMM)
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10
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A Practical Guide on Computational Tools and Databases for Transposable Elements in Plants. Methods Mol Biol 2021. [PMID: 33900590 DOI: 10.1007/978-1-0716-1134-0_3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/01/2023]
Abstract
In the age of big data, obtaining precise information about the research topic of interesting is extremely important. Keeping this in mind, this chapter focuses on providing a practical knowledge guide about computational tools and databases of transposable elements (TE) in plants. For that, we organize and present this text in three sections: (1) a discussion about tools and databases on this theme; (2) hands-on of how to use a few of them; (3) an exploratory data analysis on public TE data. Finally, we are going deep to present the main challenges and possible solutions to improve resources and tools.
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11
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Tahir Ul Qamar M, Zhu X, Khan MS, Xing F, Chen LL. Pan-genome: A promising resource for noncoding RNA discovery in plants. THE PLANT GENOME 2020; 13:e20046. [PMID: 33217199 DOI: 10.1002/tpg2.20046] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/14/2020] [Revised: 06/08/2020] [Accepted: 06/22/2020] [Indexed: 05/05/2023]
Abstract
Plant genomes contain both protein-coding and noncoding sequences including transposable elements (TEs) and noncoding RNAs (ncRNAs). The ncRNAs are recognized as important elements that play fundamental roles in the structural organization and function of plant genomes. Despite various hypotheses, TEs are believed to be a major precursor of ncRNAs. Transposable elements are also prime factors that cause genomic variation among members of a species. Hence, TEs pose a major challenge in the discovery and analysis of ncRNAs. With the increase in the number of sequenced plant genomes, it is now accepted that a single reference genome is insufficient to represent the complete genomic diversity and contents of a species, and exploring the pan-genome of a species is critical. In this review, we summarize the recent progress in the field of plant pan-genomes. We also discuss TEs and their roles in ncRNA biogenesis and present our perspectives on the application of pan-genomes for the discovery of ncRNAs to fully explore and exploit their biological roles in plants.
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Affiliation(s)
- Muhammad Tahir Ul Qamar
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Life Science and Technology, Guangxi University, Nanning, 530004, P. R. China
- Hubei Key Laboratory of Agricultural Bioinformatics, College of Informatics, Huazhong Agricultural University, Wuhan, 430070, P. R. China
| | - Xitong Zhu
- Hubei Key Laboratory of Agricultural Bioinformatics, College of Informatics, Huazhong Agricultural University, Wuhan, 430070, P. R. China
| | - Muhammad Sarwar Khan
- Center of Agricultural Biochemistry and Biotechnology, University of Agriculture, Faisalabad, 38000, Pakistan
| | - Feng Xing
- College of Life Science, Xinyang Normal University, Xinyang, 464000, P. R. China
| | - Ling-Ling Chen
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Life Science and Technology, Guangxi University, Nanning, 530004, P. R. China
- Hubei Key Laboratory of Agricultural Bioinformatics, College of Informatics, Huazhong Agricultural University, Wuhan, 430070, P. R. China
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12
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Measuring Performance Metrics of Machine Learning Algorithms for Detecting and Classifying Transposable Elements. Processes (Basel) 2020. [DOI: 10.3390/pr8060638] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Because of the promising results obtained by machine learning (ML) approaches in several fields, every day is more common, the utilization of ML to solve problems in bioinformatics. In genomics, a current issue is to detect and classify transposable elements (TEs) because of the tedious tasks involved in bioinformatics methods. Thus, ML was recently evaluated for TE datasets, demonstrating better results than bioinformatics applications. A crucial step for ML approaches is the selection of metrics that measure the realistic performance of algorithms. Each metric has specific characteristics and measures properties that may be different from the predicted results. Although the most commonly used way to compare measures is by using empirical analysis, a non-result-based methodology has been proposed, called measure invariance properties. These properties are calculated on the basis of whether a given measure changes its value under certain modifications in the confusion matrix, giving comparative parameters independent of the datasets. Measure invariance properties make metrics more or less informative, particularly on unbalanced, monomodal, or multimodal negative class datasets and for real or simulated datasets. Although several studies applied ML to detect and classify TEs, there are no works evaluating performance metrics in TE tasks. Here, we analyzed 26 different metrics utilized in binary, multiclass, and hierarchical classifications, through bibliographic sources, and their invariance properties. Then, we corroborated our findings utilizing freely available TE datasets and commonly used ML algorithms. Based on our analysis, the most suitable metrics for TE tasks must be stable, even using highly unbalanced datasets, multimodal negative class, and training datasets with errors or outliers. Based on these parameters, we conclude that the F1-score and the area under the precision-recall curve are the most informative metrics since they are calculated based on other metrics, providing insight into the development of an ML application.
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13
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Mustafin RN. The Role of Transposable Elements in the Differentiation of Stem Cells. MOLECULAR GENETICS MICROBIOLOGY AND VIROLOGY 2019. [DOI: 10.3103/s0891416819020071] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
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14
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Mustafin RN. Functional Dualism of Transposon Transcripts in Evolution of Eukaryotic Genomes. Russ J Dev Biol 2019. [DOI: 10.1134/s1062360418070019] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
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15
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Mustafin RN. The Relationship between Transposons and Transcription Factors in the Evolution of Eukaryotes. J EVOL BIOCHEM PHYS+ 2019. [DOI: 10.1134/s0022093019010022] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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16
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Gahlaut V, Baranwal VK, Khurana P. miRNomes involved in imparting thermotolerance to crop plants. 3 Biotech 2018; 8:497. [PMID: 30498670 PMCID: PMC6261126 DOI: 10.1007/s13205-018-1521-7] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2018] [Accepted: 11/17/2018] [Indexed: 12/20/2022] Open
Abstract
Thermal stress is one of the challenges to crop plants that negatively impacts crop yield. To overcome this ever-growing problem, utilization of regulatory mechanisms, especially microRNAs (miRNAs), that provide efficient and precise regulation in a targeted manner have been found to play determining roles. Besides their roles in plant growth and development, many recent studies have shown differential regulation of several miRNAs during abiotic stresses including heat stress (HS). Thus, understanding the underlying mechanism of miRNA-mediated gene expression during HS will enable researchers to exploit this regulatory mechanism to address HS responses. This review focuses on the miRNAs and regulatory networks that were involved in physiological, metabolic and morphological adaptations during HS in plant, specifically in crops. Illustrated examples including, the miR156-SPL, miR169-NF-YA5, miR395-APS/AST, miR396-WRKY, etc., have been discussed in specific relation to the crop plants. Further, we have also discussed the available plant miRNA databases and bioinformatics tools useful for miRNA identification and study of their regulatory role in response to HS. Finally, we have briefly discussed the future prospects about the miRNA-related mechanisms of HS for improving thermotolerance in crop plants.
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Affiliation(s)
- Vijay Gahlaut
- Department of Plant Molecular Biology, University of Delhi South Campus, Benito Juarez Road, New Delhi, 110021 India
| | - Vinay Kumar Baranwal
- Department of Plant Molecular Biology, University of Delhi South Campus, Benito Juarez Road, New Delhi, 110021 India
- Department of Botany, Swami Devanand Post Graduate College, Math-lar, Lar, Deoria, Uttar Pradesh 274502 India
| | - Paramjit Khurana
- Department of Plant Molecular Biology, University of Delhi South Campus, Benito Juarez Road, New Delhi, 110021 India
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Mustafin RN, Khusnutdinova EK. INTERRELATION OF PRIONS WITH NON-CODING RNAS. Vavilovskii Zhurnal Genet Selektsii 2018. [DOI: 10.18699/vj18.377] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Prions are alternative infectious conformations for some cellular proteins. For the protein PrPC(PrP – prion protein, С – common), a prion conformation, called PrPSc(S – scrapie), is pathological. For example, in mammals the PrPScprion causes transmissible spongiform encephalopathies accumulating in the brain tissues of PrPScaggregates that have amyloid properties. MicroRNAs and long non-coding RNAs can be translated into functional peptides. These peptides can have a regulatory effect on genes from which their non-coding RNAs are transcribed. It has been assumed that prions, like peptides, due to the presence of specific domains, can also activate certain non-coding RNAs. Some of the activated non-coding RNAs can catalyze the formation of new prions from normal protein, playing their role in the pathogenesis of prion diseases. Confirmation of this assumption is the presence of the association of alleles of microRNA with the development of the disease, which indicates the role of the specific sequences of noncoding RNAs in the catalysis of prion formation. In the brain tissues of patients with prion diseases, as well as in exosomes containing an abnormal PrPScisoform, changes in the levels of microRNA have been observed. A possible cause is the interaction of the spatial domains of PrPScwith the sequences of the non-coding RNA genes, which causes a change in their expression. MicroRNAs, in turn, affect the synthesis of long non-coding RNAs. We hypothesize that long noncoding RNAs and possibly microRNAs can interact with PrPCcatalyzing its transformation into PrPSc. As a result, the number of PrPScincreases exponentially. In the brain of animals and humans, transposon activity has been observed, which has a regulatory effect on the differentiation of neuronal stem cells. Transposons form the basis of domain structures of long non-coding RNAs. In addition, they are important sources of microRNA. Since prion diseases can arise as sporadic and hereditary cases, and hereditary predisposition is important for the development of pathology, we hypothesize the role of individual features of activation of transposons in the pathogenesis of prion diseases. The activation of transposons in the brain at certain stages of development, as well as under the influence of stress, is reflected in the peculiarities of expression of specific non-coding RNAs that are capable of catalyzing the transition of the PrPCprotein to PrPSc. Research in this direction can be the basis for targeted anti-microRNA therapy of prion diseases.
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Mustafin RN, Khusnutdinova EK. Epigenetic Hypothesis of the Role of Peptides in Aging. ADVANCES IN GERONTOLOGY 2018. [DOI: 10.1134/s2079057018030128] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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19
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Pedro DLF, Lorenzetti APR, Domingues DS, Paschoal AR. PlaNC-TE: a comprehensive knowledgebase of non-coding RNAs and transposable elements in plants. DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION 2018; 2018:1-7. [PMID: 30101318 PMCID: PMC6146122 DOI: 10.1093/database/bay078] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/19/2018] [Accepted: 06/28/2018] [Indexed: 12/20/2022]
Abstract
Transposable elements (TEs) play an essential role in the genetic variability of eukaryotic species. In plants, they may comprise up to 90% of the total genome. Non-coding RNAs (ncRNAs) are known to control gene expression and regulation. Although the relationship between ncRNAs and TEs is known, obtaining the organized data for sequenced genomes is not straightforward. In this study, we describe the PlaNC-TE (http://planc-te.cp.utfpr.edu.br), a user-friendly portal harboring a knowledgebase created by integrating and analysing plant ncRNA-TE data. We identified a total of 14 350 overlaps between ncRNAs and TEs in 40 plant genomes. The database allows users to browse, search and download all ncRNA and TE data analysed. Overall, PlaNC-TE not only organizes data and provides insights about the relationship between ncRNA and TEs in plants but also helps improve genome annotation strategies. Moreover, this is the first database to provide resources to broadly investigate functions and mechanisms involving TEs and ncRNAs in plants.
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Affiliation(s)
- Daniel Longhi Fernandes Pedro
- Department of Computer Science, Bioinformatics Graduation Program (PPGBIOINFO), Federal University of Technology - Paraná, Cornélio Procópio, PR, Brazil
| | | | - Douglas Silva Domingues
- Department of Computer Science, Bioinformatics Graduation Program (PPGBIOINFO), Federal University of Technology - Paraná, Cornélio Procópio, PR, Brazil.,Department of Botany, Institute of Biosciences, São Paulo State University, UNESP, Rio Claro, SP, Brazil
| | - Alexandre Rossi Paschoal
- Department of Computer Science, Bioinformatics Graduation Program (PPGBIOINFO), Federal University of Technology - Paraná, Cornélio Procópio, PR, Brazil
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20
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Modulating signaling networks by CRISPR/Cas9-mediated transposable element insertion. Curr Genet 2017; 64:405-412. [DOI: 10.1007/s00294-017-0765-9] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2017] [Revised: 10/01/2017] [Accepted: 10/09/2017] [Indexed: 12/11/2022]
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21
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Wang J, Meng X, Dobrovolskaya OB, Orlov YL, Chen M. Non-coding RNAs and Their Roles in Stress Response in Plants. GENOMICS PROTEOMICS & BIOINFORMATICS 2017; 15:301-312. [PMID: 29017967 PMCID: PMC5673675 DOI: 10.1016/j.gpb.2017.01.007] [Citation(s) in RCA: 109] [Impact Index Per Article: 15.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/28/2016] [Revised: 01/04/2017] [Accepted: 01/26/2017] [Indexed: 02/04/2023]
Abstract
Eukaryotic genomes encode thousands of non-coding RNAs (ncRNAs), which play crucial roles in transcriptional and post-transcriptional regulation of gene expression. Accumulating evidence indicates that ncRNAs, especially microRNAs (miRNAs) and long ncRNAs (lncRNAs), have emerged as key regulatory molecules in plant stress responses. In this review, we have summarized the current progress on the understanding of plant miRNA and lncRNA identification, characteristics, bioinformatics tools, and resources, and provided examples of mechanisms of miRNA- and lncRNA-mediated plant stress tolerance.
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Affiliation(s)
- Jingjing Wang
- Department of Bioinformatics, State Key Laboratory of Plant Physiology and Biochemistry, College of Life Sciences, Zhejiang University, Hangzhou 310058, China; James D. Watson Institute of Genome Sciences, Zhejiang University, Hangzhou 310058, China
| | - Xianwen Meng
- Department of Bioinformatics, State Key Laboratory of Plant Physiology and Biochemistry, College of Life Sciences, Zhejiang University, Hangzhou 310058, China
| | - Oxana B Dobrovolskaya
- Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, Novosibirsk 630090, Russia; Novosibirsk State University, Novosibirsk 630090, Russia
| | - Yuriy L Orlov
- Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, Novosibirsk 630090, Russia
| | - Ming Chen
- Department of Bioinformatics, State Key Laboratory of Plant Physiology and Biochemistry, College of Life Sciences, Zhejiang University, Hangzhou 310058, China; James D. Watson Institute of Genome Sciences, Zhejiang University, Hangzhou 310058, China.
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Karakülah G, Suner A. PlanTEnrichment: A tool for enrichment analysis of transposable elements in plants. Genomics 2017; 109:336-340. [DOI: 10.1016/j.ygeno.2017.05.008] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2017] [Revised: 05/29/2017] [Accepted: 05/31/2017] [Indexed: 02/01/2023]
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Ragupathy R, Ravichandran S, Mahdi MSR, Huang D, Reimer E, Domaratzki M, Cloutier S. Deep sequencing of wheat sRNA transcriptome reveals distinct temporal expression pattern of miRNAs in response to heat, light and UV. Sci Rep 2016; 6:39373. [PMID: 28004741 PMCID: PMC5177929 DOI: 10.1038/srep39373] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2016] [Accepted: 11/15/2016] [Indexed: 01/30/2023] Open
Abstract
Understanding of plant adaptation to abiotic stresses has implications in plant breeding, especially in the context of climate change. MicroRNAs (miRNAs) and short interfering RNAs play a crucial role in gene regulation. Here, wheat plants were exposed to one of the following stresses: continuous light, heat or ultraviolet radiations over five consecutive days and leaf tissues from three biological replicates were harvested at 0, 1, 2, 3, 7 and 10 days after treatment (DAT). A total of 72 small RNA libraries were sequenced on the Illumina platform generating ~524 million reads corresponding to ~129 million distinct tags from which 232 conserved miRNAs were identified. The expression levels of 1, 2 and 79 miRNAs were affected by ultraviolet radiation, continuous light and heat, respectively. Approximately 55% of the differentially expressed miRNAs were downregulated at 0 and 1 DAT including miR398, miR528 and miR156 that control mRNAs involved in activation of signal transduction pathways and flowering. Other putative targets included histone variants and methyltransferases. These results suggest a temporal miRNA-guided post-transcriptional regulation that enables wheat to respond to abiotic stresses, particularly heat. Designing novel wheat breeding strategies such as regulatory gene-based marker assisted selection depends on accurate identification of stress induced miRNAs.
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Affiliation(s)
- Raja Ragupathy
- Plant Science Department, University of Manitoba, Winnipeg, Manitoba, Canada
| | - Sridhar Ravichandran
- Agriculture and Agri-Food Canada, Ottawa Research and Development Centre, Ottawa, Ontario, Canada
| | | | - Douglas Huang
- Agriculture and Agri-Food Canada, Ottawa Research and Development Centre, Ottawa, Ontario, Canada
| | - Elsa Reimer
- Agriculture and Agri-Food Canada, Morden Research and Development Centre, Morden, Manitoba, Canada
| | - Michael Domaratzki
- Department of Computer Science, University of Manitoba, Winnipeg, Manitoba, Canada
| | - Sylvie Cloutier
- Agriculture and Agri-Food Canada, Ottawa Research and Development Centre, Ottawa, Ontario, Canada
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The emergence of molecular profiling and omics techniques in seagrass biology; furthering our understanding of seagrasses. Funct Integr Genomics 2016; 16:465-80. [DOI: 10.1007/s10142-016-0501-4] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2016] [Revised: 06/09/2016] [Accepted: 06/16/2016] [Indexed: 12/23/2022]
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25
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Shriram V, Kumar V, Devarumath RM, Khare TS, Wani SH. MicroRNAs As Potential Targets for Abiotic Stress Tolerance in Plants. FRONTIERS IN PLANT SCIENCE 2016; 7:817. [PMID: 27379117 PMCID: PMC4906921 DOI: 10.3389/fpls.2016.00817] [Citation(s) in RCA: 174] [Impact Index Per Article: 21.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/21/2016] [Accepted: 05/25/2016] [Indexed: 05/19/2023]
Abstract
The microRNAs (miRNAs) are small (20-24 nt) sized, non-coding, single stranded riboregulator RNAs abundant in higher organisms. Recent findings have established that plants assign miRNAs as critical post-transcriptional regulators of gene expression in sequence-specific manner to respond to numerous abiotic stresses they face during their growth cycle. These small RNAs regulate gene expression via translational inhibition. Usually, stress induced miRNAs downregulate their target mRNAs, whereas, their downregulation leads to accumulation and function of positive regulators. In the past decade, investigations were mainly aimed to identify plant miRNAs, responsive to individual or multiple environmental factors, profiling their expression patterns and recognizing their roles in stress responses and tolerance. Altered expressions of miRNAs implicated in plant growth and development have been reported in several plant species subjected to abiotic stress conditions such as drought, salinity, extreme temperatures, nutrient deprivation, and heavy metals. These findings indicate that miRNAs may hold the key as potential targets for genetic manipulations to engineer abiotic stress tolerance in crop plants. This review is aimed to provide recent updates on plant miRNAs, their biogenesis and functions, target prediction and identification, computational tools and databases available for plant miRNAs, and their roles in abiotic stress-responses and adaptive mechanisms in major crop plants. Besides, the recent case studies for overexpressing the selected miRNAs for miRNA-mediated enhanced abiotic stress tolerance of transgenic plants have been discussed.
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Affiliation(s)
- Varsha Shriram
- Department of Botany, Prof. Ramkrishna More Arts, Commerce and Science College, Savitribai Phule Pune UniversityPune, India
| | - Vinay Kumar
- Department of Biotechnology, Modern College of Arts, Science and Commerce, Savitribai Phule Pune UniversityPune, India
- *Correspondence: Vinay Kumar
| | - Rachayya M. Devarumath
- Molecular Biology and Genetic Engineering Section, Vasantdada Sugar InstitutePune, India
| | - Tushar S. Khare
- Department of Biotechnology, Modern College of Arts, Science and Commerce, Savitribai Phule Pune UniversityPune, India
| | - Shabir H. Wani
- Division of Genetics and Plant Breeding, Faculty of Agriculture WADURA, Sher-e-Kashmir University of Agricultural Sciences and TechnologyKashmir, India
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