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Wagner V, Meese E, Keller A. The intricacies of isomiRs: from classification to clinical relevance. Trends Genet 2024:S0168-9525(24)00124-0. [PMID: 38862304 DOI: 10.1016/j.tig.2024.05.007] [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: 03/22/2024] [Revised: 05/14/2024] [Accepted: 05/15/2024] [Indexed: 06/13/2024]
Abstract
MicroRNAs (miRNAs) and isoforms of their archetype, called isomiRs, regulate gene expression via complementary base-pair binding to messenger RNAs (mRNAs). The partially evolutionarily conserved isomiR sequence variations are differentially expressed among tissues, populations, and genders, and between healthy and diseased states. Aiming towards the clinical use of isomiRs as diagnostic biomarkers and for therapeutic purposes, several challenges need to be addressed, including (i) clarification of isomiR definition, (ii) improved annotation in databases with new standardization (such as the mirGFF3 format), and (iii) improved methods of isomiR detection, functional verification, and in silico analysis. In this review we discuss the respective challenges, and highlight the opportunities for clinical use of isomiRs, especially in the light of increasing amounts of next-generation sequencing (NGS) data.
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Affiliation(s)
- Viktoria Wagner
- Chair for Clinical Bioinformatics, Center for Bioinformatics, Saarland University, 66123 Saarbrücken, Germany; Helmholtz-Institute for Pharmaceutical Research Saarland (HIPS), Saarland University Campus, 66123 Saarbrücken, Germany
| | - Eckart Meese
- Department of Human Genetics, Saarland University, 66421 Homburg/Saar, Germany
| | - Andreas Keller
- Chair for Clinical Bioinformatics, Center for Bioinformatics, Saarland University, 66123 Saarbrücken, Germany; Helmholtz-Institute for Pharmaceutical Research Saarland (HIPS), Saarland University Campus, 66123 Saarbrücken, Germany.
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2
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Non-coding RNAs in human health and disease: potential function as biomarkers and therapeutic targets. Funct Integr Genomics 2023; 23:33. [PMID: 36625940 PMCID: PMC9838419 DOI: 10.1007/s10142-022-00947-4] [Citation(s) in RCA: 43] [Impact Index Per Article: 43.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2022] [Revised: 12/14/2022] [Accepted: 12/15/2022] [Indexed: 01/11/2023]
Abstract
Human diseases have been a critical threat from the beginning of human history. Knowing the origin, course of action and treatment of any disease state is essential. A microscopic approach to the molecular field is a more coherent and accurate way to explore the mechanism, progression, and therapy with the introduction and evolution of technology than a macroscopic approach. Non-coding RNAs (ncRNAs) play increasingly important roles in detecting, developing, and treating all abnormalities related to physiology, pathology, genetics, epigenetics, cancer, and developmental diseases. Noncoding RNAs are becoming increasingly crucial as powerful, multipurpose regulators of all biological processes. Parallel to this, a rising amount of scientific information has revealed links between abnormal noncoding RNA expression and human disorders. Numerous non-coding transcripts with unknown functions have been found in addition to advancements in RNA-sequencing methods. Non-coding linear RNAs come in a variety of forms, including circular RNAs with a continuous closed loop (circRNA), long non-coding RNAs (lncRNA), and microRNAs (miRNA). This comprises specific information on their biogenesis, mode of action, physiological function, and significance concerning disease (such as cancer or cardiovascular diseases and others). This study review focuses on non-coding RNA as specific biomarkers and novel therapeutic targets.
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3
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Dindhoria K, Monga I, Thind AS. Computational approaches and challenges for identification and annotation of non-coding RNAs using RNA-Seq. Funct Integr Genomics 2022; 22:1105-1112. [DOI: 10.1007/s10142-022-00915-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2022] [Revised: 11/04/2022] [Accepted: 11/04/2022] [Indexed: 11/22/2022]
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4
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Huang L, Zhang L, Chen X. Updated review of advances in microRNAs and complex diseases: experimental results, databases, webservers and data fusion. Brief Bioinform 2022; 23:6696143. [PMID: 36094095 DOI: 10.1093/bib/bbac397] [Citation(s) in RCA: 37] [Impact Index Per Article: 18.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2022] [Revised: 07/19/2022] [Accepted: 08/15/2022] [Indexed: 12/14/2022] Open
Abstract
MicroRNAs (miRNAs) are gene regulators involved in the pathogenesis of complex diseases such as cancers, and thus serve as potential diagnostic markers and therapeutic targets. The prerequisite for designing effective miRNA therapies is accurate discovery of miRNA-disease associations (MDAs), which has attracted substantial research interests during the last 15 years, as reflected by more than 55 000 related entries available on PubMed. Abundant experimental data gathered from the wealth of literature could effectively support the development of computational models for predicting novel associations. In 2017, Chen et al. published the first-ever comprehensive review on MDA prediction, presenting various relevant databases, 20 representative computational models, and suggestions for building more powerful ones. In the current review, as the continuation of the previous study, we revisit miRNA biogenesis, detection techniques and functions; summarize recent experimental findings related to common miRNA-associated diseases; introduce recent updates of miRNA-relevant databases and novel database releases since 2017, present mainstream webservers and new webserver releases since 2017 and finally elaborate on how fusion of diverse data sources has contributed to accurate MDA prediction.
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Affiliation(s)
- Li Huang
- Academy of Arts and Design, Tsinghua University, Beijing, 10084, China.,The Future Laboratory, Tsinghua University, Beijing, 10084, China
| | - Li Zhang
- School of Information and Control Engineering, China University of Mining and Technology, Xuzhou, 221116, China
| | - Xing Chen
- School of Information and Control Engineering, China University of Mining and Technology, Xuzhou, 221116, China.,Artificial Intelligence Research Institute, China University of Mining and Technology, Xuzhou, 221116, China
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5
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Chao H, Hu Y, Zhao L, Xin S, Ni Q, Zhang P, Chen M. Biogenesis, Functions, Interactions, and Resources of Non-Coding RNAs in Plants. Int J Mol Sci 2022; 23:ijms23073695. [PMID: 35409060 PMCID: PMC8998614 DOI: 10.3390/ijms23073695] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Revised: 03/19/2022] [Accepted: 03/23/2022] [Indexed: 12/14/2022] Open
Abstract
Plant transcriptomes encompass a large number of functional non-coding RNAs (ncRNAs), only some of which have protein-coding capacity. Since their initial discovery, ncRNAs have been classified into two broad categories based on their biogenesis and mechanisms of action, housekeeping ncRNAs and regulatory ncRNAs. With advances in RNA sequencing technology and computational methods, bioinformatics resources continue to emerge and update rapidly, including workflow for in silico ncRNA analysis, up-to-date platforms, databases, and tools dedicated to ncRNA identification and functional annotation. In this review, we aim to describe the biogenesis, biological functions, and interactions with DNA, RNA, protein, and microorganism of five major regulatory ncRNAs (miRNA, siRNA, tsRNA, circRNA, lncRNA) in plants. Then, we systematically summarize tools for analysis and prediction of plant ncRNAs, as well as databases. Furthermore, we discuss the silico analysis process of these ncRNAs and present a protocol for step-by-step computational analysis of ncRNAs. In general, this review will help researchers better understand the world of ncRNAs at multiple levels.
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Affiliation(s)
| | | | | | | | | | - Peijing Zhang
- Correspondence: (P.Z.); (M.C.); Tel./Fax: +86-(0)571-88206612 (M.C.)
| | - Ming Chen
- Correspondence: (P.Z.); (M.C.); Tel./Fax: +86-(0)571-88206612 (M.C.)
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6
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Khatun MS, Alam MA, Shoombuatong W, Mollah MNH, Kurata H, Hasan MM. Recent development of bioinformatics tools for microRNA target prediction. Curr Med Chem 2021; 29:865-880. [PMID: 34348604 DOI: 10.2174/0929867328666210804090224] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2021] [Revised: 06/10/2021] [Accepted: 06/15/2021] [Indexed: 11/22/2022]
Abstract
MicroRNAs (miRNAs) are central players that regulate the post-transcriptional processes of gene expression. Binding of miRNAs to target mRNAs can repress their translation by inducing the degradation or by inhibiting the translation of the target mRNAs. High-throughput experimental approaches for miRNA target identification are costly and time-consuming, depending on various factors. It is vitally important to develop the bioinformatics methods for accurately predicting miRNA targets. With the increase of RNA sequences in the post-genomic era, bioinformatics methods are being developed for miRNA studies specially for miRNA target prediction. This review summarizes the current development of state-of-the-art bioinformatics tools for miRNA target prediction, points out the progress and limitations of the available miRNA databases, and their working principles. Finally, we discuss the caveat and perspectives of the next-generation algorithms for the prediction of miRNA targets.
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Affiliation(s)
- Mst Shamima Khatun
- Department of Bioscience and Bioinformatics, Kyushu Institute of Technology, 680-4 Kawazu, Iizuka, Fukuoka 820-8502. Japan
| | - Md Ashad Alam
- Tulane Center for Biomedical Informatics and Genomics, Division of Biomedical Informatics and Genomics, John W. Deming Department of Medicine, School of Medicine, Tulane University, New Orleans, LA 70112. United States
| | - Watshara Shoombuatong
- Center of Data Mining and Biomedical Informatics, Faculty of Medical Technology, Mahidol University, Bangkok 10700. Thailand
| | - Md Nurul Haque Mollah
- Laboratory of Bioinformatics, Department of Statistics, University of Rajshahi, Rajshahi, Bangladesh. 5Japan Society for the Promotion of Science, 5-3-1 Kojimachi, Chiyoda-ku, Tokyo 102-0083. Japan
| | - Hiroyuki Kurata
- Department of Bioscience and Bioinformatics, Kyushu Institute of Technology, 680-4 Kawazu, Iizuka, Fukuoka 820-8502. Japan
| | - Md Mehedi Hasan
- Department of Bioscience and Bioinformatics, Kyushu Institute of Technology, 680-4 Kawazu, Iizuka, Fukuoka 820-8502. Japan
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7
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Perdiguero P, Rodrigues AS, Chaves I, Costa B, Alves A, de María N, Vélez MD, Díaz-Sala C, Cervera MT, Miguel CM. Comprehensive analysis of the isomiRome in the vegetative organs of the conifer Pinus pinaster under contrasting water availability. PLANT, CELL & ENVIRONMENT 2021; 44:706-728. [PMID: 33314160 DOI: 10.1111/pce.13976] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/03/2020] [Accepted: 11/30/2020] [Indexed: 06/12/2023]
Abstract
An increasing number of microRNAs (miRNAs) and miRNA-related sequences produced during miRNA biogenesis, comprising the isomiRome, have been recently highlighted in different species as critical mediators of environmental stress responses. Conifers have some of the largest known genomes but an extensive characterization of the isomiRome from any conifer species has been lacking. We provide here a comprehensive overview of the Pinus pinaster isomiRome expressed in roots, stem and needles under well-watered and drought conditions. From the 13,441 unique small RNA sequences identified, 2,980 were annotated as canonical miRNAs or miRNA* and the remaining were classified as isomiRNA or miRNA-like sequences. A survey of their expression patterns highlighted roots as the most responsive organ under drought, where specific sequences of which a 24-nt novel miRNA stood out, were strongly down-regulated. Given the putative roles of the miRNA-targeted transcripts validated specifically in root tissues, some of the miRNAs, conserved and novel, are shortlisted as potential regulators of drought response. These results provide a valuable resource for comparative studies between gymnosperms and angiosperms. Furthermore, it evidences high transferability of the isomiRome between pine species being a useful basis for further molecular regulation and physiological studies, and especially those focused on adaptation to drought conditions.
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Affiliation(s)
- Pedro Perdiguero
- iBET, Instituto de Biologia Experimental e Tecnológica, Oeiras, Portugal
- Centro de Investigación en Sanidad Animal (CISA-INIA), Madrid, Spain
| | - Andreia Santos Rodrigues
- iBET, Instituto de Biologia Experimental e Tecnológica, Oeiras, Portugal
- ITQB NOVA, Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Oeiras, Portugal
| | - Inês Chaves
- iBET, Instituto de Biologia Experimental e Tecnológica, Oeiras, Portugal
- ITQB NOVA, Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Oeiras, Portugal
| | - Bruno Costa
- iBET, Instituto de Biologia Experimental e Tecnológica, Oeiras, Portugal
- BioISI-Biosystems & Integrative Sciences Institute, Faculdade de Ciências, Universidade de Lisboa, Lisbon, Portugal
| | - Ana Alves
- BioISI-Biosystems & Integrative Sciences Institute, Faculdade de Ciências, Universidade de Lisboa, Lisbon, Portugal
| | - Nuria de María
- Departamento de Ecología y Genética Forestal, INIA-CIFOR, Madrid, Spain
- Unidad Mixta de Genómica y Ecofisiología Forestal, INIA/UPM, Madrid, Spain
| | - María Dolores Vélez
- Departamento de Ecología y Genética Forestal, INIA-CIFOR, Madrid, Spain
- Unidad Mixta de Genómica y Ecofisiología Forestal, INIA/UPM, Madrid, Spain
| | - Carmen Díaz-Sala
- Departamento de Ciencias de la Vida, Universidad de Alcalá, Madrid, Spain
| | - María Teresa Cervera
- Departamento de Ecología y Genética Forestal, INIA-CIFOR, Madrid, Spain
- Unidad Mixta de Genómica y Ecofisiología Forestal, INIA/UPM, Madrid, Spain
| | - Célia Maria Miguel
- iBET, Instituto de Biologia Experimental e Tecnológica, Oeiras, Portugal
- BioISI-Biosystems & Integrative Sciences Institute, Faculdade de Ciências, Universidade de Lisboa, Lisbon, Portugal
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8
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Heydarzadeh S, Ranjbar M, Karimi F, Seif F, Alivand MR. Overview of host miRNA properties and their association with epigenetics, long non-coding RNAs, and Xeno-infectious factors. Cell Biosci 2021; 11:43. [PMID: 33632341 PMCID: PMC7905430 DOI: 10.1186/s13578-021-00552-1] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2020] [Accepted: 02/06/2021] [Indexed: 12/19/2022] Open
Abstract
MicroRNA-derived structures play impressive roles in various biological processes. So dysregulation of miRNAs can lead to different human diseases. Recent studies have extended our comprehension of the control of miRNA function and features. Here, we overview some remarkable miRNA properties that have potential implications for the miRNA functions, including different variants of a miRNA called isomiRs, miRNA arm selection/arm switching, and the effect of these factors on miRNA target selection. Besides, we review some aspects of miRNA interactions such as the interaction between epigenetics and miRNA (different miRNAs and their related processing enzymes are epigenetically regulated by multiple DNA methylation enzymes. moreover, DNA methylation could be controlled by diverse mechanisms related to miRNAs), direct and indirect crosstalk between miRNA and lnc (Long Non-Coding) RNAs as a further approach to conduct intercellular regulation called "competing endogenous RNA" (ceRNA) that is involved in the pathogenesis of different diseases, and the interaction of miRNA activities and some Xeno-infectious (virus/bacteria/parasite) factors, which result in modulation of the pathogenesis of infections. This review provides some related studies to a better understanding of miRNA involvement mechanisms and overcoming the complexity of related diseases that may be applicable and useful to prognostic, diagnostic, therapeutic purposes and personalized medicine in the future.
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Affiliation(s)
- Samaneh Heydarzadeh
- Department of Medical Genetics, Faculty of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Maryam Ranjbar
- Immunology Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Farokh Karimi
- Department of Biotechnology, Faculty of Science, University of Maragheh, Maragheh, Iran
| | - Farhad Seif
- Department of Immunology and Allergy, Academic Center for Education, Culture, and Research (ACECR), Tehran, Iran
- Neuroscience Research Center, Iran University of Medical Sciences, Tehran, Iran
| | - Mohammad Reza Alivand
- Department of Medical Genetics, Faculty of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran.
- Immunology Research Center, Tabriz University of Medical Sciences, Tabriz, Iran.
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9
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Vasconcelos AM, Carmo MB, Ferreira B, Viegas I, Gama-Carvalho M, Ferreira A, Amaral AJ. IsomiR_Window: a system for analyzing small-RNA-seq data in an integrative and user-friendly manner. BMC Bioinformatics 2021; 22:37. [PMID: 33522913 PMCID: PMC7852101 DOI: 10.1186/s12859-021-03955-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2020] [Accepted: 01/01/2021] [Indexed: 12/30/2022] Open
Abstract
BACKGROUND IsomiRs are miRNA variants that vary in length and/or sequence when compared to their canonical forms. These variants display differences in length and/or sequence, including additions or deletions of one or more nucleotides (nts) at the 5' and/or 3' end, internal editings or untemplated 3' end additions. Most available tools for small RNA-seq data analysis do not allow the identification of isomiRs and often require advanced knowledge of bioinformatics. To overcome this, we have developed IsomiR Window, a platform that supports the systematic identification, quantification and functional exploration of isomiR expression in small RNA-seq datasets, accessible to users with no computational skills. METHODS IsomiR Window enables the discovery of isomiRs and identification of all annotated non-coding RNAs in RNA-seq datasets from animals and plants. It comprises two main components: the IsomiR Window pipeline for data processing; and the IsomiR Window Browser interface. It integrates over ten third-party softwares for the analysis of small-RNA-seq data and holds a new algorithm that allows the detection of all possible types of isomiRs. These include 3' and 5'end isomiRs, 3' end tailings, isomiRs with single nucleotide polymorphisms (SNPs) or potential RNA editings, as well as all possible fuzzy combinations. IsomiR Window includes all required databases for analysis and annotation, and is freely distributed as a Linux virtual machine, including all required software. RESULTS IsomiR Window processes several datasets in an automated manner, without restrictions of input file size. It generates high quality interactive figures and tables which can be exported into different formats. The performance of isomiR detection and quantification was assessed using simulated small-RNA-seq data. For correctly mapped reads, it identified different types of isomiRs with high confidence and 100% accuracy. The analysis of a small RNA-seq data from Basal Cell Carcinomas (BCCs) using isomiR Window confirmed that miR-183-5p is up-regulated in Nodular BCCs, but revealed that this effect was predominantly due to a novel 5'end variant. This variant displays a different seed region motif and 1756 isoform-exclusive mRNA targets that are significantly associated with disease pathways, underscoring the biological relevance of isomiR-focused analysis. IsomiR Window is available at https://isomir.fc.ul.pt/ .
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Affiliation(s)
- Ana M Vasconcelos
- Lasige - Faculdade de Ciências, Universidade de Lisboa, Lisbon, Portugal
| | | | - Beatriz Ferreira
- BioISI - Biosystems & Integrative Sciences Institute, University of Lisboa, Faculty of Sciences, Lisbon, Portugal
| | - Inês Viegas
- BioISI - Biosystems & Integrative Sciences Institute, University of Lisboa, Faculty of Sciences, Lisbon, Portugal
| | - Margarida Gama-Carvalho
- BioISI - Biosystems & Integrative Sciences Institute, University of Lisboa, Faculty of Sciences, Lisbon, Portugal
| | - António Ferreira
- Lasige - Faculdade de Ciências, Universidade de Lisboa, Lisbon, Portugal
| | - Andreia J Amaral
- CIISA - Centro de Investigação Interdisciplinar Em Sanidade Animal, Faculdade de Medicina Veterinária, Universidade de Lisboa, Lisbon, Portugal.
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Loher P, Karathanasis N, Londin E, Bray P, Pliatsika V, Telonis AG, Rigoutsos I. IsoMiRmap-fast, deterministic, and exhaustive mining of isomiRs from short RNA-seq datasets. Bioinformatics 2021; 37:1828-1838. [PMID: 33471076 PMCID: PMC8317110 DOI: 10.1093/bioinformatics/btab016] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2020] [Revised: 11/30/2020] [Accepted: 01/10/2021] [Indexed: 01/21/2023] Open
Abstract
MOTIVATION MicroRNA (miRNA) precursor arms give rise to multiple isoforms simultaneously called "isomiRs." IsomiRs from the same arm typically differ by a few nucleotides at either their 5´ or 3´ termini, or both. In humans, the identities and abundances of isomiRs depend on a person's sex, population of origin, race/ethnicity, and on tissue type, tissue state, and disease type/subtype. Moreover, nearly half of the time the most abundant isomiR differs from the miRNA sequence found in public databases. Accurate mining of isomiRs from deep sequencing data is thus important. RESULTS We developed isoMiRmap, a fast, standalone, user-friendly mining tool that identifies and quantifies all isomiRs by directly processing short RNA-seq datasets. IsoMiRmap is a portable "plug-and-play" tool, requires minimal setup, has modest computing and storage requirements, and can process an RNA-seq dataset with 50 million reads in just a few minutes on an average laptop. IsoMiRmap deterministically and exhaustively reports all isomiRs in a given deep sequencing dataset and quantifies them accurately (no double-counting). IsoMiRmap comprehensively reports all miRNA precursor locations from which an isomiR may be transcribed, tags as 'ambiguous' isomiRs whose sequences exist both inside and outside of the space of known miRNA sequences and reports the public identifiers of common single-nucleotide polymorphisms and documented somatic mutations that may be present in an isomiR. IsoMiRmap also identifies isomiRs with 3´ non-templated post-transcriptional additions. Compared to similar tools, isoMiRmap is the fastest, reports more bona fide isomiRs, and provides the most comprehensive information related to an isomiR's transcriptional origin. AVAILABILITY The codes for isoMiRmap are freely available at https://cm.jefferson.edu/isoMiRmap/ and https://github.com/TJU-CMC-Org/isoMiRmap/. IsomiR profiles for the datasets of the 1000 Genomes Project, spanning five population groups, and The Cancer Genome Atlas (TCGA), spanning 33 cancer studies, are also available at https://cm.jefferson.edu/isoMiRmap/. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Phillipe Loher
- Computational Medicine Center, Sidney Kimmel Medical College, Thomas Jefferson University, 1020 Locust Street, Philadelphia, PA, 19107, USA
| | - Nestoras Karathanasis
- Computational Medicine Center, Sidney Kimmel Medical College, Thomas Jefferson University, 1020 Locust Street, Philadelphia, PA, 19107, USA
| | - Eric Londin
- Computational Medicine Center, Sidney Kimmel Medical College, Thomas Jefferson University, 1020 Locust Street, Philadelphia, PA, 19107, USA
| | - Paul Bray
- Department of Medicine, University of Utah, Salt Lake City, Utah, 84112
| | - Venetia Pliatsika
- Computational Medicine Center, Sidney Kimmel Medical College, Thomas Jefferson University, 1020 Locust Street, Philadelphia, PA, 19107, USA
| | - Aristeidis G Telonis
- Computational Medicine Center, Sidney Kimmel Medical College, Thomas Jefferson University, 1020 Locust Street, Philadelphia, PA, 19107, USA
| | - Isidore Rigoutsos
- Computational Medicine Center, Sidney Kimmel Medical College, Thomas Jefferson University, 1020 Locust Street, Philadelphia, PA, 19107, USA
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11
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MicroRNAs Regulating Autophagy in Neurodegeneration. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2021; 1208:191-264. [PMID: 34260028 DOI: 10.1007/978-981-16-2830-6_11] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Social and economic impacts of neurodegenerative diseases (NDs) become more prominent in our constantly aging population. Currently, due to the lack of knowledge about the aetiology of most NDs, only symptomatic treatment is available for patients. Hence, researchers and clinicians are in need of solid studies on pathological mechanisms of NDs. Autophagy promotes degradation of pathogenic proteins in NDs, while microRNAs post-transcriptionally regulate multiple signalling networks including autophagy. This chapter will critically discuss current research advancements in the area of microRNAs regulating autophagy in NDs. Moreover, we will introduce basic strategies and techniques used in microRNA research. Delineation of the mechanisms contributing to NDs will result in development of better approaches for their early diagnosis and effective treatment.
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12
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Vivek AT, Kumar S. Computational methods for annotation of plant regulatory non-coding RNAs using RNA-seq. Brief Bioinform 2020; 22:6041165. [PMID: 33333550 DOI: 10.1093/bib/bbaa322] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2020] [Revised: 10/19/2020] [Accepted: 10/20/2020] [Indexed: 12/19/2022] Open
Abstract
Plant transcriptome encompasses numerous endogenous, regulatory non-coding RNAs (ncRNAs) that play a major biological role in regulating key physiological mechanisms. While studies have shown that ncRNAs are extremely diverse and ubiquitous, the functions of the vast majority of ncRNAs are still unknown. With ever-increasing ncRNAs under study, it is essential to identify, categorize and annotate these ncRNAs on a genome-wide scale. The use of high-throughput RNA sequencing (RNA-seq) technologies provides a broader picture of the non-coding component of transcriptome, enabling the comprehensive identification and annotation of all major ncRNAs across samples. However, the detection of known and emerging class of ncRNAs from RNA-seq data demands complex computational methods owing to their unique as well as similar characteristics. Here, we discuss major plant endogenous, regulatory ncRNAs in an RNA sample followed by computational strategies applied to discover each class of ncRNAs using RNA-seq. We also provide a collection of relevant software packages and databases to present a comprehensive bioinformatics toolbox for plant ncRNA researchers. We assume that the discussions in this review will provide a rationale for the discovery of all major categories of plant ncRNAs.
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Affiliation(s)
- A T Vivek
- National Institute of Plant Genome Research in New Delhi, India
| | - Shailesh Kumar
- National Institute of Plant Genome Research in New Delhi
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13
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Schmartz GP, Kern F, Fehlmann T, Wagner V, Fromm B, Keller A. Encyclopedia of tools for the analysis of miRNA isoforms. Brief Bioinform 2020; 22:6032629. [PMID: 33313643 DOI: 10.1093/bib/bbaa346] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2020] [Revised: 10/15/2020] [Accepted: 10/29/2020] [Indexed: 12/14/2022] Open
Abstract
RNA sequencing data sets rapidly increase in quantity. For microRNAs (miRNAs), frequently dozens to hundreds of billion reads are generated per study. The quantification of annotated miRNAs and the prediction of new miRNAs are leading computational tasks. Now, the increased depth of coverage allows to gain deeper insights into the variability of miRNAs. The analysis of isoforms of miRNAs (isomiRs) is a trending topic, and a range of computational tools for the analysis of isomiRs has been developed. We provide an overview on 27 available computational solutions for the analysis of isomiRs. These include both stand-alone programs (17 tools) and web-based solutions (10 tools) and span a publication time range from 2010 to 2020. Seven of the tools were published in 2019 and 2020, confirming the rising importance of the topic. While most of the analyzed tools work for a broad range of organisms or are completely independent of a reference organism, several tools have been tailored for the analysis of human miRNA data or for plants. While 14 of the tools are general analysis tools of miRNAs, and isomiR analysis is one of their features, the remaining 13 tools have specifically been developed for isomiR analysis. A direct comparison on 20 deep sequencing data sets for selected tools provides insights into the heterogeneity of results. With our work, we provide users a comprehensive overview on the landscape of isomiR analysis tools and in that support the selection of the most appropriate tool for their respective research task.
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Affiliation(s)
| | | | | | | | - Bastian Fromm
- Science for Life Laboratory, Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, Stockholm, Sweden
| | - Andreas Keller
- Saarland Center for Bioinformatics and Chair for Clinical Bioinformatics, Saarland University Building E2.1, 66123 Saarbrücken, Germany
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14
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Fard EM, Moradi S, Salekdeh NN, Bakhshi B, Ghaffari MR, Zeinalabedini M, Salekdeh GH. Plant isomiRs: origins, biogenesis, and biological functions. Genomics 2020; 112:3382-3395. [DOI: 10.1016/j.ygeno.2020.06.019] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2020] [Revised: 05/22/2020] [Accepted: 06/10/2020] [Indexed: 12/14/2022]
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15
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Morgado L, Johannes F. Computational tools for plant small RNA detection and categorization. Brief Bioinform 2020; 20:1181-1192. [PMID: 29059285 PMCID: PMC6781577 DOI: 10.1093/bib/bbx136] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2017] [Revised: 09/09/2017] [Indexed: 01/06/2023] Open
Abstract
Small RNAs (sRNAs) are important short-length molecules with regulatory functions essential for plant development and plasticity. High-throughput sequencing of total sRNA populations has revealed that the largest share of sRNA remains uncategorized. To better understand the role of sRNA-mediated cellular regulation, it is necessary to create accurate and comprehensive catalogues of sRNA and their sequence features, a task that currently relies on nontrivial bioinformatic approaches. Although a large number of computational tools have been developed to predict features of sRNA sequences, these tools are mostly dedicated to microRNAs and none integrates the functionalities necessary to describe units from all sRNA pathways thus far discovered in plants. Here, we review the different classes of sRNA found in plants and describe available bioinformatics tools that can help in their detection and categorization.
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Affiliation(s)
- Lionel Morgado
- Corresponding author: Lionel Morgado, Groningen Bioinformatics Centre, University of Groningen, Nijenborgh 25 7, 9747 AG Groningen, The Netherlands. Tel.: +31 685 585 827; E-mail:
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16
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Model-Based Integration Analysis Revealed Presence of Novel Prognostic miRNA Targets and Important Cancer Driver Genes in Triple-Negative Breast Cancers. Cancers (Basel) 2020; 12:cancers12030632. [PMID: 32182819 PMCID: PMC7139587 DOI: 10.3390/cancers12030632] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2020] [Revised: 02/21/2020] [Accepted: 03/05/2020] [Indexed: 12/24/2022] Open
Abstract
Background: miRNAs (microRNAs) play a key role in triple-negative breast cancer (TNBC) progression, and its heterogeneity at the expression, pathological and clinical levels. Stratification of breast cancer subtypes on the basis of genomics and transcriptomics profiling, along with the known biomarkers’ receptor status, has revealed the existence of subgroups known to have diverse clinical outcomes. Recently, several studies have analysed expression profiles of matched mRNA and miRNA to investigate the underlying heterogeneity of TNBC and the potential role of miRNA as a biomarker within cancers. However, the miRNA-mRNA regulatory network within TNBC has yet to be understood. Results and Findings: We performed model-based integrated analysis of miRNA and mRNA expression profiles on breast cancer, primarily focusing on triple-negative, to identify subtype-specific signatures involved in oncogenic pathways and their potential role in patient survival outcome. Using univariate and multivariate Cox analysis, we identified 25 unique miRNAs associated with the prognosis of overall survival (OS) and distant metastases-free survival (DMFS) with “risky” and “protective” outcomes. The association of these prognostic miRNAs with subtype-specific mRNA genes was established to investigate their potential regulatory role in the canonical pathways using anti-correlation analysis. The analysis showed that miRNAs contribute to the positive regulation of known breast cancer driver genes as well as the activation of respective oncogenic pathway during disease formation. Further analysis on the “risk associated” miRNAs group revealed significant regulation of critical pathways such as cell growth, voltage-gated ion channel function, ion transport and cell-to-cell signalling. Conclusion: The study findings provide new insights into the potential role of miRNAs in TNBC disease progression through the activation of key oncogenic pathways. The results showed previously unreported subtype-specific prognostic miRNAs associated with clinical outcome that may be used for further clinical evaluation.
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17
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Correia de Sousa M, Gjorgjieva M, Dolicka D, Sobolewski C, Foti M. Deciphering miRNAs' Action through miRNA Editing. Int J Mol Sci 2019; 20:E6249. [PMID: 31835747 PMCID: PMC6941098 DOI: 10.3390/ijms20246249] [Citation(s) in RCA: 514] [Impact Index Per Article: 102.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2019] [Revised: 12/04/2019] [Accepted: 12/06/2019] [Indexed: 12/13/2022] Open
Abstract
MicroRNAs (miRNAs) are small non-coding RNAs with the capability of modulating gene expression at the post-transcriptional level either by inhibiting messenger RNA (mRNA) translation or by promoting mRNA degradation. The outcome of a myriad of physiological processes and pathologies, including cancer, cardiovascular and metabolic diseases, relies highly on miRNAs. However, deciphering the precise roles of specific miRNAs in these pathophysiological contexts is challenging due to the high levels of complexity of their actions. Indeed, regulation of mRNA expression by miRNAs is frequently cell/organ specific; highly dependent on the stress and metabolic status of the organism; and often poorly correlated with miRNA expression levels. Such biological features of miRNAs suggest that various regulatory mechanisms control not only their expression, but also their activity and/or bioavailability. Several mechanisms have been described to modulate miRNA action, including genetic polymorphisms, methylation of miRNA promoters, asymmetric miRNA strand selection, interactions with RNA-binding proteins (RBPs) or other coding/non-coding RNAs. Moreover, nucleotide modifications (A-to-I or C-to-U) within the miRNA sequences at different stages of their maturation are also critical for their functionality. This regulatory mechanism called "RNA editing" involves specific enzymes of the adenosine/cytidine deaminase family, which trigger single nucleotide changes in primary miRNAs. These nucleotide modifications greatly influence a miRNA's stability, maturation and activity by changing its specificity towards target mRNAs. Understanding how editing events impact miRNA's ability to regulate stress responses in cells and organs, or the development of specific pathologies, e.g., metabolic diseases or cancer, should not only deepen our knowledge of molecular mechanisms underlying complex diseases, but can also facilitate the design of new therapeutic approaches based on miRNA targeting. Herein, we will discuss the current knowledge on miRNA editing and how this mechanism regulates miRNA biogenesis and activity.
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Affiliation(s)
| | | | | | | | - Michelangelo Foti
- Department of Cell Physiology and Metabolism, Faculty of Medicine, University of Geneva, CH-1211 Geneva, Switzerland; (M.C.d.S.); (M.G.); (D.D.); (C.S.)
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18
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Ma M, Yin Z, Zhong H, Liang T, Guo L. Analysis of the expression, function, and evolution of miR-27 isoforms and their responses in metabolic processes. Genomics 2019; 111:1249-1257. [DOI: 10.1016/j.ygeno.2018.08.004] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2018] [Revised: 07/31/2018] [Accepted: 08/08/2018] [Indexed: 12/13/2022]
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19
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Chen L, Heikkinen L, Wang C, Yang Y, Sun H, Wong G. Trends in the development of miRNA bioinformatics tools. Brief Bioinform 2019; 20:1836-1852. [PMID: 29982332 PMCID: PMC7414524 DOI: 10.1093/bib/bby054] [Citation(s) in RCA: 344] [Impact Index Per Article: 68.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2018] [Revised: 05/18/2018] [Indexed: 12/13/2022] Open
Abstract
MicroRNAs (miRNAs) are small noncoding RNAs that regulate gene expression via recognition of cognate sequences and interference of transcriptional, translational or epigenetic processes. Bioinformatics tools developed for miRNA study include those for miRNA prediction and discovery, structure, analysis and target prediction. We manually curated 95 review papers and ∼1000 miRNA bioinformatics tools published since 2003. We classified and ranked them based on citation number or PageRank score, and then performed network analysis and text mining (TM) to study the miRNA tools development trends. Five key trends were observed: (1) miRNA identification and target prediction have been hot spots in the past decade; (2) manual curation and TM are the main methods for collecting miRNA knowledge from literature; (3) most early tools are well maintained and widely used; (4) classic machine learning methods retain their utility; however, novel ones have begun to emerge; (5) disease-associated miRNA tools are emerging. Our analysis yields significant insight into the past development and future directions of miRNA tools.
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Affiliation(s)
- Liang Chen
- Faculty of Health Sciences, University of Macau, Taipa, Macau S.A.R, China
| | - Liisa Heikkinen
- Faculty of Health Sciences, University of Macau, Taipa, Macau S.A.R, China
| | - Changliang Wang
- Faculty of Health Sciences, University of Macau, Taipa, Macau S.A.R, China
| | - Yang Yang
- Faculty of Health Sciences, University of Macau, Taipa, Macau S.A.R, China
| | - Huiyan Sun
- Key Laboratory of Symbolic Computation and Knowledge Engineering of the Ministry of Education, College of Computer Science and Technology, Jilin University, Changchun, China
| | - Garry Wong
- Faculty of Health Sciences, University of Macau, Taipa, Macau S.A.R, China
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20
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An Approach to Identify Individual Functional Single Nucleotide Polymorphisms and Isoform MicroRNAs. BIOMED RESEARCH INTERNATIONAL 2019; 2019:6193673. [PMID: 31467902 PMCID: PMC6699389 DOI: 10.1155/2019/6193673] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/07/2019] [Revised: 05/28/2019] [Accepted: 06/24/2019] [Indexed: 01/08/2023]
Abstract
MicroRNAs (miRNAs) and single nucleotide polymorphisms (SNPs) play important roles in disease risk and development, especially cancer. Importantly, when SNPs are located in pre-miRNAs, they affect their splicing mechanism and change the function of miRNAs. To improve disease risk assessment, we propose an approach and developed a software tool, IsomiR_Find, to identify disease/phenotype-related SNPs and isomiRs in individuals. Our approach is based on the individual's samples, with SNP information extracted from the 1000 Genomes Project. SNPs were mapped to pre-miRNAs based on whole-genome coordinates and then SNP-pre-miRNA sequences were constructed. Moreover, we developed matpred2, a software tool to identify the four splicing sites of mature miRNAs. Using matpred2, we identified isomiRs and then verified them by searching within individual miRNA sequencing data. Our approach yielded biomarkers for biological experiments, mined functions of miRNAs and SNPs, improved disease risk assessment, and provided a way to achieve individualized precision medicine.
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21
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Computational Resources for Prediction and Analysis of Functional miRNA and Their Targetome. Methods Mol Biol 2019; 1912:215-250. [PMID: 30635896 DOI: 10.1007/978-1-4939-8982-9_9] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
microRNAs are evolutionarily conserved, endogenously produced, noncoding RNAs (ncRNAs) of approximately 19-24 nucleotides (nts) in length known to exhibit gene silencing of complementary target sequence. Their deregulated expression is reported in various disease conditions and thus has therapeutic implications. In the last decade, various computational resources are published in this field. In this chapter, we have reviewed bioinformatics resources, i.e., miRNA-centered databases, algorithms, and tools to predict miRNA targets. First section has enlisted more than 75 databases, which mainly covers information regarding miRNA registries, targets, disease associations, differential expression, interactions with other noncoding RNAs, and all-in-one resources. In the algorithms section, we have compiled about 140 algorithms from eight subcategories, viz. for the prediction of precursor (pre-) and mature miRNAs. These algorithms are developed on various sequence, structure, and thermodynamic based features incorporated into different machine learning techniques (MLTs). In addition, computational identification of miRNAs from high-throughput next generation sequencing (NGS) data and their variants, viz. isomiRs, differential expression, miR-SNPs, and functional annotation, are discussed. Prediction and analysis of miRNAs and their associated targets are also evaluated under miR-targets section providing knowledge regarding novel miRNA targets and complex host-pathogen interactions. In conclusion, we have provided comprehensive review of in silico resources published in miRNA research to help scientific community be updated and choose the appropriate tool according to their needs.
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22
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Yang K, Wen X, Mudunuri S, Varma GPS, Sablok G. Diff isomiRs: Large-scale detection of differential isomiRs for understanding non-coding regulated stress omics in plants. Sci Rep 2019; 9:1406. [PMID: 30723229 PMCID: PMC6363768 DOI: 10.1038/s41598-019-38932-w] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2018] [Accepted: 01/14/2019] [Indexed: 11/11/2022] Open
Abstract
Plants have an amazing ability to cope with wide variety of stresses by regulating the expression of genes and thus by altering the physiological status. In the past few years, canonical microRNA variants (isomiRs) have been shown to play pivotal roles by acting as regulators of the transcriptional machinery. In the present research, we present Diff isomiRs, a web-based exploratory repository of differential isomiRs across 16 sequenced plant species representing a total of 433 datasets across 21 different stresses and 158 experimental states. Diff isomiRs provides the high-throughput detection of differential isomiRs using mapping-based and model-based differential analysis revealing a total of 16,157 and 2,028 differential isomiRs, respectively. Easy-to-use and web-based exploration of differential isomiRs provides several features such as browsing of the differential isomiRs according to stress or species, as well as association of the differential isomiRs to targets and plant endogenous target mimics (PeTMs). Diff isomiRs also provides the relationship between the canonical miRNAs, isomiRs and the miRNA-target interactions. This is the first web-based large-scale repository for browsing differential isomiRs and will facilitate better understanding of the regulatory role of the isomiRs with respect to the canonical microRNAs. Diff isomiRs can be accessed at: www.mcr.org.in/diffisomirs.
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Affiliation(s)
- Kun Yang
- Key Laboratory of Plant Resources Conservation and Germplasm Innovation in Mountainous Region (Guizhou University), Ministry of Education, Institute of Agro-bioengineering/College of Life Sciences, Guizhou University, Guiyang, 550025, Guizhou Province, P. R. China
| | - Xiaopeng Wen
- Key Laboratory of Plant Resources Conservation and Germplasm Innovation in Mountainous Region (Guizhou University), Ministry of Education, Institute of Agro-bioengineering/College of Life Sciences, Guizhou University, Guiyang, 550025, Guizhou Province, P. R. China.
| | - Suresh Mudunuri
- Centre for Bioinformatics Research, SRKR Engineering College, Chinna Amiram, Bhimavaram, West Godavari District, Andhra Pradesh, 534204, India
| | - G P Saradhi Varma
- Centre for Bioinformatics Research, SRKR Engineering College, Chinna Amiram, Bhimavaram, West Godavari District, Andhra Pradesh, 534204, India
| | - Gaurav Sablok
- Finnish Museum of Natural History, Helsinki, Finland. .,Organismal and Evolutionary Biology (OEB) Research Programme, Department of Biological and Environmental Sciences, University of Helsinki, Helsinki, Finland.
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23
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Devi K, Dey KK, Singh S, Mishra SK, Modi MK, Sen P. Identification and validation of plant miRNA from NGS data—an experimental approach. Brief Funct Genomics 2018; 18:13-22. [DOI: 10.1093/bfgp/ely034] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2017] [Revised: 09/17/2018] [Accepted: 10/02/2018] [Indexed: 12/18/2022] Open
Affiliation(s)
- Kamalakshi Devi
- Department of Agricultural Biotechnology, Assam Agricultural University, Jorhat, India
| | - Kuntal Kumar Dey
- Distributed Information Centre, Department of Agricultural Biotechnology, Assam Agricultural University, Jorhat, India
| | - Sanjay Singh
- Department of Agricultural Biotechnology, Assam Agricultural University, Jorhat, India
| | | | - Mahendra Kumar Modi
- Department of Agricultural Biotechnology, Assam Agricultural University, Jorhat, India
- Distributed Information Centre, Department of Agricultural Biotechnology, Assam Agricultural University, Jorhat, India
| | - Priyabrata Sen
- Department of Agricultural Biotechnology, Assam Agricultural University, Jorhat, India
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24
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Menezes MR, Balzeau J, Hagan JP. 3' RNA Uridylation in Epitranscriptomics, Gene Regulation, and Disease. Front Mol Biosci 2018; 5:61. [PMID: 30057901 PMCID: PMC6053540 DOI: 10.3389/fmolb.2018.00061] [Citation(s) in RCA: 43] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2018] [Accepted: 06/14/2018] [Indexed: 12/31/2022] Open
Abstract
Emerging evidence implicates a wide range of post-transcriptional RNA modifications that play crucial roles in fundamental biological processes including regulating gene expression. Collectively, they are known as epitranscriptomics. Recent studies implicate 3' RNA uridylation, the non-templated addition of uridine(s) to the terminal end of RNA, as a key player in epitranscriptomics. In this review, we describe the functional roles and significance of 3' terminal RNA uridylation that has diverse functions in regulating both mRNAs and non-coding RNAs. In mammals, three Terminal Uridylyl Transferases (TUTases) are primarily responsible for 3' RNA uridylation. These enzymes are also referred to as polyU polymerases. TUTase 1 (TUT1) is implicated in U6 snRNA maturation via uridylation. The TUTases TUT4 and/or TUT7 are the predominant mediators of all other cellular uridylation. Terminal uridylation promotes turnover for many polyadenylated mRNAs, replication-dependent histone mRNAs that lack polyA-tails, and aberrant structured noncoding RNAs. In addition, uridylation regulates biogenesis of a subset of microRNAs and generates isomiRs, sequent variant microRNAs that have altered function in specific cases. For example, the RNA binding protein and proto-oncogene LIN28A and TUT4 work together to polyuridylate pre-let-7, thereby blocking biogenesis and function of the tumor suppressor let-7 microRNA family. In contrast, monouridylation of Group II pre-miRNAs creates an optimal 3' overhang that promotes recognition and subsequent cleavage by the Dicer-TRBP complex that then yields the mature microRNA. Also, uridylation may play a role in non-canonical microRNA biogenesis. The overall significance of 3' RNA uridylation is discussed with an emphasis on mammalian development, gene regulation, and disease, including cancer and Perlman syndrome. We also introduce recent changes to the HUGO-approved gene names for multiple terminal nucleotidyl transferases that affects in part TUTase nomenclature (TUT1/TENT1, TENT2/PAPD4/GLD2, TUT4/ZCCHC11/TENT3A, TUT7/ZCCHC6/TENT3B, TENT4A/PAPD7, TENT4B/PAPD5, TENT5A/FAM46A, TENT5B/FAM46B, TENT5C/FAM46C, TENT5D/FAM46D, MTPAP/TENT6/PAPD1).
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Affiliation(s)
- Miriam R Menezes
- Department of Neurosurgery, University of Texas Health Science Center at Houston, Houston, TX, United States
| | - Julien Balzeau
- Department of Neurosurgery, University of Texas Health Science Center at Houston, Houston, TX, United States
| | - John P Hagan
- Department of Neurosurgery, University of Texas Health Science Center at Houston, Houston, TX, United States
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25
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Tripathi A, Chacon O, Singla-Pareek SL, Sopory SK, Sanan-Mishra N. Mapping the microRNA Expression Profiles in Glyoxalase Over-expressing Salinity Tolerant Rice. Curr Genomics 2018; 19:21-35. [PMID: 29491730 PMCID: PMC5817874 DOI: 10.2174/1389202918666170228134530] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2016] [Revised: 09/08/2016] [Accepted: 09/20/2016] [Indexed: 12/01/2022] Open
Abstract
In the recent years, glyoxalase pathway has been an active area of research in both human and plants. This pathway is reported to confer stress tolerance in plants, by modulating the glutathione homeostasis to achieve detoxification of a potent cytotoxic and mutagenic compound, methylglyoxal. The microRNAs (miRNAs) are also reported to play significant role in stress tolerance for plants. However, the cross-talk of miRNAs with the metabolism regulated by glyoxalase in the salinity-tolerance is unexplored. We therefore investigated whether expression profiles of miRNAs are altered in response to glyoxalase overexpression, and if any of these are also responsible for modulating the stress responses of plants. In this study, the Next Generation Sequencing (NGS) was employed to profile miRNA expression levels from glyoxalase overexpressing transgenic lines. The associated targets of differentially expressed miRNAs were predicted and their functional annotation was carried out using Gene Ontology (GO) and KEGG Orthology (KO), which showed their involvement in several crucial biological pathways. The analysis of NGS datasets also identified other isoforms or isomiRs of selected miRNAs, which may have an active role in developing tolerance against salt stress. Different aspects of miRNA modifications were also studied in glyoxalase overexpressing lines.
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Affiliation(s)
- Anita Tripathi
- International Center for Genetic Engineering and Biotechnology, Aruna Asaf Ali Marg, New Delhi, India
| | - Osmani Chacon
- International Center for Genetic Engineering and Biotechnology, Aruna Asaf Ali Marg, New Delhi, India
| | - Sneh Lata Singla-Pareek
- International Center for Genetic Engineering and Biotechnology, Aruna Asaf Ali Marg, New Delhi, India
| | - Sudhir K. Sopory
- International Center for Genetic Engineering and Biotechnology, Aruna Asaf Ali Marg, New Delhi, India
| | - Neeti Sanan-Mishra
- International Center for Genetic Engineering and Biotechnology, Aruna Asaf Ali Marg, New Delhi, India
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26
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Janszky N, Süsal C. Circulating and urinary microRNAs as possible biomarkers in kidney transplantation. Transplant Rev (Orlando) 2017; 32:110-118. [PMID: 29366537 DOI: 10.1016/j.trre.2017.12.001] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2017] [Revised: 12/03/2017] [Accepted: 12/14/2017] [Indexed: 02/07/2023]
Affiliation(s)
- Noémi Janszky
- Transplantation Immunology, Institute of Immunology, University of Heidelberg, Germany.
| | - Caner Süsal
- Transplantation Immunology, Institute of Immunology, University of Heidelberg, Germany
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27
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Amsel D, Vilcinskas A, Billion A. Evaluation of high-throughput isomiR identification tools: illuminating the early isomiRome of Tribolium castaneum. BMC Bioinformatics 2017; 18:359. [PMID: 28774263 PMCID: PMC5543545 DOI: 10.1186/s12859-017-1772-z] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2017] [Accepted: 07/30/2017] [Indexed: 01/01/2023] Open
Abstract
Background MicroRNAs carry out post-transcriptional gene regulation in animals by binding to the 3' untranslated regions of mRNAs, causing their degradation or translational repression. MicroRNAs influence many biological functions, and dysregulation can therefore disrupt development or even cause death. High-throughput sequencing and the mining of animal small RNA data has shown that microRNA genes can yield differentially expressed isoforms, known as isomiRs. Such isoforms are particularly relevant during early development, and the extension or truncation of the 5' end can change the profile of mRNA targets compared to the original mature sequence. We used the publicly available small RNA dataset of the model beetle Tribolium castaneum to create the first comparative isomiRome of early developmental stages in this species. Standard microRNA analysis software does not specifically account for isomiRs. We therefore carried out the first comparative evaluation of the specialized tools isomiRID, isomiR-SEA and miraligner, which can be downloaded for local use and can handle next generation sequencing data. Results We compared the performance of isomiRID, isomiR-SEA and miraligner using simulated Illumina HiSeq2000 and MiSeq data to test the impact of technical errors. We also created artificial microRNA isoforms to determine the effect of biological variants on the performance of each algorithm. We found that isomiRID achieved the best true positive rate among the three algorithms, but only accounted for one mutation at a time. In contrast, miraligner reported all variations simultaneously but with 78% sensitivity, yielding isomiRs with 3' or 5' deletions. Finally, isomiR-SEA achieved a sensitivity of 25–33% when the seed region was mutated or partly deleted, but was the only tool that could accommodate more than one mismatch. Using the best tool, we performed a complete isomiRome analysis of the early developmental stages of T. castaneum. Conclusions Our findings will help researchers to select the most suitable isomiR analysis tools for their experiments. We confirmed the dynamic expression of 3′ non-template isomiRs and expanded the isomiRome by all known isomiR modifications during the early development of T. castaneum. Electronic supplementary material The online version of this article (doi:10.1186/s12859-017-1772-z) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Daniel Amsel
- Fraunhofer Institute for Molecular Biology and Applied Ecology, Department of Bioresources, Winchester Str. 2, 35394, Giessen, Germany.
| | - Andreas Vilcinskas
- Fraunhofer Institute for Molecular Biology and Applied Ecology, Department of Bioresources, Winchester Str. 2, 35394, Giessen, Germany.,Institute for Insect Biotechnology, Heinrich-Buff-Ring 26-32, 35392, Giessen, Germany
| | - André Billion
- Fraunhofer Institute for Molecular Biology and Applied Ecology, Department of Bioresources, Winchester Str. 2, 35394, Giessen, Germany
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28
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Chaves I, Costa BV, Rodrigues AS, Bohn A, Miguel CM. miRPursuit-a pipeline for automated analyses of small RNAs in model and nonmodel plants. FEBS Lett 2017; 591:2261-2268. [PMID: 28686301 DOI: 10.1002/1873-3468.12746] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2017] [Revised: 04/30/2017] [Accepted: 07/03/2017] [Indexed: 11/07/2022]
Abstract
miRPursuit is a pipeline developed for running end-to-end analyses of high-throughput small RNA (sRNA) sequence data in model and nonmodel plants, from raw data to identified and annotated conserved and novel sequences. It consists of a series of UNIX shell scripts, which connect open-source sRNA analysis software. The involved parameters can be combined with convenient workflow management by users without advanced computational skills. miRPursuit presents several advantages when compared to other tools, including the possibility of processing several sRNA libraries in parallel, thus easily allowing a comparison of the differences in sRNA read accumulation among sRNA libraries. We validate miRPursuit by using datasets from a model plant and discuss its performance with the analysis of sRNAs from non-model species.
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Affiliation(s)
- Inês Chaves
- Instituto de Biologia Experimental e Tecnológica (iBET), Oeiras, Portugal.,Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa (ITQB NOVA), Oeiras, Portugal
| | - Bruno Vasques Costa
- Instituto de Biologia Experimental e Tecnológica (iBET), Oeiras, Portugal.,Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa (ITQB NOVA), Oeiras, Portugal
| | - Andreia S Rodrigues
- Instituto de Biologia Experimental e Tecnológica (iBET), Oeiras, Portugal.,Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa (ITQB NOVA), Oeiras, Portugal
| | - Andreas Bohn
- Instituto de Biologia Experimental e Tecnológica (iBET), Oeiras, Portugal.,Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa (ITQB NOVA), Oeiras, Portugal
| | - Célia M Miguel
- Instituto de Biologia Experimental e Tecnológica (iBET), Oeiras, Portugal.,Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa (ITQB NOVA), Oeiras, Portugal.,Biosystems & Integrative Sciences Institute, Faculdade de Ciências, Universidade de Lisboa (FCUL), Lisboa, Portugal
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29
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Yang K, Sablok G, Qiao G, Nie Q, Wen X. isomiR2Function: An Integrated Workflow for Identifying MicroRNA Variants in Plants. FRONTIERS IN PLANT SCIENCE 2017; 8:322. [PMID: 28377776 PMCID: PMC5359237 DOI: 10.3389/fpls.2017.00322] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/08/2016] [Accepted: 02/22/2017] [Indexed: 05/28/2023]
Abstract
In plants, post transcriptional regulation by non-coding RNAs (ncRNAs), in particular miRNAs (19-24 nt) has been involved in modulating the transcriptional landscape in developmental, biotic and abiotic interactions. In past few years, considerable focus has been leveraged on delineating and deciphering the role of miRNAs and their canonical isomiRs in plants. However, proper classification and accurate prediction of plant isomiRs taking into account the relative features by which we define isomiRs, such as templated or non-templated is still lacking. In the present research, we present isomiR2Function, a standalone easily deployable tool that allows for the robust and high-throughput discovery of templated and non-templated isomiRs. Additionally, isomiR2Function allows for identification of differentially expressed isomiRs and in parallel target prediction based on both transcripts or PARE-Seq either using Targetfinder or Cleaveland. isomiR2Function allows for the functional enrichment of the detected targets using TopGO package. Benchmarking of isomiR2Function revealed highly accurate prediction and classification of isomiRs as compared to the previously developed isomiR prediction tools. Additionally, the downstream implementation of additional features allows isomiR2Function to be classified as a single standalone tool for isomiR profiling from discovery to functional roles. All in all, isomiR2Function allows the streamline processing of the miRNA-seq for the identification and characterization of isomiRs with minimal efforts. isomiR2Function can be accessed through: https://github.com/347033139/isomiR2Function.
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Affiliation(s)
- Kun Yang
- Key Laboratory of Plant Resources Conservation and Germplasm Innovation in Mountainous Region – Ministry of Education, Institute of Agro-bioengineering, Guizhou UniversityGuiyang, China
- College of Life Sciences, Guizhou UniversityGuiyang, China
| | - Gaurav Sablok
- Climate Change Cluster (C3), University of Technology SydneySydney, NSW, Australia
| | - Guang Qiao
- Key Laboratory of Plant Resources Conservation and Germplasm Innovation in Mountainous Region – Ministry of Education, Institute of Agro-bioengineering, Guizhou UniversityGuiyang, China
- College of Life Sciences, Guizhou UniversityGuiyang, China
| | - Qiong Nie
- Key Laboratory of Plant Resources Conservation and Germplasm Innovation in Mountainous Region – Ministry of Education, Institute of Agro-bioengineering, Guizhou UniversityGuiyang, China
- College of Life Sciences, Guizhou UniversityGuiyang, China
| | - Xiaopeng Wen
- Key Laboratory of Plant Resources Conservation and Germplasm Innovation in Mountainous Region – Ministry of Education, Institute of Agro-bioengineering, Guizhou UniversityGuiyang, China
- College of Life Sciences, Guizhou UniversityGuiyang, China
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30
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Bousios A, Gaut BS, Darzentas N. Considerations and complications of mapping small RNA high-throughput data to transposable elements. Mob DNA 2017; 8:3. [PMID: 28228849 PMCID: PMC5311732 DOI: 10.1186/s13100-017-0086-z] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2016] [Accepted: 01/31/2017] [Indexed: 12/21/2022] Open
Abstract
BACKGROUND High-throughput sequencing (HTS) has revolutionized the way in which epigenetic research is conducted. When coupled with fully-sequenced genomes, millions of small RNA (sRNA) reads are mapped to regions of interest and the results scrutinized for clues about epigenetic mechanisms. However, this approach requires careful consideration in regards to experimental design, especially when one investigates repetitive parts of genomes such as transposable elements (TEs), or when such genomes are large, as is often the case in plants. RESULTS Here, in an attempt to shed light on complications of mapping sRNAs to TEs, we focus on the 2,300 Mb maize genome, 85% of which is derived from TEs, and scrutinize methodological strategies that are commonly employed in TE studies. These include choices for the reference dataset, the normalization of multiply mapping sRNAs, and the selection among sRNA metrics. We further examine how these choices influence the relationship between sRNAs and the critical feature of TE age, and contrast their effect on low copy genomic regions and other popular HTS data. CONCLUSIONS Based on our analyses, we share a series of take-home messages that may help with the design, implementation, and interpretation of high-throughput TE epigenetic studies specifically, but our conclusions may also apply to any work that involves analysis of HTS data.
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Affiliation(s)
- Alexandros Bousios
- School of Life Sciences, University of Sussex, Brighton, East Sussex BN1 9RH UK
| | - Brandon S. Gaut
- Department of Ecology and Evolutionary Biology, UC Irvine, Irvine, CA 92697 USA
| | - Nikos Darzentas
- Central European Institute of Technology, Masaryk University, Brno, 62500 Czech Republic
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31
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32
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Guo L, Liang T. MicroRNAs and their variants in an RNA world: implications for complex interactions and diverse roles in an RNA regulatory network. Brief Bioinform 2016; 19:245-253. [DOI: 10.1093/bib/bbw124] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2016] [Indexed: 01/09/2023] Open
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33
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Zhang Y, Zang Q, Zhang H, Ban R, Yang Y, Iqbal F, Li A, Shi Q. DeAnnIso: a tool for online detection and annotation of isomiRs from small RNA sequencing data. Nucleic Acids Res 2016; 44:W166-75. [PMID: 27179030 PMCID: PMC4987950 DOI: 10.1093/nar/gkw427] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2016] [Accepted: 05/05/2016] [Indexed: 12/19/2022] Open
Abstract
Small RNA (sRNA) Sequencing technology has revealed that microRNAs (miRNAs) are capable of exhibiting frequent variations from their canonical sequences, generating multiple variants: the isoforms of miRNAs (isomiRs). However, integrated tool to precisely detect and systematically annotate isomiRs from sRNA sequencing data is still in great demand. Here, we present an online tool, DeAnnIso (Detection and Annotation of IsomiRs from sRNA sequencing data). DeAnnIso can detect all the isomiRs in an uploaded sample, and can extract the differentially expressing isomiRs from paired or multiple samples. Once the isomiRs detection is accomplished, detailed annotation information, including isomiRs expression, isomiRs classification, SNPs in miRNAs and tissue specific isomiR expression are provided to users. Furthermore, DeAnnIso provides a comprehensive module of target analysis and enrichment analysis for the selected isomiRs. Taken together, DeAnnIso is convenient for users to screen for isomiRs of their interest and useful for further functional studies. The server is implemented in PHP + Perl + R and available to all users for free at: http://mcg.ustc.edu.cn/bsc/deanniso/ and http://mcg2.ustc.edu.cn/bsc/deanniso/.
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Affiliation(s)
- Yuanwei Zhang
- Molecular and Cell Genetics Laboratory, The CAS Key Laboratory of Innate Immunity and Chronic Disease, Hefei National Laboratory for Physical Sciences at Microscale and School of Life Sciences, University of Science and Technology of China, Hefei 230027, China Hefei Institute of Physical Science, China Academy of Science, Hefei 230027, China
| | - Qiguang Zang
- School of Information Science and Technology, University of Science and Technology of China, Hefei 230027, China
| | - Huan Zhang
- Molecular and Cell Genetics Laboratory, The CAS Key Laboratory of Innate Immunity and Chronic Disease, Hefei National Laboratory for Physical Sciences at Microscale and School of Life Sciences, University of Science and Technology of China, Hefei 230027, China
| | - Rongjun Ban
- School of Information Science and Technology, University of Science and Technology of China, Hefei 230027, China
| | - Yifan Yang
- Department of statistics, University of Kentucky, Lexington, KY 40536, USA
| | - Furhan Iqbal
- Molecular and Cell Genetics Laboratory, The CAS Key Laboratory of Innate Immunity and Chronic Disease, Hefei National Laboratory for Physical Sciences at Microscale and School of Life Sciences, University of Science and Technology of China, Hefei 230027, China Institute of Pure and Applied Biology, Bahauddin Zakariya University, Multan 60800, Pakistan
| | - Ao Li
- School of Information Science and Technology, University of Science and Technology of China, Hefei 230027, China Research Centers for Biomedical Engineering, University of Science and Technology of China, Hefei 230027, China
| | - Qinghua Shi
- Molecular and Cell Genetics Laboratory, The CAS Key Laboratory of Innate Immunity and Chronic Disease, Hefei National Laboratory for Physical Sciences at Microscale and School of Life Sciences, University of Science and Technology of China, Hefei 230027, China Hefei Institute of Physical Science, China Academy of Science, Hefei 230027, China
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34
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Guo L, Yu J, Liang T, Zou Q. miR-isomiRExp: a web-server for the analysis of expression of miRNA at the miRNA/isomiR levels. Sci Rep 2016; 6:23700. [PMID: 27009551 PMCID: PMC4806314 DOI: 10.1038/srep23700] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2016] [Accepted: 03/09/2016] [Indexed: 12/22/2022] Open
Abstract
MicroRNA (miRNA) locus has been found that can generate a series of varied isomiR sequences. Most studies always focus on determining miRNA level, however, the canonical miRNA sequence is only a specific member in the multiple isomiRs. Some studies have shown that isomiR sequences play versatile roles in biological progress, and the analysis and research should be simultaneously performed at the miRNA/isomiR levels. Based on the biological characteristics of miRNA and isomiR, we developed miR-isomiRExp to analyze expression pattern of miRNA at the miRNA/isomiR levels, provide insights into tracking miRNA/isomiR maturation and processing mechanisms, and reveal functional characteristics of miRNA/isomiR. Simultaneously, we also performed expression analysis of specific human diseases using public small RNA sequencing datasets based on the analysis platform, which may help in surveying the potential deregulated miRNA/isomiR expression profiles, especially sequence and function-related isomiRs for further interaction analysis and study. The miR-isomiRExp platform provides miRNA/isomiR expression patterns and more information to study deregulated miRNA loci and detailed isomiR sequences. This comprehensive analysis will enrich experimental miRNA studies. miR-isomiRExp is available at http://server.malab.cn/miRisomiRExp/.
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Affiliation(s)
- Li Guo
- Department of Bioinformatics, School of Geographic and Biologic Information, Nanjing University of Posts and Telecommunications, Nanjing, 210023, China
| | - Jiafeng Yu
- Shandong Provincial Key Laboratory of Functional Macromolecular Biophysics, Institute of Biophysics, Dezhou University, Dezhou, 253023, China
| | - Tingming Liang
- Jiangsu Key Laboratory for Molecular and Medical Biotechnology, College of Life Science, Nanjing Normal University, Nanjing, 210023, China
| | - Quan Zou
- School of Computer Science and Technology, Tianjin University, Tianjin, 300072, China
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35
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Zhang Y, Zang Q, Xu B, Zheng W, Ban R, Zhang H, Yang Y, Hao Q, Iqbal F, Li A, Shi Q. IsomiR Bank: a research resource for tracking IsomiRs. Bioinformatics 2016; 32:2069-71. [DOI: 10.1093/bioinformatics/btw070] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2015] [Accepted: 02/01/2016] [Indexed: 12/14/2022] Open
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36
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Wang S, Xu Y, Li M, Tu J, Lu Z. Dysregulation of miRNA isoform level at 5' end in Alzheimer's disease. Gene 2016; 584:167-72. [PMID: 26899870 DOI: 10.1016/j.gene.2016.02.020] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2015] [Revised: 01/09/2016] [Accepted: 02/15/2016] [Indexed: 01/10/2023]
Abstract
Alzheimer's disease (AD) is the most common form of dementia, whose mechanism is still not yet fully understood. A miRNA-based signature method, commonly according to the changes of expression levels, is widely used for AD analysis in previous studies. Recently, miRNA isoforms called as isomiR variants, which is considered to play important biological roles, have been demonstrated as the applications of high throughput sequencing platforms. Here, we presented an entropy-based model to detect the miRNA isoform level at the 5' end, and found many miRNAs with significant changes of isoform levels between the early stage and the late stage of AD by the application of this model to the public data. The statistical significance of the overlap between isoform-level changed miRNAs and AD related miRNAs extracted from HMDD2 supports that these miRNA isoforms are not degradation products. Based on the most common isomiR seed analysis of isoform-level changed AD related miRNAs, the predicted targets are also found to be enriched for genes involved in transcriptional regulation and the nervous system. After comparing with the expression level based method, we detected that changes of 5' isoform levels are more stable than those of expression levels for AD related miRNA detecting.
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Affiliation(s)
- Shengqin Wang
- College of Life and Environmental Science, Wenzhou University, Wenzhou 325035, China; State Key Lab of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing 210096, China
| | - Yuming Xu
- State Key Lab of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing 210096, China
| | - Musheng Li
- State Key Lab of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing 210096, China
| | - Jing Tu
- State Key Lab of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing 210096, China
| | - Zuhong Lu
- State Key Lab of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing 210096, China; Department of Biomedical Engineering, College of Engineering, Peking University, Beijing 100781, China.
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37
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Tripathi A, Goswami K, Sanan-Mishra N. Role of bioinformatics in establishing microRNAs as modulators of abiotic stress responses: the new revolution. Front Physiol 2015; 6:286. [PMID: 26578966 PMCID: PMC4620411 DOI: 10.3389/fphys.2015.00286] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2015] [Accepted: 09/28/2015] [Indexed: 12/15/2022] Open
Abstract
microRNAs (miRs) are a class of 21-24 nucleotide long non-coding RNAs responsible for regulating the expression of associated genes mainly by cleavage or translational inhibition of the target transcripts. With this characteristic of silencing, miRs act as an important component in regulation of plant responses in various stress conditions. In recent years, with drastic change in environmental and soil conditions different type of stresses have emerged as a major challenge for plants growth and productivity. The identification and profiling of miRs has itself been a challenge for research workers given their small size and large number of many probable sequences in the genome. Application of computational approaches has expedited the process of identification of miRs and their expression profiling in different conditions. The development of High-Throughput Sequencing (HTS) techniques has facilitated to gain access to the global profiles of the miRs for understanding their mode of action in plants. Introduction of various bioinformatics databases and tools have revolutionized the study of miRs and other small RNAs. This review focuses the role of bioinformatics approaches in the identification and study of the regulatory roles of plant miRs in the adaptive response to stresses.
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Affiliation(s)
- Anita Tripathi
- Plant Molecular Biology Group, International Centre for Genetic Engineering and Biotechnology New Delhi, India
| | - Kavita Goswami
- Plant Molecular Biology Group, International Centre for Genetic Engineering and Biotechnology New Delhi, India
| | - Neeti Sanan-Mishra
- Plant Molecular Biology Group, International Centre for Genetic Engineering and Biotechnology New Delhi, India
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38
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Kaushik A, Saraf S, Mukherjee SK, Gupta D. miRMOD: a tool for identification and analysis of 5' and 3' miRNA modifications in Next Generation Sequencing small RNA data. PeerJ 2015; 3:e1332. [PMID: 26623179 PMCID: PMC4662591 DOI: 10.7717/peerj.1332] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2015] [Accepted: 09/27/2015] [Indexed: 12/27/2022] Open
Abstract
In the past decade, the microRNAs (miRNAs) have emerged to be important regulators of gene expression across various species. Several studies have confirmed different types of post-transcriptional modifications at terminal ends of miRNAs. The reports indicate that miRNA modifications are conserved and functionally significant as it may affect miRNA stability and ability to bind mRNA targets, hence affecting target gene repression. Next Generation Sequencing (NGS) of the small RNA (sRNA) provides an efficient and reliable method to explore miRNA modifications. The need for dedicated software, especially for users with little knowledge of computers, to determine and analyze miRNA modifications in sRNA NGS data, motivated us to develop miRMOD. miRMOD is a user-friendly, Microsoft Windows and Graphical User Interface (GUI) based tool for identification and analysis of 5′ and 3′ miRNA modifications (non-templated nucleotide additions and trimming) in sRNA NGS data. In addition to identification of miRNA modifications, the tool also predicts and compares the targets of query and modified miRNAs. In order to compare binding affinities for the same target, miRMOD utilizes minimum free energies of the miRNA:target and modified-miRNA:target interactions. Comparisons of the binding energies may guide experimental exploration of miRNA post-transcriptional modifications. The tool is available as a stand-alone package to overcome large data transfer problems commonly faced in web-based high-throughput (HT) sequencing data analysis tools. miRMOD package is freely available at http://bioinfo.icgeb.res.in/miRMOD.
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Affiliation(s)
- Abhinav Kaushik
- Bioinformatics Laboratory, SCB Group, International Centre for Genetic Engineering & Biotechnology, New Delhi, India
| | - Shradha Saraf
- Bioinformatics Laboratory, SCB Group, International Centre for Genetic Engineering & Biotechnology, New Delhi, India
| | - Sunil K Mukherjee
- Department of Genetics, University of Delhi, South Campus, Delhi, India
| | - Dinesh Gupta
- Bioinformatics Laboratory, SCB Group, International Centre for Genetic Engineering & Biotechnology, New Delhi, India
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39
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mirPRo-a novel standalone program for differential expression and variation analysis of miRNAs. Sci Rep 2015; 5:14617. [PMID: 26434581 PMCID: PMC4592965 DOI: 10.1038/srep14617] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2015] [Accepted: 09/02/2015] [Indexed: 12/16/2022] Open
Abstract
Being involved in many important biological processes, miRNAs can regulate gene expression by targeting mRNAs to facilitate their degradation or translational inhibition. Many miRNA sequencing studies reveal that miRNA variations such as isomiRs and “arm switching” are biologically relevant. However, existing standalone tools usually do not provide comprehensive, detailed information on miRNA variations. To deepen our understanding of miRNA variability, we developed a new standalone tool called “mirPRo” to quantify known miRNAs and predict novel miRNAs. Compared with the most widely used standalone program, miRDeep2, mirPRo offers several new functions including read cataloging based on genome annotation, optional seed region check, miRNA family expression quantification, isomiR identification and categorization, and “arm switching” detection. Our comparative data analyses using three datasets from mouse, human and chicken demonstrate that mirPRo is more accurate than miRDeep2 by avoiding over-counting of sequence reads and by implementing different approaches in adapter trimming, mapping and quantification. mirPRo is an open-source standalone program (https://sourceforge.net/projects/mirpro/).
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40
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Budak H, Kantar M, Bulut R, Akpinar BA. Stress responsive miRNAs and isomiRs in cereals. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2015; 235:1-13. [PMID: 25900561 DOI: 10.1016/j.plantsci.2015.02.008] [Citation(s) in RCA: 95] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/26/2014] [Revised: 02/12/2015] [Accepted: 02/13/2015] [Indexed: 05/18/2023]
Abstract
Abiotic and biotic stress conditions are vital determinants in the production of cereals, the major caloric source in human nutrition. Small RNAs, miRNAs and isomiRs are central to post-transcriptional regulation of gene expression in a variety of cellular processes including development and stress responses. Several miRNAs have been identified using new technologies and have roles in stress responses in plants, including cereals. The overall knowledge about the cereal miRNA repertoire, as well as an understanding of complex miRNA mediated mechanisms of target regulation in response to stress conditions, is far from complete. Ongoing efforts that add to our understanding of complex miRNA machinery have implications in plant response to stress conditions. Additionally, sequence variants of miRNAs (isomiRNAs or isomiRs), regulation of their expression through dissection of upstream regulatory elements, the role of Processing-bodies (P-bodies) in miRNA exerted gene regulation and yet unveiled organellar plant miRNAs are newly emerging topics, which will contribute to the elucidation of the miRNA machinery and its role in cereal tolerance against abiotic and biotic stresses.
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Affiliation(s)
- Hikmet Budak
- Molecular Biology, Genetics and Bioengineering Program, Faculty of Engineering and Natural Sciences, Sabanci University, 34956 Istanbul, Turkey.
| | - Melda Kantar
- Molecular Biology, Genetics and Bioengineering Program, Faculty of Engineering and Natural Sciences, Sabanci University, 34956 Istanbul, Turkey
| | - Reyyan Bulut
- Molecular Biology, Genetics and Bioengineering Program, Faculty of Engineering and Natural Sciences, Sabanci University, 34956 Istanbul, Turkey
| | - Bala Ani Akpinar
- Molecular Biology, Genetics and Bioengineering Program, Faculty of Engineering and Natural Sciences, Sabanci University, 34956 Istanbul, Turkey
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41
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Sablok G, Srivastva AK, Suprasanna P, Baev V, Ralph PJ. isomiRs: Increasing Evidences of isomiRs Complexity in Plant Stress Functional Biology. FRONTIERS IN PLANT SCIENCE 2015; 6:949. [PMID: 26617614 PMCID: PMC4639611 DOI: 10.3389/fpls.2015.00949] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/15/2015] [Accepted: 10/17/2015] [Indexed: 05/11/2023]
Affiliation(s)
- Gaurav Sablok
- Plant Functional Biology and Climate Change Cluster (C3), University of Technology SydneySydney, NSW, Australia
- *Correspondence: Gaurav Sablok
| | - Ashish K. Srivastva
- Nuclear Agriculture and Biotechnology Division, Bhabha Atomic Research CentreMumbai, India
| | - Penna Suprasanna
- Nuclear Agriculture and Biotechnology Division, Bhabha Atomic Research CentreMumbai, India
| | - Vesselin Baev
- Department of Plant Physiology and Molecular Biology, University of PlovdivPlovdiv, Bulgaria
| | - Peter J. Ralph
- Plant Functional Biology and Climate Change Cluster (C3), University of Technology SydneySydney, NSW, Australia
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42
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Lee HY, Han SS, Rhee H, Park JH, Lee JS, Oh YM, Choi SS, Shin SH, Kim WJ. Differential expression of microRNAs and their target genes in non-small-cell lung cancer. Mol Med Rep 2014; 11:2034-40. [PMID: 25376560 DOI: 10.3892/mmr.2014.2890] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2014] [Accepted: 09/09/2014] [Indexed: 11/06/2022] Open
Abstract
MicroRNAs (miRNAs) are single‑stranded RNA species that constitute a class of non‑coding RNAs, and are emerging as key regulators of gene expression. Since each miRNA is capable of regulating multiple genes, miRNAs are attractive markers for studies of coordinated gene expression. In this study, we investigated miRNA expression profiling using a massively parallel sequencing technique to compare non‑small‑cell lung cancer (NSCLC) tissue and normal lung tissue. Lung cancer tissue and normal lung tissue were obtained from nine NSCLC patients. RNA isolated from these samples was processed using RNA sequencing (RNA Seq) and the HiSeq 2000 system. Differentially expressed miRNAs and mRNAs were analyzed using a t‑test. We selected target pairs that showed a negative correlation among significantly differentially expressed miRNAs and their putative target mRNAs using miRBase Targets. The differences in the expression levels of 222 miRNAs and 1,597 genes were statistically significant, as indicated by an absolute fold change ≥1.5 and P<0.05. miR‑577, miR‑301b, miR‑944, miR‑891a and miR‑615‑3p were generally upregulated, and miR‑338‑3p was generally downregulated. miRNA‑mRNA target pair analysis revealed that 49 miRNAs had 696 target mRNAs. There were significantly differentially expressed miRNAs and mRNAs between lung cancer and normal tissue. Further investigation of miRNAs and their target genes is warranted to better understand NSCLC.
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Affiliation(s)
- Hui-Young Lee
- Department of Internal Medicine, Kangwon National University Hospital, Kangwon National University School of Medicine, Chuncheon-si, Gangwon-do 200-722, Republic of Korea
| | - Seon-Sook Han
- Department of Internal Medicine, Kangwon National University Hospital, Kangwon National University School of Medicine, Chuncheon-si, Gangwon-do 200-722, Republic of Korea
| | - Hwanseok Rhee
- Macrogen Bioinformatics Center, Macrogen, Seoul 153-023, Republic of Korea
| | - Jung Hoon Park
- Macrogen Bioinformatics Center, Macrogen, Seoul 153-023, Republic of Korea
| | - Jae Seung Lee
- Department of Pulmonary and Critical Care Medicine, Asan Medical Center, University of Ulsan College of Medicine, Seoul 138-736, Republic of Korea
| | - Yeon-Mok Oh
- Department of Pulmonary and Critical Care Medicine, Asan Medical Center, University of Ulsan College of Medicine, Seoul 138-736, Republic of Korea
| | - Sun Shim Choi
- Department of Medical Biotechnology, College of Biomedical Science and Institute of Bioscience and Biotechnology, Kangwon National University, Chuncheon-si, Gangwon-do 200-701, Republic of Korea
| | - Seung-Ho Shin
- Department of Medical Biotechnology, College of Biomedical Science and Institute of Bioscience and Biotechnology, Kangwon National University, Chuncheon-si, Gangwon-do 200-701, Republic of Korea
| | - Woo Jin Kim
- Department of Internal Medicine, Kangwon National University Hospital, Kangwon National University School of Medicine, Chuncheon-si, Gangwon-do 200-722, Republic of Korea
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Baev V, Milev I, Naydenov M, Vachev T, Apostolova E, Mehterov N, Gozmanva M, Minkov G, Sablok G, Yahubyan G. Insight into small RNA abundance and expression in high- and low-temperature stress response using deep sequencing in Arabidopsis. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2014; 84:105-114. [PMID: 25261853 DOI: 10.1016/j.plaphy.2014.09.007] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/30/2014] [Accepted: 09/15/2014] [Indexed: 05/25/2023]
Abstract
Small RNA profiling and assessing its dependence on changing environmental factors have expanded our understanding of the transcriptional and post-transcriptional regulation of plant stress responses. Insufficient data have been documented earlier to depict the profiling of small RNA classes in temperature-associated stress which has a wide implication for climate change biology. In the present study, we report a comparative assessment of the genome-wide profiling of small RNAs in Arabidopsis thaliana using two conditional responses, induced by high- and low-temperature. Genome-wide profiling of small RNAs revealed an abundance of 21 nt small RNAs at low temperature, while high temperature showed an abundance of 21 nt and 24 nt small RNAs. The two temperature treatments altered the expression of a specific subset of mature miRNAs and displayed differential expression of a number of miRNA isoforms (isomiRs). Comparative analysis demonstrated that a large number of protein-coding genes can give rise to differentially expressed small RNAs following temperature shifts. Low temperature caused accumulation of small RNAs, corresponding to the sense strand of a number of cold-responsive genes. In contrast, high temperature stimulated the production of small RNAs of both polarities from genes encoding functionally diverse proteins.
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Affiliation(s)
- Vesselin Baev
- Department of Plant Physiology and Molecular Biology, University of Plovdiv, 24 Tsar Assen St, 4000 Plovdiv, Bulgaria.
| | - Ivan Milev
- Department of Plant Physiology and Molecular Biology, University of Plovdiv, 24 Tsar Assen St, 4000 Plovdiv, Bulgaria
| | - Mladen Naydenov
- Department of Plant Physiology and Molecular Biology, University of Plovdiv, 24 Tsar Assen St, 4000 Plovdiv, Bulgaria
| | - Tihomir Vachev
- Department of Plant Physiology and Molecular Biology, University of Plovdiv, 24 Tsar Assen St, 4000 Plovdiv, Bulgaria
| | - Elena Apostolova
- Department of Plant Physiology and Molecular Biology, University of Plovdiv, 24 Tsar Assen St, 4000 Plovdiv, Bulgaria
| | - Nikolay Mehterov
- Department of Plant Physiology and Molecular Biology, University of Plovdiv, 24 Tsar Assen St, 4000 Plovdiv, Bulgaria
| | - Mariyana Gozmanva
- Department of Plant Physiology and Molecular Biology, University of Plovdiv, 24 Tsar Assen St, 4000 Plovdiv, Bulgaria
| | - Georgi Minkov
- Department of Plant Physiology and Molecular Biology, University of Plovdiv, 24 Tsar Assen St, 4000 Plovdiv, Bulgaria
| | - Gaurav Sablok
- Department of Biodiversity and Molecular Ecology, Fondazione Edmund Mach, IASMA, San Michele 38010, Italy
| | - Galina Yahubyan
- Department of Plant Physiology and Molecular Biology, University of Plovdiv, 24 Tsar Assen St, 4000 Plovdiv, Bulgaria.
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44
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Muller H, Marzi MJ, Nicassio F. IsomiRage: From Functional Classification to Differential Expression of miRNA Isoforms. Front Bioeng Biotechnol 2014; 2:38. [PMID: 25325056 PMCID: PMC4179619 DOI: 10.3389/fbioe.2014.00038] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2014] [Accepted: 09/12/2014] [Indexed: 01/29/2023] Open
Abstract
As more small RNA sequencing libraries are becoming available, it clearly emerges that microRNAs (miRNAs) are highly heterogeneous both in length and sequence. In comparison to canonical miRNAs, miRNA isoforms (termed as “isomiRs”) might exhibit different biological properties, such as a different target repertoire, or enhanced/reduced stability. Nonetheless, this layer of information has remained largely unexplored due to the scarcity of small RNA NGS-datasets and the absence of proper analytical tools. Here, we present a workflow for the characterization and analysis of miRNAs and their variants in next-generation sequencing datasets. IsomiRs can originate from an alternative dicing event (“templated” forms) or from the addition of nucleotides through an enzymatic activity or target-dependent mechanisms (“non-templated” forms). Our pipeline allows distinguishing canonical miRNAs from templated and non-templated isomiRs by alignment to a custom database, which comprises all possible 3′-, 5′-, and trimmed variants. Functionally equivalent isomiRs can be grouped together according to the type of modification (e.g., uridylation, adenylation, trimming …) to assess which miRNAs are more intensively modified in a given biological context. When applied to the analysis of primary epithelial breast cancer cells, our methodology provided a 40% increase in the number of detected miRNA species and allowed to easily identify and classify more than 1000 variants. Most modifications were compatible with templated IsomiRs, as a consequence of imprecise Drosha or Dicer cleavage. However, some non-templated variants were consistently found either in the normal or in the cancer cells, with the 3′-end adenylation and uridylation as the most frequent events, suggesting that miRNA post-transcriptional modification frequently occurs. In conclusion, our analytical tool permits the deconvolution of miRNA heterogeneity and could be used to explore the functional role of miRNA isoforms.
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Affiliation(s)
- Heiko Muller
- Center for Genomic Science of IIT@SEMM, Istituto Italiano di Tecnologia (IIT) , Milan , Italy
| | - Matteo Jacopo Marzi
- Center for Genomic Science of IIT@SEMM, Istituto Italiano di Tecnologia (IIT) , Milan , Italy
| | - Francesco Nicassio
- Center for Genomic Science of IIT@SEMM, Istituto Italiano di Tecnologia (IIT) , Milan , Italy
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45
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Maghuly F, Ramkat RC, Laimer M. Virus versus host plant microRNAs: who determines the outcome of the interaction? PLoS One 2014; 9:e98263. [PMID: 24896088 PMCID: PMC4045720 DOI: 10.1371/journal.pone.0098263] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2014] [Accepted: 04/30/2014] [Indexed: 12/23/2022] Open
Abstract
Considering the importance of microRNAs (miRNAs) in the regulation of essential processes in plant pathogen interactions, it is not surprising that, while plant miRNA sequences counteract viral attack via antiviral RNA silencing, viruses in turn have developed antihost defense mechanisms blocking these RNA silencing pathways and establish a counter-defense. In the current study, computational and stem-loop Reverse Transcription – Polymerase Chain Reaction (RT-PCR) approaches were employed to a) predict and validate virus encoded mature miRNAs (miRs) in 39 DNA-A sequences of the bipartite genomes of African cassava mosaic virus (ACMV) and East African cassava mosaic virus-Uganda (EACMV-UG) isolates, b) determine whether virus encoded miRs/miRs* generated from the 5′/3′ harpin arms have the capacity to bind to genomic sequences of the host plants Jatropha or cassava and c) investigate whether plant encoded miR/miR* sequences have the potential to bind to the viral genomes. Different viral pre-miRNA hairpin sequences and viral miR/miR* length variants occurring as isomiRs were predicted in both viruses. These miRNAs were located in three Open Reading Frames (ORFs) and in the Intergenic Region (IR). Moreover, various target genes for miRNAs from both viruses were predicted and annotated in the host plant genomes indicating that they are involved in biotic response, metabolic pathways and transcription factors. Plant miRs/miRs* from conserved and highly expressed families were identified, which were shown to have potential targets in the genome of both begomoviruses, representing potential plant miRNAs mediating antiviral defense. This is the first assessment of predicted viral miRs/miRs* of ACMV and EACMV-UG and host plant miRNAs, providing a reference point for miRNA identification in pathogens and their hosts. These findings will improve the understanding of host- pathogen interaction pathways and the function of viral miRNAs in Euphorbiaceous crop plants.
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Affiliation(s)
- Fatemeh Maghuly
- Plant Biotechnology Unit (PBU), Department Biotechnology, University of Natural Resources and Life Sciences, BOKU-VIBT, Vienna, Austria
| | - Rose C. Ramkat
- Plant Biotechnology Unit (PBU), Department Biotechnology, University of Natural Resources and Life Sciences, BOKU-VIBT, Vienna, Austria
- Department of Biological Sciences, Egerton University, Nakuru, Kenya
| | - Margit Laimer
- Plant Biotechnology Unit (PBU), Department Biotechnology, University of Natural Resources and Life Sciences, BOKU-VIBT, Vienna, Austria
- * E-mail:
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46
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A challenge for miRNA: multiple isomiRs in miRNAomics. Gene 2014; 544:1-7. [PMID: 24768184 DOI: 10.1016/j.gene.2014.04.039] [Citation(s) in RCA: 83] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2014] [Revised: 04/11/2014] [Accepted: 04/18/2014] [Indexed: 11/22/2022]
Abstract
Accumulating evidence suggests that a single microRNA (miRNA) locus can generate a series of sequences during miRNA maturation process. These multiple sequences, called miRNA variants, or isomiRs, have different lengths and different 5' and 3' ends. Some of these isomiRs are detected as varied nucleotides and 3' additional non-template nucleotides. As physiological miRNA isoforms, they have drawn attention for possible regulatory biological roles. The present work mainly reviews miRNA/isomiR biogenesis, isomiR expression patterns, and functional and evolutionary implications, especially between isomiRs from homologous and clustered miRNA loci. The phenomenon of multiple isomiRs and their biological roles indicates that analysis performed at the miRNA and isomiR levels should be included in miRNA studies. This may enrich and complicate miRNA biogenesis and coding-non-coding RNA regulatory networks.
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47
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Luo GZ, Yang W, Ma YK, Wang XJ. ISRNA: an integrative online toolkit for short reads from high-throughput sequencing data. ACTA ACUST UNITED AC 2013; 30:434-6. [PMID: 24300438 DOI: 10.1093/bioinformatics/btt678] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
UNLABELLED Integrative Short Reads NAvigator (ISRNA) is an online toolkit for analyzing high-throughput small RNA sequencing data. Besides the high-speed genome mapping function, ISRNA provides statistics for genomic location, length distribution and nucleotide composition bias analysis of sequence reads. Number of reads mapped to known microRNAs and other classes of short non-coding RNAs, coverage of short reads on genes, expression abundance of sequence reads as well as some other analysis functions are also supported. The versatile search functions enable users to select sequence reads according to their sub-sequences, expression abundance, genomic location, relationship to genes, etc. A specialized genome browser is integrated to visualize the genomic distribution of short reads. ISRNA also supports management and comparison among multiple datasets. AVAILABILITY ISRNA is implemented in Java/C++/Perl/MySQL and can be freely accessed at http://omicslab.genetics.ac.cn/ISRNA/.
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Affiliation(s)
- Guan-Zheng Luo
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences and Graduate University of Chinese Academy of Sciences, Beijing 100101, China
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48
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Piva R, Spandidos DA, Gambari R. From microRNA functions to microRNA therapeutics: novel targets and novel drugs in breast cancer research and treatment (Review). Int J Oncol 2013; 43:985-94. [PMID: 23939688 PMCID: PMC3829774 DOI: 10.3892/ijo.2013.2059] [Citation(s) in RCA: 99] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2013] [Accepted: 08/12/2013] [Indexed: 12/12/2022] Open
Abstract
MicroRNAs (miRNAs or miRs) are a family of small non-coding RNAs that regulate gene expression by the sequence-selective targeting of mRNAs, leading to translational repression or mRNA degradation, depending on the degree of complementarity with target mRNA sequences. miRNAs play a crucial role in cancer. In the case of breast tumors, several studies have demonstrated a correlation between: i) the expression profile of oncogenic miRNAs (oncomiRs) or tumor suppressor miRNAs and ii) the tumorigenic potential of triple-negative [estrogen receptor (ER), progesterone receptor (PR) and Her2/neu] primary breast cancers. Among the miRNAs involved in breast cancer, miR-221 plays a crucial role for the following reasons: i) miR-221 is significantly overexpressed in triple-negative primary breast cancers; ii) the oncosuppressor p27
Kip1
, a validated miR-221 target, is downregulated in aggressive cancer cell lines; and iii) the upregulation of a key transcription factor, Slug, appears to be crucial, since it binds to the miR-221/miR-222 promoter and is responsible for the high expression of the miR-221/miR-222 cluster in breast cancer cells. A Slug/miR-221 network has been suggested, linking miR-221 activity with the downregulation of a Slug repressor, leading to Slug/miR-221 upregulation and p27
Kip1
downregulation. Interference with this process can be achieved using antisense miRNA (antagomiR) molecules targeting miR-221, inducing the down-regulation of Slug and the upregulation of p27
Kip1
.
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Affiliation(s)
- Roberta Piva
- Department of Biomedical and Specialty Surgical Sciences, Ferrara University, Ferrara, Italy
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