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Agrawal M, Mani A. Integrative in silico approaches to analyse microRNA-mediated responses in human diseases. J Gene Med 2024; 26:e3734. [PMID: 39197943 DOI: 10.1002/jgm.3734] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2024] [Revised: 07/23/2024] [Accepted: 08/13/2024] [Indexed: 09/01/2024] Open
Abstract
Advancements in sequencing technologies have facilitated omics level information generation for various diseases in human. High-throughput technologies have become a powerful tool to understand differential expression studies and transcriptional network analysis. An understanding of complex transcriptional networks in human diseases requires integration of datasets representing different RNA species including microRNA (miRNA) and messenger RNA (mRNA). This review emphasises on conceptual explanation of generalized workflow and methodologies to the miRNA mediated responses in human diseases by using different in silico analysis. Although, there have been many prior explorations in miRNA-mediated responses in human diseases, the advantages, limitations and overcoming the limitation through different statistical techniques have not yet been discussed. This review focuses on miRNAs as important gene regulators in human diseases, methodologies for miRNA-target gene prediction and data driven methods for enrichment and network analysis for miRnome-targetome interactions. Additionally, it proposes an integrative workflow to analyse structural components of networks obtained from high-throughput data. This review explains how to apply the existing methods to analyse miRNA-mediated responses in human diseases. It addresses unique characteristics of different analysis, its limitations and its statistical solutions influencing the choice of methods for the analysis through a workflow. Moreover, it provides an overview of promising common integrative approaches to comprehend miRNA-mediated gene regulatory events in biological processes in humans. The proposed methodologies and workflow shall help in the analysis of multi-source data to identify molecular signatures of various human diseases.
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Affiliation(s)
- Meghna Agrawal
- Department of Biotechnology, Motilal Nehru Institute of Technology Allahabad, Prayagraj, India
| | - Ashutosh Mani
- Department of Biotechnology, Motilal Nehru Institute of Technology Allahabad, Prayagraj, India
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2
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Hadad E, Rokach L, Veksler-Lublinsky I. Empowering prediction of miRNA-mRNA interactions in species with limited training data through transfer learning. Heliyon 2024; 10:e28000. [PMID: 38560149 PMCID: PMC10981012 DOI: 10.1016/j.heliyon.2024.e28000] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2023] [Revised: 03/06/2024] [Accepted: 03/11/2024] [Indexed: 04/04/2024] Open
Abstract
MicroRNAs (miRNAs) play a crucial role in mRNA regulation. Identifying functionally important mRNA targets of a specific miRNA is essential for uncovering its biological function and assisting miRNA-based drug development. Datasets of high-throughput direct bona fide miRNA-target interactions (MTIs) exist only for a few model organisms, prompting the need for computational prediction. However, the scarcity of data poses a challenge in training accurate machine learning models for MTI prediction. In this study, we explored the potential of transfer learning technique (with ANN and XGB) to address the limited data challenge by leveraging the similarities in interaction rules between species. Furthermore, we introduced a novel approach called TransferSHAP for estimating the feature importance of transfer learning in tabular dataset tasks. We demonstrated that transfer learning improves MTI prediction accuracy for species with limited datasets and identified the specific interaction features the models employed to transfer information across different species.
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Affiliation(s)
- Eyal Hadad
- Department of Software and Information Systems Engineering, Ben-Gurion University of the Negev, David Ben-Gurion Blvd. 1, Beer-Sheva 8410501, Israel
| | - Lior Rokach
- Department of Software and Information Systems Engineering, Ben-Gurion University of the Negev, David Ben-Gurion Blvd. 1, Beer-Sheva 8410501, Israel
| | - Isana Veksler-Lublinsky
- Department of Software and Information Systems Engineering, Ben-Gurion University of the Negev, David Ben-Gurion Blvd. 1, Beer-Sheva 8410501, Israel
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3
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Nakanishi K. When Argonaute takes out the ribonuclease sword. J Biol Chem 2024; 300:105499. [PMID: 38029964 PMCID: PMC10772731 DOI: 10.1016/j.jbc.2023.105499] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2023] [Revised: 11/11/2023] [Accepted: 11/15/2023] [Indexed: 12/01/2023] Open
Abstract
Argonaute (AGO) proteins in all three domains of life form ribonucleoprotein or deoxyribonucleoprotein complexes by loading a guide RNA or DNA, respectively. Since all AGOs retain a PIWI domain that takes an RNase H fold, the ancestor was likely an endoribonuclease (i.e., a slicer). In animals, most miRNA-mediated gene silencing occurs slicer independently. However, the slicer activity of AGO is indispensable in specific events, such as development and differentiation, which are critical for vertebrates and thus cannot be replaced by the slicer-independent regulation. This review highlights the distinctions in catalytic activation mechanisms among slicing-competent AGOs, shedding light on the roles of two metal ions in target recognition and cleavage. The precision of the target specificity by the RNA-induced silencing complexes is reevaluated and redefined. The possible coevolutionary relationship between slicer-independent gene regulation and AGO-binding protein, GW182, is also explored. These discussions reveal that numerous captivating questions remain unanswered regarding the timing and manner in which AGOs employ their slicing activity.
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Affiliation(s)
- Kotaro Nakanishi
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio, USA; Center for RNA Biology, The Ohio State University, Columbus, Ohio, USA.
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4
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Vishwakarma S, Kaur I. Molecular Mediators and Regulators of Retinal Angiogenesis. Semin Ophthalmol 2023; 38:124-133. [PMID: 36536520 DOI: 10.1080/08820538.2022.2152706] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
BACKGROUND Retinal neovascularization is the major cause of vision loss that affects both adults and young children including premature babies. It has been a major pathology in several retinal diseases like age-related macular degeneration (AMD), diabetic retinopathy (DR) and retinopathy of prematurity (ROP). Current treatment modalities such as anti-VEGF therapy, laser are not suitable for every patient and response to these therapies is highly variable. Thus, there is a need to investigate newer therapeutic targets for DR, ROP and AMD, based on a clear understanding of disease pathology and regulatory mechanisms involved. METHOD Appropriate articles published till February 2021 were extracted from PUBMED using keywords like ocular angiogenesis, DR, ROP, AMD, miRNA, mRNA, and cirMiRNA and containvaluable information regarding the involvement of miRNA in causing neovascularization. After compiling the list of miRNA regulating mRNA expression in angiogenesis and neovascularaization, their interactions were studied using online available tool MIENTURNET (http://userver.bio.uniroma1.it/apps/mienturnet/). The pathways involved in these processes were also predicted using the same tool. RESULTS Most of the studies have explored potential targets like HIF1-α, PDGF, TGFβ, FGF, etc., for their involvement in pathological angiogenesis in different retinal diseases. The regulatory role of microRNA (miRNA) has also been explored in various retinal ocular pathologies. This review highlights regulatory mechanism of cellular and circulatory miRNAs and their interactions with the genes involved in retinal neovascularization. The role of long noncoding RNA (ncRNA) in the regulation of genes involved in different pathways is also noteworthy and discussed in this review. CONCLUSION This review highlights the potential regulatory mechanism/pathways involved in retinal neovascularization and its implications in retinal diseases and for identifying new drug targets.
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Affiliation(s)
- Sushma Vishwakarma
- Prof Brien Holden Eye Research Centre, LV Prasad Eye Institute, Hyderabad, India.,Manipal Academy of Higher Education, Manipal, India
| | - Inderjeet Kaur
- Prof Brien Holden Eye Research Centre, LV Prasad Eye Institute, Hyderabad, India
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5
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Schmitz U. Overview of Computational and Experimental Methods to Identify Tissue-Specific MicroRNA Targets. Methods Mol Biol 2023; 2630:155-177. [PMID: 36689183 DOI: 10.1007/978-1-0716-2982-6_12] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
As ubiquitous posttranscriptional regulators of gene expression, microRNAs (miRNAs) play key roles in cell physiology and function across taxa. In the last two decades, we have gained a good understanding about miRNA biogenesis pathways, modes of action, and consequences of miRNA-mediated gene regulation. More recently, research has focused on exploring causes for miRNA dysregulation, miRNA-mediated crosstalk between genes and signaling pathways, and the role of miRNAs in disease.This chapter discusses methods for the identification of miRNA-target interactions and causes for tissue-specific miRNA-target regulation. Computational approaches for predicting miRNA target sites and assessing tissue-specific target regulation are discussed. Moreover, there is an emphasis on features that affect miRNA target recognition and how high-throughput sequencing protocols can help in assessing miRNA-mediated gene regulation on a genome-wide scale. In addition, this chapter introduces some experimental approaches for the validation of miRNA targets as well as web-based resources sharing predicted and validated miRNA-target interactions.
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Affiliation(s)
- Ulf Schmitz
- Department of Molecular & Cell Biology, College of Public Health, Medical & Vet Sciences, James Cook University, Douglas, Australia.
- Centre for Tropical Bioinformatics and Molecular Biology, Australian Institute of Tropical Health and Medicine, James Cook University, Cairns, Australia.
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6
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Small RNA Targets: Advances in Prediction Tools and High-Throughput Profiling. BIOLOGY 2022; 11:biology11121798. [PMID: 36552307 PMCID: PMC9775672 DOI: 10.3390/biology11121798] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/14/2022] [Revised: 11/27/2022] [Accepted: 12/08/2022] [Indexed: 12/14/2022]
Abstract
MicroRNAs (miRNAs) are an abundant class of small non-coding RNAs that regulate gene expression at the post-transcriptional level. They are suggested to be involved in most biological processes of the cell primarily by targeting messenger RNAs (mRNAs) for cleavage or translational repression. Their binding to their target sites is mediated by the Argonaute (AGO) family of proteins. Thus, miRNA target prediction is pivotal for research and clinical applications. Moreover, transfer-RNA-derived fragments (tRFs) and other types of small RNAs have been found to be potent regulators of Ago-mediated gene expression. Their role in mRNA regulation is still to be fully elucidated, and advancements in the computational prediction of their targets are in their infancy. To shed light on these complex RNA-RNA interactions, the availability of good quality high-throughput data and reliable computational methods is of utmost importance. Even though the arsenal of computational approaches in the field has been enriched in the last decade, there is still a degree of discrepancy between the results they yield. This review offers an overview of the relevant advancements in the field of bioinformatics and machine learning and summarizes the key strategies utilized for small RNA target prediction. Furthermore, we report the recent development of high-throughput sequencing technologies, and explore the role of non-miRNA AGO driver sequences.
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Feitosa RM, Prieto-Oliveira P, Brentani H, Machado-Lima A. MicroRNA target prediction tools for animals: Where we are at and where we are going to - A systematic review. Comput Biol Chem 2022; 100:107729. [DOI: 10.1016/j.compbiolchem.2022.107729] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2021] [Revised: 07/08/2022] [Accepted: 07/09/2022] [Indexed: 11/26/2022]
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8
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Deng F, Zeng F, Shen Q, Abbas A, Cheng J, Jiang W, Chen G, Shah AN, Holford P, Tanveer M, Zhang D, Chen ZH. Molecular evolution and functional modification of plant miRNAs with CRISPR. TRENDS IN PLANT SCIENCE 2022; 27:890-907. [PMID: 35165036 DOI: 10.1016/j.tplants.2022.01.009] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/14/2021] [Revised: 01/06/2022] [Accepted: 01/20/2022] [Indexed: 06/14/2023]
Abstract
Gene editing using clustered regularly interspaced short palindromic repeat/CRISPR-associated proteins (CRISPR/Cas) has revolutionized biotechnology and provides genetic tools for medicine and life sciences. However, the application of this technology to miRNAs, with the function as negative gene regulators, has not been extensively reviewed in plants. Here, we summarize the evolution, biogenesis, and structure of miRNAs, as well as their interactions with mRNAs and computational models for predicting target genes. In addition, we review current advances in CRISPR/Cas for functional analysis and for modulating miRNA genes in plants. Extending our knowledge of miRNAs and their manipulation with CRISPR will provide fundamental understanding of the functions of plant miRNAs and facilitate more sustainable and publicly acceptable genetic engineering of crops.
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Affiliation(s)
- Fenglin Deng
- Collaborative Innovation Center for Grain Industry, College of Agriculture, Yangtze University, Jingzhou, China
| | - Fanrong Zeng
- Collaborative Innovation Center for Grain Industry, College of Agriculture, Yangtze University, Jingzhou, China
| | - Qiufang Shen
- College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China
| | - Asad Abbas
- School of Horticulture, Anhui Agricultural University, Hefei 230036, China
| | - Jianhui Cheng
- Collaborative Innovation Center for Grain Industry, College of Agriculture, Yangtze University, Jingzhou, China
| | - Wei Jiang
- Collaborative Innovation Center for Grain Industry, College of Agriculture, Yangtze University, Jingzhou, China
| | - Guang Chen
- Central Laboratory, Zhejiang Academy of Agricultural Science, Hangzhou, China
| | - Adnan Noor Shah
- Department of Agricultural Engineering, Khawaja Fareed University of Engineering and Information Technology, Rahim Yar Khan, 64200, Pakistan
| | - Paul Holford
- School of Science, Western Sydney University, Penrith, NSW 2751, Australia
| | - Mohsin Tanveer
- Tasmanian Institute of Agriculture, University of Tasmania, Hobart, TAS 7004, Australia.
| | - Dabing Zhang
- Joint International Research Laboratory of Metabolic and Developmental Sciences, Shanghai Jiao Tong University-University of Adelaide Joint Centre for Agriculture and Health, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China; School of Agriculture, Food, and Wine, University of Adelaide, Glen Osmond, SA, Australia.
| | - Zhong-Hua Chen
- School of Science, Western Sydney University, Penrith, NSW 2751, Australia; Hawkesbury Institute for the Environment, Western Sydney University, Penrith, NSW 2751, Australia.
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Abbas A, Shah AN, Tanveer M, Ahmed W, Shah AA, Fiaz S, Waqas MM, Ullah S. MiRNA fine tuning for crop improvement: using advance computational models and biotechnological tools. Mol Biol Rep 2022; 49:5437-5450. [PMID: 35182321 DOI: 10.1007/s11033-022-07231-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2021] [Accepted: 02/04/2022] [Indexed: 12/17/2022]
Abstract
MiRNAs modulate target genes expression at post-transcriptional levels, by reducing spatial abundance of mRNAs. MiRNAs regulats plant metabolism, and emerged as regulators of plant stress responses. Which make miRNAs promising candidates for fine tuning to affectively alter crop stress tolerance and other important traits. With recent advancements in the computational biology and biotechnology miRNAs structure and target prediction is possible resulting in pin point editing; miRNA modulation can be done by up or down regulating miRNAs using recently available biotechnological tools (CRISPR Cas9, TALENS and RNAi). In this review we have focused on miRNA biogenesis, miRNA roles in plant development, plant stress responses and roles in signaling pathways. Additionally we have discussed latest computational prediction models for miRNA to target gene interaction and biotechnological systems used recently for miRNA modulation. We have also highlighted setbacks and limitations in the way of miRNA modulation; providing entirely a new direction for improvement in plant genomics primarily focusing miRNAs.
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Affiliation(s)
- Asad Abbas
- School of Horticulture, Anhui Agricultural University, Hefei, 230036, China
| | - Adnan Noor Shah
- Department of Agricultural Engineering, Khwaja Fareed University of Engineering and Information Technology, Rahim Yar Khan 64200, Punjab, Pakistan.
| | - Mohsin Tanveer
- Tasmanian Institute of Agriculture, University of Tasmania, Hobart, Australia
| | - Waseem Ahmed
- Department of Horticulture, The University of Haripur, Hatatr Road, Haripur, 22620, Pakistan
| | - Anis Ali Shah
- Department of Botany, Division of Science and Technology, University of Education, Lahore, Pakistan
| | - Sajid Fiaz
- Department of Plant Breeding and Genetics, The University of Haripur, Haripur, Pakistan
| | - Muhammad Mohsin Waqas
- Department of Agricultural Engineering, Khwaja Fareed University of Engineering and Information Technology, Rahim Yar Khan 64200, Punjab, Pakistan
| | - Sami Ullah
- Department of Chemistry, College of Science, King Khalid University, Abha, 61413, Saudi Arabia
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Mahlab-Aviv S, Linial N, Linial M. miRNA Combinatorics and its Role in Cell State Control-A Probabilistic Approach. Front Mol Biosci 2022; 8:772852. [PMID: 34993232 PMCID: PMC8724548 DOI: 10.3389/fmolb.2021.772852] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2021] [Accepted: 11/29/2021] [Indexed: 12/16/2022] Open
Abstract
A hallmark of cancer evolution is that the tumor may change its cell identity and improve its survival and fitness. Drastic change in microRNA (miRNA) composition and quantities accompany such dynamic processes. Cancer samples are composed of cells’ mixtures of varying stages of cancerous progress. Therefore, cell-specific molecular profiling represents cellular averaging. In this study, we consider the degree to which altering miRNAs composition shifts cell behavior. We used COMICS, an iterative framework that simulates the stochastic events of miRNA-mRNA pairing, using a probabilistic approach. COMICS simulates the likelihood that cells change their transcriptome following many iterations (100 k). Results of COMICS from the human cell line (HeLa) confirmed that most genes are resistant to miRNA regulation. However, COMICS results suggest that the composition of the abundant miRNAs dictates the nature of the cells (across three cell lines) regardless of its actual mRNA steady-state. In silico perturbations of cell lines (i.e., by overexpressing miRNAs) allowed to classify genes according to their sensitivity and resilience to any combination of miRNA perturbations. Our results expose an overlooked quantitative dimension for a set of genes and miRNA regulation in living cells. The immediate implication is that even relatively modest overexpression of specific miRNAs may shift cell identity and impact cancer evolution.
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Affiliation(s)
- Shelly Mahlab-Aviv
- The Rachel and Selim Benin School of Computer Science and Engineering, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Nathan Linial
- The Rachel and Selim Benin School of Computer Science and Engineering, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Michal Linial
- Department of Biological Chemistry, Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem, Israel
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11
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Machine Learning Based Methods and Best Practices of microRNA-Target Prediction and Validation. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2022; 1385:109-131. [DOI: 10.1007/978-3-031-08356-3_4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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12
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Quillet A, Anouar Y, Lecroq T, Dubessy C. Prediction methods for microRNA targets in bilaterian animals: Toward a better understanding by biologists. Comput Struct Biotechnol J 2021; 19:5811-5825. [PMID: 34765096 PMCID: PMC8567327 DOI: 10.1016/j.csbj.2021.10.025] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2021] [Revised: 09/20/2021] [Accepted: 10/15/2021] [Indexed: 12/13/2022] Open
Abstract
MicroRNAs (miRNAs) are small noncoding RNAs that regulate gene expression at the posttranscriptional level. Because of their wide network of interactions, miRNAs have become the focus of many studies over the past decade, particularly in animal species. To streamline the number of potential wet lab experiments, the use of miRNA target prediction tools is currently the first step undertaken. However, the predictions made may vary considerably depending on the tool used, which is mostly due to the complex and still not fully understood mechanism of action of miRNAs. The discrepancies complicate the choice of the tool for miRNA target prediction. To provide a comprehensive view of this issue, we highlight in this review the main characteristics of miRNA-target interactions in bilaterian animals, describe the prediction models currently used, and provide some insights for the evaluation of predictor performance.
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Affiliation(s)
- Aurélien Quillet
- Normandie Université, UNIROUEN, INSERM, Laboratoire Différenciation et Communication Neuronale et Neuroendocrine, 76000 Rouen, France
| | - Youssef Anouar
- Normandie Université, UNIROUEN, INSERM, Laboratoire Différenciation et Communication Neuronale et Neuroendocrine, 76000 Rouen, France
| | - Thierry Lecroq
- Normandie Université, UNIROUEN, UNIHAVRE, INSA Rouen, Laboratoire d'Informatique du Traitement de l'Information et des Systèmes, 76000 Rouen, France
| | - Christophe Dubessy
- Normandie Université, UNIROUEN, INSERM, Laboratoire Différenciation et Communication Neuronale et Neuroendocrine, 76000 Rouen, France.,Normandie Université, UNIROUEN, INSERM, PRIMACEN, 76000 Rouen, France
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Sindhu KJ, Venkatesan N, Karunagaran D. MicroRNA Interactome Multiomics Characterization for Cancer Research and Personalized Medicine: An Expert Review. OMICS-A JOURNAL OF INTEGRATIVE BIOLOGY 2021; 25:545-566. [PMID: 34448651 DOI: 10.1089/omi.2021.0087] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
MicroRNAs (miRNAs) that are mutually modulated by their interacting partners (interactome) are being increasingly noted for their significant role in pathogenesis and treatment of various human cancers. Recently, miRNA interactome dissected with multiomics approaches has been the subject of focus since individual tools or methods failed to provide the necessary comprehensive clues on the complete interactome. Even though single-omics technologies such as proteomics can uncover part of the interactome, the biological and clinical understanding still remain incomplete. In this study, we present an expert review of studies involving multiomics approaches to identification of miRNA interactome and its application in mechanistic characterization, classification, and therapeutic target identification in a variety of cancers, and with a focus on proteomics. We also discuss individual or multiple miRNA-based interactome identification in various pathological conditions of relevance to clinical medicine. Various new single-omics methods that can be integrated into multiomics cancer research and the computational approaches to analyze and predict miRNA interactome are also highlighted in this review. In all, we contextulize the power of multiomics approaches and the importance of the miRNA interactome to achieve the vision and practice of predictive, preventive, and personalized medicine in cancer research and clinical oncology.
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Affiliation(s)
- K J Sindhu
- Department of Biotechnology, Bhupat and Jyoti Mehta School of Biosciences, Indian Institute of Technology Madras, Chennai, India
| | - Nalini Venkatesan
- Department of Biotechnology, Bhupat and Jyoti Mehta School of Biosciences, Indian Institute of Technology Madras, Chennai, India
| | - Devarajan Karunagaran
- Department of Biotechnology, Bhupat and Jyoti Mehta School of Biosciences, Indian Institute of Technology Madras, Chennai, India
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Ben Or G, Veksler-Lublinsky I. Comprehensive machine-learning-based analysis of microRNA-target interactions reveals variable transferability of interaction rules across species. BMC Bioinformatics 2021; 22:264. [PMID: 34030625 PMCID: PMC8146624 DOI: 10.1186/s12859-021-04164-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2020] [Accepted: 05/04/2021] [Indexed: 12/18/2022] Open
Abstract
BACKGROUND MicroRNAs (miRNAs) are small non-coding RNAs that regulate gene expression post-transcriptionally via base-pairing with complementary sequences on messenger RNAs (mRNAs). Due to the technical challenges involved in the application of high-throughput experimental methods, datasets of direct bona fide miRNA targets exist only for a few model organisms. Machine learning (ML)-based target prediction models were successfully trained and tested on some of these datasets. There is a need to further apply the trained models to organisms in which experimental training data are unavailable. However, it is largely unknown how the features of miRNA-target interactions evolve and whether some features have remained fixed during evolution, raising questions regarding the general, cross-species applicability of currently available ML methods. RESULTS We examined the evolution of miRNA-target interaction rules and used data science and ML approaches to investigate whether these rules are transferable between species. We analyzed eight datasets of direct miRNA-target interactions in four species (human, mouse, worm, cattle). Using ML classifiers, we achieved high accuracy for intra-dataset classification and found that the most influential features of all datasets overlap significantly. To explore the relationships between datasets, we measured the divergence of their miRNA seed sequences and evaluated the performance of cross-dataset classification. We found that both measures coincide with the evolutionary distance between the compared species. CONCLUSIONS The transferability of miRNA-targeting rules between species depends on several factors, the most associated factors being the composition of seed families and evolutionary distance. Furthermore, our feature-importance results suggest that some miRNA-target features have evolved while others remained fixed during the evolution of the species. Our findings lay the foundation for the future development of target prediction tools that could be applied to "non-model" organisms for which minimal experimental data are available. AVAILABILITY AND IMPLEMENTATION The code is freely available at https://github.com/gbenor/TPVOD .
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Affiliation(s)
- Gilad Ben Or
- Department of Software and Information Systems Engineering, Ben-Gurion University of the Negev, Beer Sheva, Israel
| | - Isana Veksler-Lublinsky
- Department of Software and Information Systems Engineering, Ben-Gurion University of the Negev, Beer Sheva, Israel
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Kozar I, Philippidou D, Margue C, Gay LA, Renne R, Kreis S. Cross-Linking Ligation and Sequencing of Hybrids (qCLASH) Reveals an Unpredicted miRNA Targetome in Melanoma Cells. Cancers (Basel) 2021; 13:1096. [PMID: 33806450 PMCID: PMC7961530 DOI: 10.3390/cancers13051096] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2021] [Revised: 02/18/2021] [Accepted: 02/26/2021] [Indexed: 01/13/2023] Open
Abstract
MicroRNAs are key post-transcriptional gene regulators often displaying aberrant expression patterns in cancer. As microRNAs are promising disease-associated biomarkers and modulators of responsiveness to anti-cancer therapies, a solid understanding of their targetome is crucial. Despite enormous research efforts, the success rates of available tools to reliably predict microRNAs (miRNA)-target interactions remains limited. To investigate the disease-associated miRNA targetome, we have applied modified cross-linking ligation and sequencing of hybrids (qCLASH) to BRAF-mutant melanoma cells. The resulting RNA-RNA hybrid molecules provide a comprehensive and unbiased snapshot of direct miRNA-target interactions. The regulatory effects on selected miRNA target genes in predicted vs. non-predicted binding regions was validated by miRNA mimic experiments. Most miRNA-target interactions deviate from the central dogma of miRNA targeting up to 60% interactions occur via non-canonical seed pairing with a strong contribution of the 3' miRNA sequence, and over 50% display a clear bias towards the coding sequence of mRNAs. miRNAs targeting the coding sequence can directly reduce gene expression (miR-34a/CD68), while the majority of non-canonical miRNA interactions appear to have roles beyond target gene suppression (miR-100/AXL). Additionally, non-mRNA targets of miRNAs (lncRNAs) whose interactions mainly occur via non-canonical binding were identified in melanoma. This first application of CLASH sequencing to cancer cells identified over 8 K distinct miRNA-target interactions in melanoma cells. Our data highlight the importance non-canonical interactions, revealing further layers of complexity of post-transcriptional gene regulation in melanoma, thus expanding the pool of miRNA-target interactions, which have so far been omitted in the cancer field.
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Affiliation(s)
- Ines Kozar
- Department of Life Sciences and Medicine, University of Luxembourg, 6, Avenue du Swing, L-4367 Belvaux, Luxembourg; (I.K.); (D.P.); (C.M.)
| | - Demetra Philippidou
- Department of Life Sciences and Medicine, University of Luxembourg, 6, Avenue du Swing, L-4367 Belvaux, Luxembourg; (I.K.); (D.P.); (C.M.)
| | - Christiane Margue
- Department of Life Sciences and Medicine, University of Luxembourg, 6, Avenue du Swing, L-4367 Belvaux, Luxembourg; (I.K.); (D.P.); (C.M.)
| | - Lauren A. Gay
- Department of Molecular Genetics and Microbiology, University of Florida, 1200 Newell Drive, Gainesville, FL 32610, USA; (L.A.G.); (R.R.)
| | - Rolf Renne
- Department of Molecular Genetics and Microbiology, University of Florida, 1200 Newell Drive, Gainesville, FL 32610, USA; (L.A.G.); (R.R.)
| | - Stephanie Kreis
- Department of Life Sciences and Medicine, University of Luxembourg, 6, Avenue du Swing, L-4367 Belvaux, Luxembourg; (I.K.); (D.P.); (C.M.)
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16
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MicroRNAs and Their Targetomes in Tumor-Immune Communication. Cancers (Basel) 2020; 12:cancers12082025. [PMID: 32722019 PMCID: PMC7465095 DOI: 10.3390/cancers12082025] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2020] [Revised: 07/18/2020] [Accepted: 07/21/2020] [Indexed: 01/14/2023] Open
Abstract
The development of cancer is a complex and dynamically regulated multiple-step process that involves many changes in gene expression. Over the last decade, microRNAs (miRNAs), a class of short regulatory non-coding RNAs, have emerged as key molecular effectors and regulators of tumorigenesis. While aberrant expression of miRNAs or dysregulated miRNA-mediated gene regulation in tumor cells have been shown to be capable of directly promoting or inhibiting tumorigenesis, considering the well-reported role of the immune system in cancer, tumor-derived miRNAs could also impact tumor growth through regulating anti-tumor immune responses. Here, we discuss howmiRNAs can function as central mediators that influence the crosstalk between cancer and the immune system. Moreover, we also review the current progress in the development of novel experimental approaches for miRNA target identification that will facilitate our understanding of miRNA-mediated gene regulation in not only human malignancies, but also in other genetic disorders.
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17
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Talukder A, Li X, Hu H. Position-wise binding preference is important for miRNA target site prediction. Bioinformatics 2020; 36:3680-3686. [PMID: 32186709 PMCID: PMC8453239 DOI: 10.1093/bioinformatics/btaa195] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2019] [Revised: 01/16/2020] [Accepted: 03/17/2020] [Indexed: 01/21/2023] Open
Abstract
MOTIVATION It is a fundamental task to identify microRNAs (miRNAs) targets and accurately locate their target sites. Genome-scale experiments for miRNA target site detection are still costly. The prediction accuracies of existing computational algorithms and tools are often not up to the expectation due to a large number of false positives. One major obstacle to achieve a higher accuracy is the lack of knowledge of the target binding features of miRNAs. The published high-throughput experimental data provide an opportunity to analyze position-wise preference of miRNAs in terms of target binding, which can be an important feature in miRNA target prediction algorithms. RESULTS We developed a Markov model to characterize position-wise pairing patterns of miRNA-target interactions. We further integrated this model as a scoring method and developed a dynamic programming (DP) algorithm, MDPS (Markov model-scored Dynamic Programming algorithm for miRNA target site Selection) that can screen putative target sites of miRNA-target binding. The MDPS algorithm thus can take into account both the dependency of neighboring pairing positions and the global pairing information. Based on the trained Markov models from both miRNA-specific and general datasets, we discovered that the position-wise binding information specific to a given miRNA would benefit its target prediction. We also found that miRNAs maintain region-wise similarity in their target binding patterns. Combining MDPS with existing methods significantly improves their precision while only slightly reduces their recall. Therefore, position-wise pairing patterns have the promise to improve target prediction if incorporated into existing software tools. AVAILABILITY AND IMPLEMENTATION The source code and tool to calculate MDPS score is available at http://hulab.ucf.edu/research/projects/MDPS/index.html. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
| | - Xiaoman Li
- Burnett School of Biomedical Science, College of Medicine, University of Central Orlando, FL 32816, USA
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18
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Plotnikova O, Baranova A, Skoblov M. Comprehensive Analysis of Human microRNA-mRNA Interactome. Front Genet 2019; 10:933. [PMID: 31649721 PMCID: PMC6792129 DOI: 10.3389/fgene.2019.00933] [Citation(s) in RCA: 94] [Impact Index Per Article: 18.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2019] [Accepted: 09/05/2019] [Indexed: 01/20/2023] Open
Abstract
MicroRNAs play a key role in the regulation of gene expression. A majority of microRNA–mRNA interactions remain unidentified. Despite extensive research, our ability to predict human microRNA-mRNA interactions using computational algorithms remains limited by a complexity of the models for non-canonical interactions, and an abundance of false-positive results. Here, we present the landscape of human microRNA–mRNA interactions derived from comprehensive analysis of HEK293 and Huh7.5 datasets, along with publicly available microRNA and mRNA expression data. We show that, while only 1–2% of human genes were the most regulated by microRNAs, few cell line–specific RNAs, including EEF1A1 and HSPA1B in HEK293 and AFP, APOB, and MALAT1 genes in Huh7.5, display substantial “sponge-like” properties. We revealed a group of microRNAs that are expressed at a very high level, while interacting with only a few mRNAs, which, indeed, serve as their specific expression regulators. In order to establish reliable microRNA-binding regions, we collected and systematically analyzed the data from 79 CLIP datasets of microRNA-binding sites. We report 46,805 experimentally confirmed mRNA–miRNA duplex regions. Resulting dataset is available at http://score.generesearch.ru/services/mirna/. Our study provides initial insight into the complexity of human microRNA–mRNA interactions.
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Affiliation(s)
- Olga Plotnikova
- Laboratory of Functional Genome Analysis, Moscow Institute of Physics and Technology, Moscow, Russia.,Laboratory of Functional Genomics, Research Centre for Medical Genetics, Moscow, Russia
| | - Ancha Baranova
- Laboratory of Functional Genomics, Research Centre for Medical Genetics, Moscow, Russia.,School of Systems Biology, George Mason University, Fairfax, VA, United States
| | - Mikhail Skoblov
- Laboratory of Functional Genomics, Research Centre for Medical Genetics, Moscow, Russia
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19
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Fadaka AO, Pretorius A, Klein A. MicroRNA Assisted Gene Regulation in Colorectal Cancer. Int J Mol Sci 2019; 20:E4899. [PMID: 31623294 PMCID: PMC6801675 DOI: 10.3390/ijms20194899] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2019] [Revised: 08/25/2019] [Accepted: 08/29/2019] [Indexed: 02/06/2023] Open
Abstract
Colorectal cancer (CRC) is the second-leading cause of cancer death and a major public health problem. Nearly 80% CRC cases are diagnosed after the disease have metastasized and are often too advanced for treatment. Small non-coding RNA guides argonaute protein to their specific target for regulation as the sole of RNA induced silencing complex for gene silencing. These non-coding RNA for example microRNA, are thought to play a key role in affecting the efficiency of gene regulation in cancer, especially CRC. Understanding the mechanism at the molecular level could lead to improved diagnosis, treatment, and management decisions for CRC. The study aimed to predict the molecular mechanism of gene regulation based microRNA-mRNA duplex as a lead in the silencing mechanism. Five candidate microRNAs were identified through the in silico approach. The MicroRNA target prediction and subsequent correlation, and prioritization were performed using miRTarBase, gbCRC and CoReCG, and DAVID databases respectively. Protein selection and preparation were carried out using PDB and Schrödinger suits. The molecular docking analysis was performed using PATCHDOCK webserver and visualized by discovery studio visualizer. The results of the study reveal that the candidate microRNAs have strong binding affinity towards their targets suggesting a crucial factor in the silencing mechanism. Furthermore, the molecular docking of the receptor to both the microRNA and microRNA-mRNA duplex were analyzed computationally to understand their interaction at the molecular level. Conclusively, the study provides an explanation for understanding the microRNAs-based gene regulation (silencing mechanism) in CRC.
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Affiliation(s)
- Adewale O Fadaka
- Department of Biotechnology, Faculty of Natural Sciences, University of the Western Cape, Private Bag X17, Bellville, 7535 Cape Town, South Africa.
| | - Ashley Pretorius
- Department of Biotechnology, Faculty of Natural Sciences, University of the Western Cape, Private Bag X17, Bellville, 7535 Cape Town, South Africa.
| | - Ashwil Klein
- Department of Biotechnology, Faculty of Natural Sciences, University of the Western Cape, Private Bag X17, Bellville, 7535 Cape Town, South Africa.
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20
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Ahmed N, Foss DV, Powdrill MH, Pezacki JP. Site-Specific Cross-Linking of a p19 Viral Suppressor of RNA Silencing Protein and Its RNA Targets Using an Expanded Genetic Code. Biochemistry 2019; 58:3520-3526. [PMID: 31329415 DOI: 10.1021/acs.biochem.9b00428] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
The p19 viral suppressor of RNA silencing protein has useful applications in biotechnology due to its high affinity for binding to small RNAs such as small interfering RNAs (siRNAs). Also, its applications for the study and modulation of microRNAs are actively expanding. Here we demonstrate the successful site-specific incorporation of a photoactivatable unnatural amino acid, p-azido-l-phenylalanine (AzF), for cross-linking to RNA substrates into the p19 sequence. Incorporation of AzF was performed at three positions in the protein near the RNA binding site: K67, R115, and T111. Incorporation of AzF at position T111 of p19 did not affect the binding affinity of p19 for siRNAs and also showed nanomolar affinity for human microRNA miR-122. The affinity was less favorable with AzF incorporation at two other positions, suggesting the sensitivity of placement of the unnatural amino acid. Exposure of the T111AzF in complex with either siRNA or miRNA to ultraviolet light resulted in cross-linking of the protein with the RNA, but no cross-linking could be detected with the wild-type protein. Our results demonstrate that p19-T111AzF can be used for detection of small RNAs, including human miR-122, with high sensitivity and to irreversibly sequester these RNAs through covalent photo-cross-linking.
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Affiliation(s)
- Noreen Ahmed
- Department of Biochemistry, Microbiology and Immunology , University of Ottawa , Ottawa , Ontario K1N 6N5 , Canada
| | - Dana V Foss
- Department of Chemistry and Biomolecular Sciences , University of Ottawa , Ottawa , Ontario K1N 6N5 , Canada
| | - Megan H Powdrill
- Department of Biochemistry, Microbiology and Immunology , University of Ottawa , Ottawa , Ontario K1N 6N5 , Canada
| | - John Paul Pezacki
- Department of Biochemistry, Microbiology and Immunology , University of Ottawa , Ottawa , Ontario K1N 6N5 , Canada.,Department of Chemistry and Biomolecular Sciences , University of Ottawa , Ottawa , Ontario K1N 6N5 , Canada
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21
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Tokar T, Pastrello C, Rossos AEM, Abovsky M, Hauschild AC, Tsay M, Lu R, Jurisica I. mirDIP 4.1-integrative database of human microRNA target predictions. Nucleic Acids Res 2019; 46:D360-D370. [PMID: 29194489 PMCID: PMC5753284 DOI: 10.1093/nar/gkx1144] [Citation(s) in RCA: 360] [Impact Index Per Article: 72.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2017] [Accepted: 10/30/2017] [Indexed: 02/07/2023] Open
Abstract
MicroRNAs are important regulators of gene expression, achieved by binding to the gene to be regulated. Even with modern high-throughput technologies, it is laborious and expensive to detect all possible microRNA targets. For this reason, several computational microRNA-target prediction tools have been developed, each with its own strengths and limitations. Integration of different tools has been a successful approach to minimize the shortcomings of individual databases. Here, we present mirDIP v4.1, providing nearly 152 million human microRNA-target predictions, which were collected across 30 different resources. We also introduce an integrative score, which was statistically inferred from the obtained predictions, and was assigned to each unique microRNA-target interaction to provide a unified measure of confidence. We demonstrate that integrating predictions across multiple resources does not cumulate prediction bias toward biological processes or pathways. mirDIP v4.1 is freely available at http://ophid.utoronto.ca/mirDIP/.
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Affiliation(s)
- Tomas Tokar
- Krembil Research Institute, University Health Network, Toronto, Ontario M5T 2S8, Canada
| | - Chiara Pastrello
- Krembil Research Institute, University Health Network, Toronto, Ontario M5T 2S8, Canada
| | - Andrea E M Rossos
- Krembil Research Institute, University Health Network, Toronto, Ontario M5T 2S8, Canada
| | - Mark Abovsky
- Krembil Research Institute, University Health Network, Toronto, Ontario M5T 2S8, Canada
| | | | - Mike Tsay
- Krembil Research Institute, University Health Network, Toronto, Ontario M5T 2S8, Canada
| | - Richard Lu
- Krembil Research Institute, University Health Network, Toronto, Ontario M5T 2S8, Canada
| | - Igor Jurisica
- Krembil Research Institute, University Health Network, Toronto, Ontario M5T 2S8, Canada.,Department of Medical Biophysics, University of Toronto, Toronto, Ontario M5G 1L7, Canada.,Department of Computer Science, University of Toronto, Toronto, Ontario M5S 3G4, Canada.,Institute of Neuroimmunology, Slovak Academy of Sciences, Bratislava, 845 10, Slovakia
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22
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Bottini S, Pratella D, Grandjean V, Repetto E, Trabucchi M. Recent computational developments on CLIP-seq data analysis and microRNA targeting implications. Brief Bioinform 2019; 19:1290-1301. [PMID: 28605404 PMCID: PMC6291801 DOI: 10.1093/bib/bbx063] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2017] [Indexed: 01/18/2023] Open
Abstract
Cross-Linking
Immunoprecipitation associated to
high-throughput sequencing (CLIP-seq) is a technique used to
identify RNA directly bound to RNA-binding proteins across the entire transcriptome in
cell or tissue samples. Recent technological and computational advances permit the
analysis of many CLIP-seq samples simultaneously, allowing us to reveal the comprehensive
network of RNA–protein interaction and to integrate it to other genome-wide analyses.
Therefore, the design and quality management of the CLIP-seq analyses are of critical
importance to extract clean and biological meaningful information from CLIP-seq
experiments. The application of CLIP-seq technique to Argonaute 2 (Ago2) protein, the main
component of the microRNA (miRNA)-induced silencing complex, reveals the direct binding
sites of miRNAs, thus providing insightful information about the role played by miRNA(s).
In this review, we summarize and discuss the most recent computational methods for
CLIP-seq analysis, and discuss their impact on Ago2/miRNA-binding site identification and
prediction with a regard toward human pathologies.
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Affiliation(s)
- Silvia Bottini
- Université Côte d'Azur, Inserm, C3M, 151 route de St-Antoine-de-Ginestière, B.P. 2 3194, 06204 Nice, France
| | - David Pratella
- Université Côte d'Azur, Inserm, C3M, 151 route de St-Antoine-de-Ginestière, B.P. 2 3194, 06204 Nice, France
| | - Valerie Grandjean
- Université Côte d'Azur, Inserm, C3M, 151 route de St-Antoine-de-Ginestière, B.P. 2 3194, 06204 Nice, France
| | - Emanuela Repetto
- Université Côte d'Azur, Inserm, C3M, 151 route de St-Antoine-de-Ginestière, B.P. 2 3194, 06204 Nice, France
| | - Michele Trabucchi
- Université Côte d'Azur, Inserm, C3M, 151 route de St-Antoine-de-Ginestière, B.P. 2 3194, 06204 Nice, France
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23
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Dubin JA, Greenberg DR, Iglinski-Benjamin KC, Abrams GD. Effect of micro-RNA on tenocytes and tendon-related gene expression: A systematic review. J Orthop Res 2018; 36:2823-2829. [PMID: 29873411 DOI: 10.1002/jor.24064] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/24/2018] [Accepted: 05/21/2018] [Indexed: 02/04/2023]
Abstract
The purpose of the review was to synthesize the current literature regarding the effect of miRNA on biological processes known to be involved in tendon and tenocyte development and homeostasis. Using multiple databases, a systematic review was performed with a customized search term crafted to identify any study examining micro-RNA in relation to tendon and/or tenocytes. Results were classified based on the following categories: Gene expression, tenocyte development and differentiation, tendon tissue repair, and tenocyte senescence. A total of 3,112 potentially relevant studies were reviewed, and after exclusion criteria was applied, 15 investigations were included in the final analysis. There were 14 specific miRNA included in this review, with 11 studies reporting on tendon-related gene expression, five reporting on tendon development and/or tenocyte differentiation, six reporting on tendon tissue repair, and five reporting on tenocyte senescence. The miR-29 family was the most commonly reported micro-RNA in the investigation. We also report on a number of micro-RNA which are associated with both positive and negative effects on tendon homeostasis. © 2018 Orthopaedic Research Society. Published by Wiley Periodicals, Inc. J Orthop Res 36:2823-2829, 2018.
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Affiliation(s)
- Jeremy A Dubin
- Veterans Administration-Palo Alto, Palo Alto, California
| | - Daniel R Greenberg
- Department of Orthopedic Surgery, Stanford University School of Medicine, 341 Galvez Street Mail Code 6175, Stanford, California
| | - Kag C Iglinski-Benjamin
- Veterans Administration-Palo Alto, Palo Alto, California.,Department of Orthopedic Surgery, Stanford University School of Medicine, 341 Galvez Street Mail Code 6175, Stanford, California
| | - Geoffrey D Abrams
- Veterans Administration-Palo Alto, Palo Alto, California.,Department of Orthopedic Surgery, Stanford University School of Medicine, 341 Galvez Street Mail Code 6175, Stanford, California
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24
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Hannigan MM, Zagore LL, Licatalosi DD. Mapping transcriptome-wide protein-RNA interactions to elucidate RNA regulatory programs. QUANTITATIVE BIOLOGY 2018; 6:228-238. [PMID: 31098334 PMCID: PMC6516777 DOI: 10.1007/s40484-018-0145-6] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2018] [Revised: 03/27/2018] [Accepted: 04/03/2018] [Indexed: 12/12/2022]
Abstract
BACKGROUND Our understanding of post-transcriptional gene regulation has increased exponentially with the development of robust methods to define protein-RNA interactions across the transcriptome. In this review, we highlight the evolution and successful applications of crosslinking and immunoprecipitation (CLIP) methods to interrogate protein-RNA interactions in a transcriptome-wide manner. RESULTS Here, we survey the vast array of in vitro and in vivo approaches used to identify protein-RNA interactions, including but not limited to electrophoretic mobility shift assays, systematic evolution of ligands by exponential enrichment (SELEX), and RIP-seq. We particularly emphasize the advancement of CLIP technologies, and detail protocol improvements and computational tools used to analyze the output data. Importantly, we discuss how profiling protein-RNA interactions can delineate biological functions including splicing regulation, alternative polyadenylation, cytoplasmic decay substrates, and miRNA targets. CONCLUSIONS In summary, this review summarizes the benefits of characterizing RNA-protein networks to further understand the regulation of gene expression and disease pathogenesis. Our review comments on how future CLIP technologies can be adapted to address outstanding questions related to many aspects of RNA metabolism and further advance our understanding of RNA biology.
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Affiliation(s)
- Molly M Hannigan
- Center for RNA Science and Therapeutics, Case Western Reserve University, Cleveland, OH 44106, USA
| | - Leah L Zagore
- Center for RNA Science and Therapeutics, Case Western Reserve University, Cleveland, OH 44106, USA
| | - Donny D Licatalosi
- Center for RNA Science and Therapeutics, Case Western Reserve University, Cleveland, OH 44106, USA
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25
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26
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Yoo SS, Hong MJ, Lee JH, Choi JE, Lee SY, Lee J, Cha SI, Kim CH, Seok Y, Lee E, Cho S, Jheon S, Park JY. Association between polymorphisms in microRNA target sites and survival in early-stage non-small cell lung cancer. Thorac Cancer 2017; 8:682-686. [PMID: 28922562 PMCID: PMC5668488 DOI: 10.1111/1759-7714.12478] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2017] [Revised: 06/12/2017] [Accepted: 06/13/2017] [Indexed: 11/27/2022] Open
Abstract
A high‐throughput mapping method of RNA–RNA interactions by crosslinking, ligation, and sequencing of hybrids (CLASH) can not only provide information about canonical but also non‐canonical interactions. We evaluated the associations between variants in microRNA target sites using CLASH data and survival outcomes of 782 early‐stage non‐small cell lung cancer (NSCLC) patients who underwent curative surgical resection. Among the 100 variants studied, two variants showed significant association with survival outcomes. The POLR2A rs2071504 C > T variant was associated with poor overall and disease‐free survival under a dominant model (hazard ratio [HR] 1.42, 95% confidence interval [CI] 1.08–1.88; P = 0.01 and HR 1.34, 95% CI 1.08–1.67; P = 0.01, respectively). Patients carrying the NR2F6 rs2288539 TT genotype showed significantly better overall survival than those with the NR2F6 rs2288539 CC or CT genotypes (HR 0.13, 95% CI 0.02–0.90; P = 0.04). These findings suggest that POLR2A rs2071504 C > T and NR2F6 rs2288539 C > T can influence prognosis in early‐stage NSCLC patients.
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Affiliation(s)
- Seung Soo Yoo
- Department of Internal Medicine, School of Medicine, Kyungpook National University, Daegu, South Korea
| | - Mi Jeong Hong
- Cell and Matrix Research Institute, School of Medicine, Kyungpook National University, Daegu, South Korea
| | - Jang Hyuck Lee
- Department of Biochemistry and Cell Biology, School of Medicine, Kyungpook National University, Daegu, South Korea
| | - Jin Eun Choi
- Cell and Matrix Research Institute, School of Medicine, Kyungpook National University, Daegu, South Korea
| | - Shin Yup Lee
- Department of Internal Medicine, School of Medicine, Kyungpook National University, Daegu, South Korea
| | - Jaehee Lee
- Department of Internal Medicine, School of Medicine, Kyungpook National University, Daegu, South Korea
| | - Seung Ick Cha
- Department of Internal Medicine, School of Medicine, Kyungpook National University, Daegu, South Korea
| | - Chang Ho Kim
- Department of Internal Medicine, School of Medicine, Kyungpook National University, Daegu, South Korea
| | - Yangki Seok
- Department of Thoracic Surgery, School of Medicine, Kyungpook National University, Daegu, South Korea
| | - Eungbae Lee
- Department of Thoracic Surgery, School of Medicine, Kyungpook National University, Daegu, South Korea
| | - Sukki Cho
- Department of Thoracic and Cardiovascular Surgery, School of Medicine, Seoul National University, Seoul, South Korea
| | - Sanghoon Jheon
- Department of Thoracic and Cardiovascular Surgery, School of Medicine, Seoul National University, Seoul, South Korea
| | - Jae Yong Park
- Department of Internal Medicine, School of Medicine, Kyungpook National University, Daegu, South Korea.,Cell and Matrix Research Institute, School of Medicine, Kyungpook National University, Daegu, South Korea.,Department of Biochemistry and Cell Biology, School of Medicine, Kyungpook National University, Daegu, South Korea
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27
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Scheel TKH, Moore MJ, Luna JM, Nishiuchi E, Fak J, Darnell RB, Rice CM. Global mapping of miRNA-target interactions in cattle (Bos taurus). Sci Rep 2017; 7:8190. [PMID: 28811507 PMCID: PMC5557892 DOI: 10.1038/s41598-017-07880-8] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2017] [Accepted: 07/04/2017] [Indexed: 12/18/2022] Open
Abstract
With roles in development, cell proliferation and disease, micro-RNA (miRNA) biology is of great importance and a potential therapeutic target. Here we used cross-linking immunoprecipitation (CLIP) and ligation of miRNA-target chimeras on the Argonaute (AGO) protein to globally map miRNA interactions in the cow. The interactome is the deepest reported to date. miRNA targeting principles are consistent with observations in other species, but with expanded pairing rules. Experimental mapping robustly predicted functional miR-17 regulatory sites. From miRNA-specific targeting for >5000 mRNAs we determined gene ontologies (GO). This confirmed repression of genes important for embryonic development and cell cycle progress by the let-7 family, and repression of those involved in cell cycle arrest by the miR-17 family, but also suggested a number of unappreciated miRNA functions. Our results provide a significant resource for understanding of bovine and species-conserved miRNA regulation, and demonstrate the power of experimental methods for establishing comprehensive interaction maps.
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Affiliation(s)
- Troels K H Scheel
- Laboratory of Virology and Infectious Disease, Center for the Study of Hepatitis C, The Rockefeller University, New York, NY, USA. .,Copenhagen Hepatitis C Program, Department of Infectious Diseases, Copenhagen University Hospital, Hvidovre, Denmark. .,Department of Immunology and Microbiology, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark.
| | - Michael J Moore
- Laboratory of Molecular Neuro-Oncology, and Howard Hughes Medical Institute, The Rockefeller University, New York, NY, USA
| | - Joseph M Luna
- Laboratory of Virology and Infectious Disease, Center for the Study of Hepatitis C, The Rockefeller University, New York, NY, USA.,Laboratory of Molecular Neuro-Oncology, and Howard Hughes Medical Institute, The Rockefeller University, New York, NY, USA
| | - Eiko Nishiuchi
- Laboratory of Virology and Infectious Disease, Center for the Study of Hepatitis C, The Rockefeller University, New York, NY, USA
| | - John Fak
- Laboratory of Molecular Neuro-Oncology, and Howard Hughes Medical Institute, The Rockefeller University, New York, NY, USA
| | - Robert B Darnell
- Laboratory of Molecular Neuro-Oncology, and Howard Hughes Medical Institute, The Rockefeller University, New York, NY, USA.,New York Genome Center, New York, NY, USA
| | - Charles M Rice
- Laboratory of Virology and Infectious Disease, Center for the Study of Hepatitis C, The Rockefeller University, New York, NY, USA.
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