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de Oliveira AC, Bovolenta LA, Figueiredo L, Ribeiro ADO, Pereira BJA, de Almeida TRA, Campos VF, Patton JG, Pinhal D. MicroRNA Transcriptomes Reveal Prevalence of Rare and Species-Specific Arm Switching Events During Zebrafish Ontogenesis. Evol Bioinform Online 2024; 20:11769343241263230. [PMID: 39055772 PMCID: PMC11271096 DOI: 10.1177/11769343241263230] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2024] [Accepted: 06/04/2024] [Indexed: 07/27/2024] Open
Abstract
In metazoans, microRNAs (miRNAs) are essential regulators of gene expression, affecting critical cellular processes from differentiation and proliferation, to homeostasis. During miRNA biogenesis, the miRNA strand that loads onto the RNA-induced Silencing Complex (RISC) can vary, leading to changes in gene targeting and modulation of biological pathways. To investigate the impact of these "arm switching" events on gene regulation, we analyzed a diverse range of tissues and developmental stages in zebrafish by comparing 5p and 3p arms accumulation dynamics between embryonic developmental stages, adult tissues, and sexes. We also compared variable arm usage patterns observed in zebrafish to other vertebrates including arm switching data from fish, birds, and mammals. Our comprehensive analysis revealed that variable arm usage events predominantly take place during embryonic development. It is also noteworthy that isomiR occurrence correlates to changes in arm selection evidencing an important role of microRNA distinct isoforms in reinforcing and modifying gene regulation by promoting dynamics switches on miRNA 5p and 3p arms accumulation. Our results shed new light on the emergence and coordination of gene expression regulation and pave the way for future investigations in this field.
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Affiliation(s)
- Arthur Casulli de Oliveira
- Department of Chemical and Biological Sciences, Institute of Biosciences of Botucatu, São Paulo State University-UNESP, Botucatu, São Paulo, Brazil
| | - Luiz Augusto Bovolenta
- Department of Structural and Functional Biology, Institute of Biosciences of Botucatu, São Paulo State University-UNESP, Botucatu, São Paulo, Brazil
| | - Lucas Figueiredo
- Department of Chemical and Biological Sciences, Institute of Biosciences of Botucatu, São Paulo State University-UNESP, Botucatu, São Paulo, Brazil
| | - Amanda De Oliveira Ribeiro
- Department of Structural and Functional Biology, Institute of Biosciences of Botucatu, São Paulo State University-UNESP, Botucatu, São Paulo, Brazil
| | - Beatriz Jacinto Alves Pereira
- Department of Chemical and Biological Sciences, Institute of Biosciences of Botucatu, São Paulo State University-UNESP, Botucatu, São Paulo, Brazil
| | - Talita Roberto Aleixo de Almeida
- Department of Chemical and Biological Sciences, Institute of Biosciences of Botucatu, São Paulo State University-UNESP, Botucatu, São Paulo, Brazil
| | - Vinicius Farias Campos
- Laboratory of Structural Genomics, Postgraduate Program in Biotechnology, Center for Technological Development, Federal University of Pelotas, Pelotas, Rio Grande do Sul, Brazil
| | - James G Patton
- Department of Biological Sciences, Vanderbilt University, Nashville TN, USA
| | - Danillo Pinhal
- Department of Chemical and Biological Sciences, Institute of Biosciences of Botucatu, São Paulo State University-UNESP, Botucatu, São Paulo, Brazil
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2
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Rac M. Synthesis and Regulation of miRNA, Its Role in Oncogenesis, and Its Association with Colorectal Cancer Progression, Diagnosis, and Prognosis. Diagnostics (Basel) 2024; 14:1450. [PMID: 39001340 PMCID: PMC11241650 DOI: 10.3390/diagnostics14131450] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2024] [Revised: 06/27/2024] [Accepted: 07/05/2024] [Indexed: 07/16/2024] Open
Abstract
The dysfunction of several types of regulators, including miRNAs, has recently attracted scientific attention for their role in cancer-associated changes in gene expression. MiRNAs are small RNAs of ~22 nt in length that do not encode protein information but play an important role in post-transcriptional mRNA regulation. Studies have shown that miRNAs are involved in tumour progression, including cell proliferation, cell cycle, apoptosis, and tumour angiogenesis and invasion, and play a complex and important role in the regulation of tumourigenesis. The detection of selected miRNAs may help in the early detection of cancer cells, and monitoring changes in their expression profile may serve as a prognostic factor in the course of the disease or its treatment. MiRNAs may serve as diagnostic and prognostic biomarkers, as well as potential therapeutic targets for colorectal cancer. In recent years, there has been increasing evidence for an epigenetic interaction between DNA methylation and miRNA expression in tumours. This article provides an overview of selected miRNAs, which are more frequently expressed in colorectal cancer cells, suggesting an oncogenic nature.
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Affiliation(s)
- Monika Rac
- Department of Biochemistry and Medical Chemistry, Pomeranian Medical University, Al. Powstańców Wielkopolskich 72, 70-111 Szczecin, Poland
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3
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Daniel Thomas S, Vijayakumar K, John L, Krishnan D, Rehman N, Revikumar A, Kandel Codi JA, Prasad TSK, S S V, Raju R. Machine Learning Strategies in MicroRNA Research: Bridging Genome to Phenome. OMICS : A JOURNAL OF INTEGRATIVE BIOLOGY 2024; 28:213-233. [PMID: 38752932 DOI: 10.1089/omi.2024.0047] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2024]
Abstract
MicroRNAs (miRNAs) have emerged as a prominent layer of regulation of gene expression. This article offers the salient and current aspects of machine learning (ML) tools and approaches from genome to phenome in miRNA research. First, we underline that the complexity in the analysis of miRNA function ranges from their modes of biogenesis to the target diversity in diverse biological conditions. Therefore, it is imperative to first ascertain the miRNA coding potential of genomes and understand the regulatory mechanisms of their expression. This knowledge enables the efficient classification of miRNA precursors and the identification of their mature forms and respective target genes. Second, and because one miRNA can target multiple mRNAs and vice versa, another challenge is the assessment of the miRNA-mRNA target interaction network. Furthermore, long-noncoding RNA (lncRNA)and circular RNAs (circRNAs) also contribute to this complexity. ML has been used to tackle these challenges at the high-dimensional data level. The present expert review covers more than 100 tools adopting various ML approaches pertaining to, for example, (1) miRNA promoter prediction, (2) precursor classification, (3) mature miRNA prediction, (4) miRNA target prediction, (5) miRNA- lncRNA and miRNA-circRNA interactions, (6) miRNA-mRNA expression profiling, (7) miRNA regulatory module detection, (8) miRNA-disease association, and (9) miRNA essentiality prediction. Taken together, we unpack, critically examine, and highlight the cutting-edge synergy of ML approaches and miRNA research so as to develop a dynamic and microlevel understanding of human health and diseases.
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Affiliation(s)
- Sonet Daniel Thomas
- Centre for Integrative Omics Data Science (CIODS), Yenepoya (Deemed to Be University), Manglore, Karnataka, India
- Centre for Systems Biology and Molecular Medicine (CSBMM), Yenepoya (Deemed to Be University), Manglore, Karnataka, India
| | - Krithika Vijayakumar
- Centre for Integrative Omics Data Science (CIODS), Yenepoya (Deemed to Be University), Manglore, Karnataka, India
| | - Levin John
- Centre for Integrative Omics Data Science (CIODS), Yenepoya (Deemed to Be University), Manglore, Karnataka, India
| | - Deepak Krishnan
- Centre for Systems Biology and Molecular Medicine (CSBMM), Yenepoya (Deemed to Be University), Manglore, Karnataka, India
| | - Niyas Rehman
- Centre for Integrative Omics Data Science (CIODS), Yenepoya (Deemed to Be University), Manglore, Karnataka, India
| | - Amjesh Revikumar
- Centre for Integrative Omics Data Science (CIODS), Yenepoya (Deemed to Be University), Manglore, Karnataka, India
- Kerala Genome Data Centre, Kerala Development and Innovation Strategic Council, Thiruvananthapuram, Kerala, India
| | - Jalaluddin Akbar Kandel Codi
- Department of Surgical Oncology, Yenepoya Medical College, Yenepoya (Deemed to Be University), Manglore, Karnataka, India
| | | | - Vinodchandra S S
- Department of Computer Science, University of Kerala, Thiruvananthapuram, Kerala, India
| | - Rajesh Raju
- Centre for Integrative Omics Data Science (CIODS), Yenepoya (Deemed to Be University), Manglore, Karnataka, India
- Centre for Systems Biology and Molecular Medicine (CSBMM), Yenepoya (Deemed to Be University), Manglore, Karnataka, India
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4
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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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5
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Yang TH, Chen JC, Lee YH, Lu SY, Wu SH, Chang FY, Huang YC, Lee MH, Tseng YY, Wu WS. Identifying Human miRNA Target Sites via Learning the Interaction Patterns between miRNA and mRNA Segments. J Chem Inf Model 2024; 64:2445-2453. [PMID: 37903033 DOI: 10.1021/acs.jcim.3c01150] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/01/2023]
Abstract
miRNAs (microRNAs) target specific mRNA (messenger RNA) sites to regulate their translation expression. Although miRNA targeting can rely on seed region base pairing, animal miRNAs, including human miRNAs, typically cooperate with several cofactors, leading to various noncanonical pairing rules. Therefore, identifying the binding sites of animal miRNAs remains challenging. Because experiments for mapping miRNA targets are costly, computational methods are preferred for extracting potential miRNA-mRNA fragment binding pairs first. However, existing prediction tools can have significant false positives due to the prevalent noncanonical miRNA binding behaviors and the information-biased training negative sets that were used while constructing these tools. To overcome these obstacles, we first prepared an information-balanced miRNA binding pair ground-truth data set. A miRNA-mRNA interaction-aware model was then designed to help identify miRNA binding events. On the test set, our model (auROC = 94.4%) outperformed existing models by at least 2.8% in auROC. Furthermore, we showed that this model can suggest potential binding patterns for miRNA-mRNA sequence interacting pairs. Finally, we made the prepared data sets and the designed model available at http://cosbi2.ee.ncku.edu.tw/mirna_binding/download.
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Affiliation(s)
- Tzu-Hsien Yang
- Department of Biomedical Engineering, National Cheng Kung University, No.1, University Road, Tainan 701, Taiwan
- Medical Device Innovation Center, National Cheng Kung University, No.1 University Road, Tainan 701, Taiwan
| | - Jhih-Cheng Chen
- Department of Electrical Engineering, National Cheng Kung University, No.1, University Road, Tainan 701, Taiwan
| | - Yuan-Han Lee
- Department of Electrical Engineering, National Cheng Kung University, No.1, University Road, Tainan 701, Taiwan
| | - Shang-Yi Lu
- Department of Electrical Engineering, National Cheng Kung University, No.1, University Road, Tainan 701, Taiwan
| | - Sheng-Hang Wu
- Department of Information Management, National University of Kaohsiung, Kaohsiung University Rd, Kaohsiung 811, Taiwan
| | - Fang-Yuan Chang
- Department of Information Management, National University of Kaohsiung, Kaohsiung University Rd, Kaohsiung 811, Taiwan
| | - Yan-Cheng Huang
- Department of Electrical Engineering, National Cheng Kung University, No.1, University Road, Tainan 701, Taiwan
| | - Mei-Hsien Lee
- Department of Mathematics, University of Taipei, No.1, Ai-Guo West Road, Taipei 100234, Taiwan
| | - Yan-Yuan Tseng
- Center for Molecular Medicine and Genetics, Wayne State University, School of Medicine, Detroit, Michigan 48201, United States
| | - Wei-Sheng Wu
- Department of Electrical Engineering, National Cheng Kung University, No.1, University Road, Tainan 701, Taiwan
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6
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Cordoba-Caballero J, Perkins JR, García-Criado F, Gallego D, Navarro-Sánchez A, Moreno-Estellés M, Garcés C, Bonet F, Romá-Mateo C, Toro R, Perez B, Sanz P, Kohl M, Rojano E, Seoane P, Ranea JAG. Exploring miRNA-target gene pair detection in disease with coRmiT. Brief Bioinform 2024; 25:bbae060. [PMID: 38436559 PMCID: PMC10939301 DOI: 10.1093/bib/bbae060] [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: 09/21/2023] [Revised: 12/14/2023] [Accepted: 01/10/2024] [Indexed: 03/05/2024] Open
Abstract
A wide range of approaches can be used to detect micro RNA (miRNA)-target gene pairs (mTPs) from expression data, differing in the ways the gene and miRNA expression profiles are calculated, combined and correlated. However, there is no clear consensus on which is the best approach across all datasets. Here, we have implemented multiple strategies and applied them to three distinct rare disease datasets that comprise smallRNA-Seq and RNA-Seq data obtained from the same samples, obtaining mTPs related to the disease pathology. All datasets were preprocessed using a standardized, freely available computational workflow, DEG_workflow. This workflow includes coRmiT, a method to compare multiple strategies for mTP detection. We used it to investigate the overlap of the detected mTPs with predicted and validated mTPs from 11 different databases. Results show that there is no clear best strategy for mTP detection applicable to all situations. We therefore propose the integration of the results of the different strategies by selecting the one with the highest odds ratio for each miRNA, as the optimal way to integrate the results. We applied this selection-integration method to the datasets and showed it to be robust to changes in the predicted and validated mTP databases. Our findings have important implications for miRNA analysis. coRmiT is implemented as part of the ExpHunterSuite Bioconductor package available from https://bioconductor.org/packages/ExpHunterSuite.
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Affiliation(s)
- Jose Cordoba-Caballero
- Departamento de Biología Molecular y Bioquímica, Facultad de Ciencias, Universidad de Málaga, Bulevar Louis Pasteur, 31, Málaga, 29010, Spain
- Research Unit, Biomedical Research and Innovation Institute of Cádiz (INiBICA), Puerta del Mar University Hospital, Cádiz, Spain
| | - James R Perkins
- Departamento de Biología Molecular y Bioquímica, Facultad de Ciencias, Universidad de Málaga, Bulevar Louis Pasteur, 31, Málaga, 29010, Spain
- Instituto de Investigación Biomédica de Málaga y Plataforma en Nanomedicina (IBIMA-Plataforma BIONAND), C/ Severo Ochoa, 35, Parque Tecnológico de Andalucía (PTA), Campanillas, Málaga, 29590, Spain
| | - Federico García-Criado
- Departamento de Biología Molecular y Bioquímica, Facultad de Ciencias, Universidad de Málaga, Bulevar Louis Pasteur, 31, Málaga, 29010, Spain
| | - Diana Gallego
- CIBER de Enfermedades Raras (CIBERER), Avda. Monforte de Lemos, 3-5, Pabellón 11, Planta 0, Madrid, 28029, Spain
- Centro de Diagnóstico de Enfermedades Moleculares, Centro de Biología Molecular-SO UAM-CSIC, Universidad Autónoma de Madrid, Campus de Cantoblanco, Madrid, Spain
- Instituto de Investigación Sanitaria IdiPaZ, Madrid, Spain
| | - Alicia Navarro-Sánchez
- CIBER de Enfermedades Raras (CIBERER), Avda. Monforte de Lemos, 3-5, Pabellón 11, Planta 0, Madrid, 28029, Spain
- Departament de Fisiologia, Facultat de Medicina i Odontologia, Universitat de València, Av. Blasco Ibáñez 15, 46010, València, Spain
| | - Mireia Moreno-Estellés
- CIBER de Enfermedades Raras (CIBERER), Avda. Monforte de Lemos, 3-5, Pabellón 11, Planta 0, Madrid, 28029, Spain
- Consejo Superior de Investigaciones Científicas, Instituto de Biomedicina de Valencia, Jaime Roig 11, 46010, Valencia, Spain
| | - Concepción Garcés
- CIBER de Enfermedades Raras (CIBERER), Avda. Monforte de Lemos, 3-5, Pabellón 11, Planta 0, Madrid, 28029, Spain
- Departament de Fisiologia, Facultat de Medicina i Odontologia, Universitat de València, Av. Blasco Ibáñez 15, 46010, València, Spain
| | - Fernando Bonet
- Research Unit, Biomedical Research and Innovation Institute of Cádiz (INiBICA), Puerta del Mar University Hospital, Cádiz, Spain
- Medicine Department, School of Medicine, University of Cádiz, Cádiz, Spain
| | - Carlos Romá-Mateo
- CIBER de Enfermedades Raras (CIBERER), Avda. Monforte de Lemos, 3-5, Pabellón 11, Planta 0, Madrid, 28029, Spain
- Departament de Fisiologia, Facultat de Medicina i Odontologia, Universitat de València, Av. Blasco Ibáñez 15, 46010, València, Spain
- Incliva Biomedical Research Institute, 46010, València, Spain
| | - Rocio Toro
- Research Unit, Biomedical Research and Innovation Institute of Cádiz (INiBICA), Puerta del Mar University Hospital, Cádiz, Spain
- Medicine Department, School of Medicine, University of Cádiz, Cádiz, Spain
| | - Belén Perez
- CIBER de Enfermedades Raras (CIBERER), Avda. Monforte de Lemos, 3-5, Pabellón 11, Planta 0, Madrid, 28029, Spain
- Centro de Diagnóstico de Enfermedades Moleculares, Centro de Biología Molecular-SO UAM-CSIC, Universidad Autónoma de Madrid, Campus de Cantoblanco, Madrid, Spain
- Instituto de Investigación Sanitaria IdiPaZ, Madrid, Spain
| | - Pascual Sanz
- CIBER de Enfermedades Raras (CIBERER), Avda. Monforte de Lemos, 3-5, Pabellón 11, Planta 0, Madrid, 28029, Spain
- Consejo Superior de Investigaciones Científicas, Instituto de Biomedicina de Valencia, Jaime Roig 11, 46010, Valencia, Spain
| | - Matthias Kohl
- Faculty of Medical and Life Sciences, Furtwangen University, Germany
| | - Elena Rojano
- Departamento de Biología Molecular y Bioquímica, Facultad de Ciencias, Universidad de Málaga, Bulevar Louis Pasteur, 31, Málaga, 29010, Spain
- Instituto de Investigación Biomédica de Málaga y Plataforma en Nanomedicina (IBIMA-Plataforma BIONAND), C/ Severo Ochoa, 35, Parque Tecnológico de Andalucía (PTA), Campanillas, Málaga, 29590, Spain
| | - Pedro Seoane
- Departamento de Biología Molecular y Bioquímica, Facultad de Ciencias, Universidad de Málaga, Bulevar Louis Pasteur, 31, Málaga, 29010, Spain
- Instituto de Investigación Biomédica de Málaga y Plataforma en Nanomedicina (IBIMA-Plataforma BIONAND), C/ Severo Ochoa, 35, Parque Tecnológico de Andalucía (PTA), Campanillas, Málaga, 29590, Spain
- CIBER de Enfermedades Raras (CIBERER), Avda. Monforte de Lemos, 3-5, Pabellón 11, Planta 0, Madrid, 28029, Spain
| | - Juan A G Ranea
- Departamento de Biología Molecular y Bioquímica, Facultad de Ciencias, Universidad de Málaga, Bulevar Louis Pasteur, 31, Málaga, 29010, Spain
- Instituto de Investigación Biomédica de Málaga y Plataforma en Nanomedicina (IBIMA-Plataforma BIONAND), C/ Severo Ochoa, 35, Parque Tecnológico de Andalucía (PTA), Campanillas, Málaga, 29590, Spain
- CIBER de Enfermedades Raras (CIBERER), Avda. Monforte de Lemos, 3-5, Pabellón 11, Planta 0, Madrid, 28029, Spain
- Instituto Nacional de Bioinformática (INB/ELIXIR-ES), Instituto de Salud Carlos III (ISCIII), C/ Sinesio Delgado, 4, Madrid, 28029, Spain
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7
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Zheng H, Wang S, Li X, Hu H. A computational modeling of pri-miRNA expression. PLoS One 2024; 19:e0290768. [PMID: 38165860 PMCID: PMC10760784 DOI: 10.1371/journal.pone.0290768] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2022] [Accepted: 08/15/2023] [Indexed: 01/04/2024] Open
Abstract
MicroRNAs (miRNAs) play crucial roles in gene regulation. Most studies focus on mature miRNAs, which leaves many unknowns about primary miRNAs (pri-miRNAs). To fill the gap, we attempted to model the expression of pri-miRNAs in 1829 primary cell types, cell lines, and tissues in this study. We demonstrated that the expression of pri-miRNAs can be modeled well by the expression of specific sets of mRNAs, which we termed their associated mRNAs. These associated mRNAs differ from their corresponding target mRNAs and are enriched with specific functions. Most associated mRNAs of a miRNA are shared across conditions, while on average, about one-fifth of the associated mRNAs are condition-specific. Our study shed new light on understanding miRNA biogenesis and general gene transcriptional regulation.
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Affiliation(s)
- Hansi Zheng
- Department of Computer Science, University of Central Florida, Orlando, Florida, United States of America
| | - Saidi Wang
- Department of Computer Science, University of Central Florida, Orlando, Florida, United States of America
| | - Xiaoman Li
- Burnett School of Biomedical Science, College of Medicine, University of Central Florida, Orlando, Florida, United States of America
| | - Haiyan Hu
- Department of Computer Science, University of Central Florida, Orlando, Florida, United States of America
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8
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Using Attribution Sequence Alignment to Interpret Deep Learning Models for miRNA Binding Site Prediction. BIOLOGY 2023; 12:biology12030369. [PMID: 36979061 PMCID: PMC10045089 DOI: 10.3390/biology12030369] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/15/2022] [Revised: 02/21/2023] [Accepted: 02/24/2023] [Indexed: 03/03/2023]
Abstract
MicroRNAs (miRNAs) are small non-coding RNAs that play a central role in the post-transcriptional regulation of biological processes. miRNAs regulate transcripts through direct binding involving the Argonaute protein family. The exact rules of binding are not known, and several in silico miRNA target prediction methods have been developed to date. Deep learning has recently revolutionized miRNA target prediction. However, the higher predictive power comes with a decreased ability to interpret increasingly complex models. Here, we present a novel interpretation technique, called attribution sequence alignment, for miRNA target site prediction models that can interpret such deep learning models on a two-dimensional representation of miRNA and putative target sequence. Our method produces a human readable visual representation of miRNA:target interactions and can be used as a proxy for the further interpretation of biological concepts learned by the neural network. We demonstrate applications of this method in the clustering of experimental data into binding classes, as well as using the method to narrow down predicted miRNA binding sites on long transcript sequences. Importantly, the presented method works with any neural network model trained on a two-dimensional representation of interactions and can be easily extended to further domains such as protein–protein interactions.
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9
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Hwang H, Chang HR, Baek D. Determinants of Functional MicroRNA Targeting. Mol Cells 2023; 46:21-32. [PMID: 36697234 PMCID: PMC9880601 DOI: 10.14348/molcells.2023.2157] [Citation(s) in RCA: 4] [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: 10/14/2022] [Revised: 11/09/2022] [Accepted: 11/15/2022] [Indexed: 01/27/2023] Open
Abstract
MicroRNAs (miRNAs) play cardinal roles in regulating biological pathways and processes, resulting in significant physiological effects. To understand the complex regulatory network of miRNAs, previous studies have utilized massivescale datasets of miRNA targeting and attempted to computationally predict the functional targets of miRNAs. Many miRNA target prediction tools have been developed and are widely used by scientists from various fields of biology and medicine. Most of these tools consider seed pairing between miRNAs and their mRNA targets and additionally consider other determinants to improve prediction accuracy. However, these tools exhibit limited prediction accuracy and high false positive rates. The utilization of additional determinants, such as RNA modifications and RNA-binding protein binding sites, may further improve miRNA target prediction. In this review, we discuss the determinants of functional miRNA targeting that are currently used in miRNA target prediction and the potentially predictive but unappreciated determinants that may improve prediction accuracy.
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Affiliation(s)
- Hyeonseo Hwang
- School of Biological Sciences, Seoul National University, Seoul 08826, Korea
| | - Hee Ryung Chang
- School of Biological Sciences, Seoul National University, Seoul 08826, Korea
| | - Daehyun Baek
- School of Biological Sciences, Seoul National University, Seoul 08826, Korea
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