1
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Polo-Generelo S, Rodríguez-Mateo C, Torres B, Pintor-Tortolero J, Guerrero-Martínez JA, König J, Vázquez J, Bonzón-Kulichenco E, Padillo-Ruiz J, de la Portilla F, Reyes JC, Pintor-Toro JA. Serpine1 mRNA confers mesenchymal characteristics to the cell and promotes CD8+ T cells exclusion from colon adenocarcinomas. Cell Death Discov 2024; 10:116. [PMID: 38448406 PMCID: PMC10917750 DOI: 10.1038/s41420-024-01886-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2023] [Revised: 02/20/2024] [Accepted: 02/23/2024] [Indexed: 03/08/2024] Open
Abstract
Serine protease inhibitor clade E member 1 (SERPINE1) inhibits extracellular matrix proteolysis and cell detachment. However, SERPINE1 expression also promotes tumor progression and plays a crucial role in metastasis. Here, we solve this apparent paradox and report that Serpine1 mRNA per se, independent of its protein-coding function, confers mesenchymal properties to the cell, promoting migration, invasiveness, and resistance to anoikis and increasing glycolytic activity by sequestering miRNAs. Expression of Serpine1 mRNA upregulates the expression of the TRA2B splicing factor without affecting its mRNA levels. Through transcriptional profiling, we found that Serpine1 mRNA expression downregulates through TRA2B the expression of genes involved in the immune response. Analysis of human colon tumor samples showed an inverse correlation between SERPINE1 mRNA expression and CD8+ T cell infiltration, unveiling the potential value of SERPINE1 mRNA as a promising therapeutic target for colon tumors.
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Affiliation(s)
- Salvador Polo-Generelo
- Department of Cell Signaling, Centro Andaluz de Biología Molecular y Medicina Regenerativa (CABIMER-CSIC), 41092, Sevilla, Spain
| | - Cristina Rodríguez-Mateo
- Department of Cell Signaling, Centro Andaluz de Biología Molecular y Medicina Regenerativa (CABIMER-CSIC), 41092, Sevilla, Spain
| | - Belén Torres
- Department of Cell Signaling, Centro Andaluz de Biología Molecular y Medicina Regenerativa (CABIMER-CSIC), 41092, Sevilla, Spain
| | - José Pintor-Tortolero
- Colorectal Surgery Unit, Department of General and Digestive Surgery, Virgen del Rocío University Hospital, IBIS, CSIC, University of Sevilla, Sevilla, Spain
| | - José A Guerrero-Martínez
- Department of Cell Signaling, Centro Andaluz de Biología Molecular y Medicina Regenerativa (CABIMER-CSIC), 41092, Sevilla, Spain
| | - Julian König
- Institute of Molecular Biology (IMB), Ackermannweg 4, 55128, Mainz, Germany
| | - Jesús Vázquez
- Cardiovascular Proteomics, Centro Nacional de Investigaciones Cardiovasculares (CNIC), 28029, Madrid, Spain
| | - Elena Bonzón-Kulichenco
- Facultad de Ciencias Ambientales y Bioquímica, Universidad de Castilla-La Mancha, Toledo, Spain
| | - Javier Padillo-Ruiz
- Hepatobiliary Surgery Unit, Department of General and Digestive Surgery, Virgen del Rocío University Hospital, IBIS, CSIC, University of Sevilla, Sevilla, Spain
| | - Fernando de la Portilla
- Colorectal Surgery Unit, Department of General and Digestive Surgery, Virgen del Rocío University Hospital, IBIS, CSIC, University of Sevilla, Sevilla, Spain
| | - José C Reyes
- Department of Cell Signaling, Centro Andaluz de Biología Molecular y Medicina Regenerativa (CABIMER-CSIC), 41092, Sevilla, Spain
| | - José A Pintor-Toro
- Department of Cell Signaling, Centro Andaluz de Biología Molecular y Medicina Regenerativa (CABIMER-CSIC), 41092, Sevilla, Spain.
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2
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Non-coding RNAs in human health and disease: potential function as biomarkers and therapeutic targets. Funct Integr Genomics 2023; 23:33. [PMID: 36625940 PMCID: PMC9838419 DOI: 10.1007/s10142-022-00947-4] [Citation(s) in RCA: 38] [Impact Index Per Article: 38.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2022] [Revised: 12/14/2022] [Accepted: 12/15/2022] [Indexed: 01/11/2023]
Abstract
Human diseases have been a critical threat from the beginning of human history. Knowing the origin, course of action and treatment of any disease state is essential. A microscopic approach to the molecular field is a more coherent and accurate way to explore the mechanism, progression, and therapy with the introduction and evolution of technology than a macroscopic approach. Non-coding RNAs (ncRNAs) play increasingly important roles in detecting, developing, and treating all abnormalities related to physiology, pathology, genetics, epigenetics, cancer, and developmental diseases. Noncoding RNAs are becoming increasingly crucial as powerful, multipurpose regulators of all biological processes. Parallel to this, a rising amount of scientific information has revealed links between abnormal noncoding RNA expression and human disorders. Numerous non-coding transcripts with unknown functions have been found in addition to advancements in RNA-sequencing methods. Non-coding linear RNAs come in a variety of forms, including circular RNAs with a continuous closed loop (circRNA), long non-coding RNAs (lncRNA), and microRNAs (miRNA). This comprises specific information on their biogenesis, mode of action, physiological function, and significance concerning disease (such as cancer or cardiovascular diseases and others). This study review focuses on non-coding RNA as specific biomarkers and novel therapeutic targets.
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3
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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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4
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Serra F, Bottini S, Pratella D, Stathopoulou MG, Sebille W, El-Hami L, Repetto E, Mauduit C, Benahmed M, Grandjean V, Trabucchi M. Systemic CLIP-seq analysis and game theory approach to model microRNA mode of binding. Nucleic Acids Res 2021; 49:e66. [PMID: 33823551 PMCID: PMC8216473 DOI: 10.1093/nar/gkab198] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2020] [Revised: 02/19/2021] [Accepted: 03/10/2021] [Indexed: 12/18/2022] Open
Abstract
microRNAs (miRNAs) associate with Ago proteins to post-transcriptionally silence gene expression by targeting mRNAs. To characterize the modes of miRNA-binding, we developed a novel computational framework, called optiCLIP, which considers the reproducibility of the identified peaks among replicates based on the peak overlap. We identified 98 999 binding sites for mouse and human miRNAs, from eleven Ago2 CLIP-seq datasets. Clustering the binding preferences, we found heterogeneity of the mode of binding for different miRNAs. Finally, we set up a quantitative model, named miRgame, based on an adaptation of the game theory. We have developed a new algorithm to translate the miRgame into a score that corresponds to a miRNA degree of occupancy for each Ago2 peak. The degree of occupancy summarizes the number of miRNA-binding sites and miRNAs targeting each binding site, and binding energy of each miRNA::RNA heteroduplex in each peak. Ago peaks were stratified accordingly to the degree of occupancy. Target repression correlates with higher score of degree of occupancy and number of miRNA-binding sites within each Ago peak. We validated the biological performance of our new method on miR-155-5p. In conclusion, our data demonstrate that miRNA-binding sites within each Ago2 CLIP-seq peak synergistically interplay to enhance target repression.
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Affiliation(s)
- Fabrizio Serra
- Inserm U1065, C3M, Team Control of Gene Expression (10), Nice, France.,Université Côte d'Azur, Inserm, C3M, Nice, France
| | - Silvia Bottini
- Inserm U1065, C3M, Team Control of Gene Expression (10), Nice, France.,Université Côte d'Azur, Inserm, C3M, Nice, France
| | - David Pratella
- Inserm U1065, C3M, Team Control of Gene Expression (10), Nice, France.,Université Côte d'Azur, Inserm, C3M, Nice, France
| | - Maria G Stathopoulou
- Inserm U1065, C3M, Team Control of Gene Expression (10), Nice, France.,Université Côte d'Azur, Inserm, C3M, Nice, France
| | - Wanda Sebille
- Inserm U1065, C3M, Team Control of Gene Expression (10), Nice, France.,Université Côte d'Azur, Inserm, C3M, Nice, France
| | - Loubna El-Hami
- Inserm U1065, C3M, Team Control of Gene Expression (10), Nice, France.,Université Côte d'Azur, Inserm, C3M, Nice, France
| | - Emanuela Repetto
- Inserm U1065, C3M, Team Control of Gene Expression (10), Nice, France.,Université Côte d'Azur, Inserm, C3M, Nice, France
| | - Claire Mauduit
- Inserm U1065, C3M, Team Control of Gene Expression (10), Nice, France.,Université Côte d'Azur, Inserm, C3M, Nice, France
| | - Mohamed Benahmed
- Inserm U1065, C3M, Team Control of Gene Expression (10), Nice, France.,Université Côte d'Azur, Inserm, C3M, Nice, France
| | - Valerie Grandjean
- Inserm U1065, C3M, Team Control of Gene Expression (10), Nice, France.,Université Côte d'Azur, Inserm, C3M, Nice, France
| | - Michele Trabucchi
- Inserm U1065, C3M, Team Control of Gene Expression (10), Nice, France.,Université Côte d'Azur, Inserm, C3M, Nice, France
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5
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Vega-Tapia F, Peñaloza E, Krause BJ. Specific arterio-venous transcriptomic and ncRNA-RNA interactions in human umbilical endothelial cells: A meta-analysis. iScience 2021; 24:102675. [PMID: 34222842 PMCID: PMC8243012 DOI: 10.1016/j.isci.2021.102675] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2021] [Revised: 04/21/2021] [Accepted: 05/27/2021] [Indexed: 01/06/2023] Open
Abstract
Whether arterial-venous differences of primary endothelial cells commonly used for vascular research are preserved in vitro remains under debate. To address this issue, a meta-analysis of Affymetrix transcriptomic data sets from human umbilical artery (HUAECs) and vein (HUVEC) endothelial cells was performed. The meta-analysis showed 2,742 transcripts differentially expressed (false discovery rate <0.05), of which 78% were downregulated in HUVECs. Comparisons with RNA-seq data sets showed high levels of agreement and correlation (p < 0.0001), identifying 84 arterial-venous identity markers. Functional analysis revealed enrichment of key vascular processes in HUAECs/HUVECs, including nitric oxide- (NO) and hypoxia-related genes, as well as differences in miRNA- and ncRNA-mRNA interaction profiles. A proof of concept of these findings in primary cells exposed to hypoxia in vitro and in vivo confirmed the arterial-venous differences in NO-related genes and miRNAs. Altogether, these data defined a cross-platform arterial-venous transcript profile for cultured HUAEC-HUVEC and support a preserved identity involving key vascular pathways post-transcriptionally regulated in vitro. Transcriptional differences among HUAEC and HUVEC are preserved in culture These differences occur even after correcting for experimental conditions The heterogenous regulation affects NO- and hypoxia-related genes Cell-specific ncRNA/mRNA interactions are found
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Affiliation(s)
- Fabian Vega-Tapia
- Instituto de Ciencias de la Salud, Universidad de O'Higgins, Avenida Libertador Bernardo O'Higgins 611, Rancagua, Chile
| | - Estefania Peñaloza
- Instituto de Ciencias de la Salud, Universidad de O'Higgins, Avenida Libertador Bernardo O'Higgins 611, Rancagua, Chile
| | - Bernardo J Krause
- Instituto de Ciencias de la Salud, Universidad de O'Higgins, Avenida Libertador Bernardo O'Higgins 611, Rancagua, Chile
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6
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Heyl F, Maticzka D, Uhl M, Backofen R. Galaxy CLIP-Explorer: a web server for CLIP-Seq data analysis. Gigascience 2020; 9:giaa108. [PMID: 33179042 PMCID: PMC7657819 DOI: 10.1093/gigascience/giaa108] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2019] [Revised: 03/01/2020] [Indexed: 12/31/2022] Open
Abstract
BACKGROUND Post-transcriptional regulation via RNA-binding proteins plays a fundamental role in every organism, but the regulatory mechanisms lack important understanding. Nevertheless, they can be elucidated by cross-linking immunoprecipitation in combination with high-throughput sequencing (CLIP-Seq). CLIP-Seq answers questions about the functional role of an RNA-binding protein and its targets by determining binding sites on a nucleotide level and associated sequence and structural binding patterns. In recent years the amount of CLIP-Seq data skyrocketed, urging the need for an automatic data analysis that can deal with different experimental set-ups. However, noncanonical data, new protocols, and a huge variety of tools, especially for peak calling, made it difficult to define a standard. FINDINGS CLIP-Explorer is a flexible and reproducible data analysis pipeline for iCLIP data that supports for the first time eCLIP, FLASH, and uvCLAP data. Individual steps like peak calling can be changed to adapt to different experimental settings. We validate CLIP-Explorer on eCLIP data, finding similar or nearly identical motifs for various proteins in comparison with other databases. In addition, we detect new sequence motifs for PTBP1 and U2AF2. Finally, we optimize the peak calling with 3 different peak callers on RBFOX2 data, discuss the difficulty of the peak-calling step, and give advice for different experimental set-ups. CONCLUSION CLIP-Explorer finally fills the demand for a flexible CLIP-Seq data analysis pipeline that is applicable to the up-to-date CLIP protocols. The article further shows the limitations of current peak-calling algorithms and the importance of a robust peak detection.
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Affiliation(s)
- Florian Heyl
- Bioinformatics Group, Department of Computer Science, University of Freiburg, Georges-Köhler-Allee 106, 79110 Freiburg, Germany
| | - Daniel Maticzka
- Bioinformatics Group, Department of Computer Science, University of Freiburg, Georges-Köhler-Allee 106, 79110 Freiburg, Germany
| | - Michael Uhl
- Bioinformatics Group, Department of Computer Science, University of Freiburg, Georges-Köhler-Allee 106, 79110 Freiburg, Germany
| | - Rolf Backofen
- Bioinformatics Group, Department of Computer Science, University of Freiburg, Georges-Köhler-Allee 106, 79110 Freiburg, Germany
- Signalling Research Centres BIOSS and CIBSS, University of Freiburg, Schaenzlestr. 18, 79104 Freiburg, Germany
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7
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Cui J, Shu J. Circulating microRNA trafficking and regulation: computational principles and practice. Brief Bioinform 2020; 21:1313-1326. [PMID: 31504144 PMCID: PMC7412956 DOI: 10.1093/bib/bbz079] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2019] [Revised: 06/07/2019] [Accepted: 06/07/2019] [Indexed: 01/18/2023] Open
Abstract
Rapid advances in genomics discovery tools and a growing realization of microRNA's implication in intercellular communication have led to a proliferation of studies of circulating microRNA sorting and regulation across cells and different species. Although sometimes, reaching controversial scientific discoveries and conclusions, these studies have yielded new insights in the functional roles of circulating microRNA and a plethora of analytical methods and tools. Here, we consider this body of work in light of key computational principles underpinning discovery of circulating microRNAs in terms of their sorting and targeting, with the goal of providing practical guidance for applications that is focused on the design and analysis of circulating microRNAs and their context-dependent regulation. We survey a broad range of informatics methods and tools that are available to the researcher, discuss their key features, applications and various unsolved problems and close this review with prospects and broader implication of this field.
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Affiliation(s)
- Juan Cui
- Systems Biology and Biomedical Informatics Laboratory, Department of Computer Science and Engineering, University of Nebraska-Lincoln, Lincoln, NE, USA
| | - Jiang Shu
- Systems Biology and Biomedical Informatics Laboratory, Department of Computer Science and Engineering, University of Nebraska-Lincoln, Lincoln, NE, USA
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8
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Chen L, Heikkinen L, Wang C, Yang Y, Sun H, Wong G. Trends in the development of miRNA bioinformatics tools. Brief Bioinform 2019; 20:1836-1852. [PMID: 29982332 PMCID: PMC7414524 DOI: 10.1093/bib/bby054] [Citation(s) in RCA: 326] [Impact Index Per Article: 65.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2018] [Revised: 05/18/2018] [Indexed: 12/13/2022] Open
Abstract
MicroRNAs (miRNAs) are small noncoding RNAs that regulate gene expression via recognition of cognate sequences and interference of transcriptional, translational or epigenetic processes. Bioinformatics tools developed for miRNA study include those for miRNA prediction and discovery, structure, analysis and target prediction. We manually curated 95 review papers and ∼1000 miRNA bioinformatics tools published since 2003. We classified and ranked them based on citation number or PageRank score, and then performed network analysis and text mining (TM) to study the miRNA tools development trends. Five key trends were observed: (1) miRNA identification and target prediction have been hot spots in the past decade; (2) manual curation and TM are the main methods for collecting miRNA knowledge from literature; (3) most early tools are well maintained and widely used; (4) classic machine learning methods retain their utility; however, novel ones have begun to emerge; (5) disease-associated miRNA tools are emerging. Our analysis yields significant insight into the past development and future directions of miRNA tools.
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Affiliation(s)
- Liang Chen
- Faculty of Health Sciences, University of Macau, Taipa, Macau S.A.R, China
| | - Liisa Heikkinen
- Faculty of Health Sciences, University of Macau, Taipa, Macau S.A.R, China
| | - Changliang Wang
- Faculty of Health Sciences, University of Macau, Taipa, Macau S.A.R, China
| | - Yang Yang
- Faculty of Health Sciences, University of Macau, Taipa, Macau S.A.R, China
| | - Huiyan Sun
- Key Laboratory of Symbolic Computation and Knowledge Engineering of the Ministry of Education, College of Computer Science and Technology, Jilin University, Changchun, China
| | - Garry Wong
- Faculty of Health Sciences, University of Macau, Taipa, Macau S.A.R, China
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9
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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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10
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Park S, Ahn SH, Cho ES, Cho YK, Jang ES, Chi SW. CLIPick: a sensitive peak caller for expression-based deconvolution of HITS-CLIP signals. Nucleic Acids Res 2019; 46:11153-11168. [PMID: 30329090 PMCID: PMC6265468 DOI: 10.1093/nar/gky917] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2018] [Accepted: 10/09/2018] [Indexed: 12/12/2022] Open
Abstract
High-throughput sequencing of RNAs isolated by crosslinking immunoprecipitation (HITS-CLIP, also called CLIP-Seq) has been used to map global RNA–protein interactions. However, a critical caveat of HITS-CLIP results is that they contain non-linear background noise—different extent of non-specific interactions caused by individual transcript abundance—that has been inconsiderately normalized, resulting in sacrifice of sensitivity. To properly deconvolute RNA–protein interactions, we have implemented CLIPick, a flexible peak calling pipeline for analyzing HITS-CLIP data, which statistically determines the signal-to-noise ratio for each transcript based on the expression-dependent background simulation. Comprising of streamlined Python modules with an easy-to-use standalone graphical user interface, CLIPick robustly identifies significant peaks and quantitatively defines footprint regions within which RNA–protein interactions were occurred. CLIPick outperforms other peak callers in accuracy and sensitivity, selecting the largest number of peaks particularly in lowly expressed transcripts where such marginal signals are hard to discriminate. Specifically, the application of CLIPick to Argonaute (Ago) HITS-CLIP data were sensitive enough to uncover extended features of microRNA target sites, and these sites were experimentally validated. CLIPick enables to resolve critical interactions in a wide spectrum of transcript levels and extends the scope of HITS-CLIP analysis. CLIPick is available at: http://clip.korea.ac.kr/clipick/
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Affiliation(s)
- Sihyung Park
- Division of Life Sciences, College of Life Sciences and Biotechnology, Korea University, Seoul 02841, Korea
| | - Seung Hyun Ahn
- Department of Life Sciences, Korea University, Seoul 02841, Korea
| | - Eun Sol Cho
- Division of Life Sciences, College of Life Sciences and Biotechnology, Korea University, Seoul 02841, Korea
| | - You Kyung Cho
- Department of Life Sciences, Korea University, Seoul 02841, Korea
| | - Eun-Sook Jang
- Department of Life Sciences, Korea University, Seoul 02841, Korea.,EncodeGEN Co. Ltd., Seoul 06329, Korea
| | - Sung Wook Chi
- Division of Life Sciences, College of Life Sciences and Biotechnology, Korea University, Seoul 02841, Korea.,Department of Life Sciences, Korea University, Seoul 02841, Korea
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11
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Chen X, Castro SA, Liu Q, Hu W, Zhang S. Practical considerations on performing and analyzing CLIP-seq experiments to identify transcriptomic-wide RNA-protein interactions. Methods 2019; 155:49-57. [PMID: 30527764 PMCID: PMC6387833 DOI: 10.1016/j.ymeth.2018.12.002] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2018] [Revised: 11/27/2018] [Accepted: 12/03/2018] [Indexed: 10/27/2022] Open
Abstract
RNA-binding proteins are important players in post-transcriptional regulation, such as modulating mRNA splicing, translation, and degradation under diverse biological settings. Identifying and characterizing the RNA substrates is a critical step in deciphering the function and molecular mechanisms of the target RNA-binding proteins. High-throughput sequencing of the RNA fragments isolated by crosslinking immunoprecipitation (CLIP-seq) is one of the standard techniques to identify the in vivo transcriptome-wide binding sites of the target RNA-binding protein. This method is widely used in functional and mechanistic characterizations of RNA-binding proteins. In this review, we provide several practical considerations on performing and analyzing CLIP-seq experiments. Particularly, we focus on how to perform CLIP-seq experiments on endogenous RNA-binding proteins. In addition, we provide a practical summary on how to choose and use computational pipelines from an increasing number of computational methods and packages that are available for analyzing the sequencing datasets from the CLIP-seq experiments. We hope these practical considerations will facilitate experimental biologists in performing and analyzing CLIP-seq experiment to obtain biologically relevant mechanistic insights.
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Affiliation(s)
- Xiaoli Chen
- Department of Computer Science, University of Central Florida, Orlando, FL 32816, USA
| | - Sarah A Castro
- Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, MN 55905, USA
| | - Qiuying Liu
- Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, MN 55905, USA
| | - Wenqian Hu
- Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, MN 55905, USA.
| | - Shaojie Zhang
- Department of Computer Science, University of Central Florida, Orlando, FL 32816, USA.
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12
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The Nefarious Nexus of Noncoding RNAs in Cancer. Int J Mol Sci 2018; 19:ijms19072072. [PMID: 30018188 PMCID: PMC6073630 DOI: 10.3390/ijms19072072] [Citation(s) in RCA: 41] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2018] [Accepted: 07/12/2018] [Indexed: 02/07/2023] Open
Abstract
The past decade has witnessed enormous progress, and has seen the noncoding RNAs (ncRNAs) turn from the so-called dark matter RNA to critical functional molecules, influencing most physiological processes in development and disease contexts. Many ncRNAs interact with each other and are part of networks that influence the cell transcriptome and proteome and consequently the outcome of biological processes. The regulatory circuits controlled by ncRNAs have become increasingly more relevant in cancer. Further understanding of these complex network interactions and how ncRNAs are regulated, is paving the way for the identification of better therapeutic strategies in cancer.
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Maticzka D, Ilik IA, Aktas T, Backofen R, Akhtar A. uvCLAP is a fast and non-radioactive method to identify in vivo targets of RNA-binding proteins. Nat Commun 2018; 9:1142. [PMID: 29559621 PMCID: PMC5861125 DOI: 10.1038/s41467-018-03575-4] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2017] [Accepted: 02/26/2018] [Indexed: 01/24/2023] Open
Abstract
RNA-binding proteins (RBPs) play important and essential roles in eukaryotic gene expression regulating splicing, localization, translation, and stability of mRNAs. We describe ultraviolet crosslinking and affinity purification (uvCLAP), an easy-to-use, robust, reproducible, and high-throughput method to determine in vivo targets of RBPs. uvCLAP is fast and does not rely on radioactive labeling of RNA. We investigate binding of 15 RBPs from fly, mouse, and human cells to test the method's performance and applicability. Multiplexing of signal and control libraries enables straightforward comparison of samples. Experiments for most proteins achieve high enrichment of signal over background. A point mutation and a natural splice isoform that change the RBP subcellular localization dramatically alter target selection without changing the targeted RNA motif, showing that compartmentalization of RBPs can be used as an elegant means to generate RNA target specificity.
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Affiliation(s)
- Daniel Maticzka
- Bioinformatics Group, Department of Computer Science, University of Freiburg, Georges-Koehler-Allee 106, 79110, Freiburg, Germany
| | - Ibrahim Avsar Ilik
- Max Planck Institute of Immunobiology and Epigenetics, Stuebeweg 51, 79108, Freiburg, Germany
| | - Tugce Aktas
- Max Planck Institute of Immunobiology and Epigenetics, Stuebeweg 51, 79108, Freiburg, Germany
| | - Rolf Backofen
- Bioinformatics Group, Department of Computer Science, University of Freiburg, Georges-Koehler-Allee 106, 79110, Freiburg, Germany.
- Centre for Biological Signalling Studies (BIOSS), University of Freiburg, Schaenzlestr. 18, 79104, Freiburg, Germany.
| | - Asifa Akhtar
- Max Planck Institute of Immunobiology and Epigenetics, Stuebeweg 51, 79108, Freiburg, Germany.
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Post-transcriptional gene silencing mediated by microRNAs is controlled by nucleoplasmic Sfpq. Nat Commun 2017; 8:1189. [PMID: 29084942 PMCID: PMC5662751 DOI: 10.1038/s41467-017-01126-x] [Citation(s) in RCA: 59] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2016] [Accepted: 08/18/2017] [Indexed: 02/06/2023] Open
Abstract
There is a growing body of evidence about the presence and the activity of the miRISC in the nucleus of mammalian cells. Here, we show by quantitative proteomic analysis that Ago2 interacts with the nucleoplasmic protein Sfpq in an RNA-dependent fashion. By a combination of HITS-CLIP and transcriptomic analyses, we demonstrate that Sfpq directly controls the miRNA targeting of a subset of binding sites by local binding. Sfpq modulates miRNA targeting in both nucleoplasm and cytoplasm, indicating a nucleoplasmic commitment of Sfpq-target mRNAs that globally influences miRNA modes of action. Mechanistically, Sfpq binds to a sizeable set of long 3′UTRs forming aggregates to optimize miRNA positioning/recruitment at selected binding sites, including let-7a binding to Lin28A 3′UTR. Our results extend the miRNA-mediated post-transcriptional gene silencing into the nucleoplasm and indicate that an Sfpq-dependent strategy for controlling miRNA activity takes place in cells, contributing to the complexity of miRNA-dependent gene expression control. MicroRNAs have been best characterized for their functions in the cytoplasm; however, there is growing evidence of a nuclear localized role. Here, the authors identify Sfpq as an Ago2-interacting protein that modulates miRNA activity in both the nucleus and cytoplasm.
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Re-evaluating Strategies to Define the Immunoregulatory Roles of miRNAs. Trends Immunol 2017; 38:558-566. [PMID: 28666937 DOI: 10.1016/j.it.2017.06.001] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2017] [Revised: 06/03/2017] [Accepted: 06/06/2017] [Indexed: 12/18/2022]
Abstract
miRNAs play an important role in fine-tuning host immune homeostasis and responses through the regulation of mRNA stability and translation. Studies have demonstrated that miRNA-mediated regulation of gene expression has a profound impact on immune cell development, function, and response to invading pathogens. As we continue to examine the mechanisms by which miRNAs maintain the balance between robust protective host immune responses and dysregulated responses that promote immune pathology, careful consideration of the complexity of post-transcriptional immune regulation is needed. Distinct tissue- and stimulus-specific RNA-RNA and RNA-protein interactions can modulate the functions of a given miRNA. Thus, new challenges emerge in the identification of post-transcriptional coregulatory modules and the genetic factors that impact miRNA function.
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