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Tav C, Fournier É, Fournier M, Khadangi F, Baguette A, Côté MC, Silveira MAD, Bérubé-Simard FA, Bourque G, Droit A, Bilodeau S. Glucocorticoid stimulation induces regionalized gene responses within topologically associating domains. Front Genet 2023; 14:1237092. [PMID: 37576549 PMCID: PMC10413275 DOI: 10.3389/fgene.2023.1237092] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2023] [Accepted: 07/07/2023] [Indexed: 08/15/2023] Open
Abstract
Transcription-factor binding to cis-regulatory regions regulates the gene expression program of a cell, but occupancy is often a poor predictor of the gene response. Here, we show that glucocorticoid stimulation led to the reorganization of transcriptional coregulators MED1 and BRD4 within topologically associating domains (TADs), resulting in active or repressive gene environments. Indeed, we observed a bias toward the activation or repression of a TAD when their activities were defined by the number of regions gaining and losing MED1 and BRD4 following dexamethasone (Dex) stimulation. Variations in Dex-responsive genes at the RNA levels were consistent with the redistribution of MED1 and BRD4 at the associated cis-regulatory regions. Interestingly, Dex-responsive genes without the differential recruitment of MED1 and BRD4 or binding by the glucocorticoid receptor were found within TADs, which gained or lost MED1 and BRD4, suggesting a role of the surrounding environment in gene regulation. However, the amplitude of the response of Dex-regulated genes was higher when the differential recruitment of the glucocorticoid receptor and transcriptional coregulators was observed, reaffirming the role of transcription factor-driven gene regulation and attributing a lesser role to the TAD environment. These results support a model where a signal-induced transcription factor induces a regionalized effect throughout the TAD, redefining the notion of direct and indirect effects of transcription factors on target genes.
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Affiliation(s)
- Christophe Tav
- Centre de Recherche du CHU de Québec—Université Laval, Axe Oncologie, Québec, QC, Canada
- Centre de Recherche sur le Cancer de l’Université Laval, Québec, QC, Canada
- Centre de Recherche en Données Massives de l’Université Laval, Québec, QC, Canada
| | - Éric Fournier
- Centre de Recherche du CHU de Québec—Université Laval, Axe Oncologie, Québec, QC, Canada
- Centre de Recherche sur le Cancer de l’Université Laval, Québec, QC, Canada
- Centre de Recherche en Données Massives de l’Université Laval, Québec, QC, Canada
| | - Michèle Fournier
- Centre de Recherche du CHU de Québec—Université Laval, Axe Oncologie, Québec, QC, Canada
- Centre de Recherche sur le Cancer de l’Université Laval, Québec, QC, Canada
| | - Fatemeh Khadangi
- Centre de Recherche du CHU de Québec—Université Laval, Axe Oncologie, Québec, QC, Canada
- Centre de Recherche sur le Cancer de l’Université Laval, Québec, QC, Canada
| | - Audrey Baguette
- Department of Human Genetics, Faculty of Medicine, McGill University, Montréal, QC, Canada
| | - Maxime C. Côté
- Centre de Recherche du CHU de Québec—Université Laval, Axe Oncologie, Québec, QC, Canada
- Centre de Recherche sur le Cancer de l’Université Laval, Québec, QC, Canada
| | - Maruhen A. D. Silveira
- Centre de Recherche du CHU de Québec—Université Laval, Axe Oncologie, Québec, QC, Canada
- Centre de Recherche sur le Cancer de l’Université Laval, Québec, QC, Canada
| | - Félix-Antoine Bérubé-Simard
- Centre de Recherche du CHU de Québec—Université Laval, Axe Oncologie, Québec, QC, Canada
- Centre de Recherche sur le Cancer de l’Université Laval, Québec, QC, Canada
| | - Guillaume Bourque
- Department of Human Genetics, Faculty of Medicine, McGill University, Montréal, QC, Canada
- Canadian Center for Computational Genomics, McGill University, Montréal, QC, Canada
| | - Arnaud Droit
- Centre de Recherche sur le Cancer de l’Université Laval, Québec, QC, Canada
- Centre de Recherche en Données Massives de l’Université Laval, Québec, QC, Canada
- Centre de Recherche du CHU de Québec—Université Laval, Axe Endocrinologie et Néphrologie, Québec, QC, Canada
- Département de Médecine Moléculaire, Faculté de Médecine, Université Laval, Québec, QC, Canada
| | - Steve Bilodeau
- Centre de Recherche du CHU de Québec—Université Laval, Axe Oncologie, Québec, QC, Canada
- Centre de Recherche sur le Cancer de l’Université Laval, Québec, QC, Canada
- Centre de Recherche en Données Massives de l’Université Laval, Québec, QC, Canada
- Département de Biologie Moléculaire, Biochimie Médicale et Pathologie, Faculté de Médecine, Université Laval, Québec, QC, Canada
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Postic G, Tav C, Platon L, Zehraoui F, Tahi F. IRSOM2: a web server for predicting bifunctional RNAs. Nucleic Acids Res 2023:7157516. [PMID: 37158254 DOI: 10.1093/nar/gkad381] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2023] [Revised: 04/16/2023] [Accepted: 04/28/2023] [Indexed: 05/10/2023] Open
Abstract
Recent advances have shown that some biologically active non-coding RNAs (ncRNAs) are actually translated into polypeptides that have a physiological function as well. This paradigm shift requires adapted computational methods to predict this new class of 'bifunctional RNAs'. Previously, we developed IRSOM, an open-source algorithm to classify non-coding and coding RNAs. Here, we use the binary statistical model of IRSOM as a ternary classifier, called IRSOM2, to identify bifunctional RNAs as a rejection of the two other classes. We present its easy-to-use web interface, which allows users to perform predictions on large datasets of RNA sequences in a short time, to re-train the model with their own data, and to visualize and analyze the classification results thanks to the implementation of self-organizing maps (SOM). We also propose a new benchmark of experimentally validated RNAs that play both protein-coding and non-coding roles, in different organisms. Thus, IRSOM2 showed promising performance in detecting these bifunctional transcripts among ncRNAs of different types, such as circRNAs and lncRNAs (in particular those of shorter lengths). The web server is freely available on the EvryRNA platform: https://evryrna.ibisc.univ-evry.fr.
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Affiliation(s)
- Guillaume Postic
- Université Paris-Saclay, Univ Evry, IBISC, 91020, Evry-Courcouronnes, France
| | - Christophe Tav
- Université Paris-Saclay, Univ Evry, IBISC, 91020, Evry-Courcouronnes, France
| | - Ludovic Platon
- Université Paris-Saclay, Univ Evry, IBISC, 91020, Evry-Courcouronnes, France
| | - Farida Zehraoui
- Université Paris-Saclay, Univ Evry, IBISC, 91020, Evry-Courcouronnes, France
| | - Fariza Tahi
- Université Paris-Saclay, Univ Evry, IBISC, 91020, Evry-Courcouronnes, France
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Boibessot C, Molina O, Lachance G, Tav C, Champagne A, Neveu B, Pelletier J, Pouliot F, Fradet V, Bilodeau S, Fradet Y, Bergeron A, Toren P. Subversion of infiltrating prostate macrophages to a mixed immunosuppressive tumor-associated macrophage phenotype. Clin Transl Med 2022; 12:e581. [PMID: 35075795 PMCID: PMC8786699 DOI: 10.1002/ctm2.581] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2021] [Revised: 09/05/2021] [Accepted: 09/07/2021] [Indexed: 12/21/2022] Open
Abstract
Tumor-associated macrophages (TAMs) support tumor progression within the tumor microenvironment (TME). Many questions remain as to the origin, development, and function of TAMs within the prostate TME. Evaluation of TAMs in prostate cancer (PCa) patients identified the immunosuppressive TAM marker CD163 in adjacent normal epithelium as an independent predictor of metastases or PCa death. Flow cytometry analyses identified prostate TAMs as frequently expressing both proinflammatory M1 (CCR7+) and immunosuppressive M2 (CD163+) markers. In vitro, we demonstrate PCa cells similarly subvert human M1 macrophages toward a mixed M1/M2 macrophage phenotype favoring tumor growth. Further the cytokine milieu-induced transition between immunosuppressive M2 to proinflammatory M1 (M2→M1) macrophages is abrogated by the presence of PCa cells. RNA sequencing suggests alterations in chemokine expression in prostate TAMs due to the presence of PCa cells. Together, our results suggest that prostate TAMs originate from inflammatory infiltrating macrophages, which are then reprogrammed mainly by PCa cells, but also the cytokine milieu. A better understanding of this subversion of macrophages within the prostate may lead to novel treatment strategies.
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Affiliation(s)
- Clovis Boibessot
- Centre de recherche du CHU de Québec—Université LavalAxe OncologieQuébecCanada
- Centre de recherche sur le cancer de l'Université LavalQuébecCanada
| | - Oscar Molina
- Centre de recherche du CHU de Québec—Université LavalAxe OncologieQuébecCanada
- Centre de recherche sur le cancer de l'Université LavalQuébecCanada
| | - Gabriel Lachance
- Centre de recherche du CHU de Québec—Université LavalAxe OncologieQuébecCanada
- Centre de recherche sur le cancer de l'Université LavalQuébecCanada
| | - Christophe Tav
- Centre de recherche du CHU de Québec—Université LavalAxe OncologieQuébecCanada
- Centre de recherche sur le cancer de l'Université LavalQuébecCanada
- Centre de Recherche en Données Massives de l'Université LavalQuébecCanada
| | - Audrey Champagne
- Centre de recherche du CHU de Québec—Université LavalAxe OncologieQuébecCanada
- Centre de recherche sur le cancer de l'Université LavalQuébecCanada
| | - Bertrand Neveu
- Centre de recherche du CHU de Québec—Université LavalAxe OncologieQuébecCanada
- Centre de recherche sur le cancer de l'Université LavalQuébecCanada
| | - Jean‐François Pelletier
- Centre de recherche du CHU de Québec—Université LavalAxe OncologieQuébecCanada
- Centre de recherche sur le cancer de l'Université LavalQuébecCanada
| | - Frédéric Pouliot
- Centre de recherche du CHU de Québec—Université LavalAxe OncologieQuébecCanada
- Centre de recherche sur le cancer de l'Université LavalQuébecCanada
- Département de chirurgieUniversité LavalQuébecCanada
| | - Vincent Fradet
- Centre de recherche du CHU de Québec—Université LavalAxe OncologieQuébecCanada
- Centre de recherche sur le cancer de l'Université LavalQuébecCanada
- Département de chirurgieUniversité LavalQuébecCanada
| | - Steve Bilodeau
- Centre de recherche du CHU de Québec—Université LavalAxe OncologieQuébecCanada
- Centre de recherche sur le cancer de l'Université LavalQuébecCanada
- Centre de Recherche en Données Massives de l'Université LavalQuébecCanada
- Département de biologie moléculairebiochimie médicale et pathologieFaculté de MédecineUniversité LavalQuébecCanada
| | - Yves Fradet
- Centre de recherche du CHU de Québec—Université LavalAxe OncologieQuébecCanada
- Centre de recherche sur le cancer de l'Université LavalQuébecCanada
- Département de chirurgieUniversité LavalQuébecCanada
| | - Alain Bergeron
- Centre de recherche du CHU de Québec—Université LavalAxe OncologieQuébecCanada
- Centre de recherche sur le cancer de l'Université LavalQuébecCanada
- Département de chirurgieUniversité LavalQuébecCanada
| | - Paul Toren
- Centre de recherche du CHU de Québec—Université LavalAxe OncologieQuébecCanada
- Centre de recherche sur le cancer de l'Université LavalQuébecCanada
- Département de chirurgieUniversité LavalQuébecCanada
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Vélot L, Lessard F, Bérubé-Simard FA, Tav C, Neveu B, Teyssier V, Boudaoud I, Dionne U, Lavoie N, Bilodeau S, Pouliot F, Bisson N. Proximity-dependent Mapping of the Androgen Receptor Identifies Kruppel-like Factor 4 as a Functional Partner. Mol Cell Proteomics 2021; 20:100064. [PMID: 33640491 PMCID: PMC8050775 DOI: 10.1016/j.mcpro.2021.100064] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2020] [Revised: 02/09/2021] [Accepted: 02/10/2021] [Indexed: 12/15/2022] Open
Abstract
Prostate cancer (PCa) is the most frequently diagnosed cancer in men and the third cause of cancer mortality. PCa initiation and growth are driven by the androgen receptor (AR). The AR is activated by androgens such as testosterone and controls prostatic cell proliferation and survival. Here, we report an AR signaling network generated using BioID proximity labeling proteomics in androgen-dependent LAPC4 cells. We identified 31 AR-associated proteins in nonstimulated cells. Strikingly, the AR signaling network increased to 182 and 200 proteins, upon 24 h or 72 h of androgenic stimulation, respectively, for a total of 267 nonredundant AR-associated candidates. Among the latter group, we identified 213 proteins that were not previously reported in databases. Many of these new AR-associated proteins are involved in DNA metabolism, RNA processing, and RNA polymerase II transcription. Moreover, we identified 44 transcription factors, including the Kru¨ppel-like factor 4 (KLF4), which were found interacting in androgen-stimulated cells. Interestingly, KLF4 repressed the well-characterized AR-dependent transcription of the KLK3 (PSA) gene; AR and KLF4 also colocalized genome-wide. Taken together, our data report an expanded high-confidence proximity network for AR, which will be instrumental to further dissect the molecular mechanisms underlying androgen signaling in PCa cells. BioID proteomics identifies 267 androgen receptor (AR)-associated candidates Krüppel-like factor 4 (KLF4) is a new AR interaction partner AR and KLF4 colocalize genome-wide on >4000 genes, including KLK3 (PSA) KLF4 acts as a repressor for the AR target gene KLK3 (PSA)
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Affiliation(s)
- Lauriane Vélot
- Centre de recherche du Centre Hospitalier Universitaire (CHU) de Québec-Université Laval, Axe Oncologie, Québec, Quebec, Canada; Centre de recherche sur le cancer de l'Université Laval, Québec, Quebec, Canada; PROTEO-Quebec Network for Research on Protein Function, Engineering, and Applications, Québec, Quebec, Canada
| | - Frédéric Lessard
- Centre de recherche du Centre Hospitalier Universitaire (CHU) de Québec-Université Laval, Axe Oncologie, Québec, Quebec, Canada; Centre de recherche sur le cancer de l'Université Laval, Québec, Quebec, Canada; PROTEO-Quebec Network for Research on Protein Function, Engineering, and Applications, Québec, Quebec, Canada
| | - Félix-Antoine Bérubé-Simard
- Centre de recherche du Centre Hospitalier Universitaire (CHU) de Québec-Université Laval, Axe Oncologie, Québec, Quebec, Canada; Centre de recherche sur le cancer de l'Université Laval, Québec, Quebec, Canada
| | - Christophe Tav
- Centre de recherche du Centre Hospitalier Universitaire (CHU) de Québec-Université Laval, Axe Oncologie, Québec, Quebec, Canada; Centre de recherche sur le cancer de l'Université Laval, Québec, Quebec, Canada; Centre de recherche en données massives de l'Université Laval, Québec, Québec, Canada
| | - Bertrand Neveu
- Centre de recherche du Centre Hospitalier Universitaire (CHU) de Québec-Université Laval, Axe Oncologie, Québec, Quebec, Canada; Centre de recherche sur le cancer de l'Université Laval, Québec, Quebec, Canada
| | - Valentine Teyssier
- Centre de recherche du Centre Hospitalier Universitaire (CHU) de Québec-Université Laval, Axe Oncologie, Québec, Quebec, Canada; Centre de recherche sur le cancer de l'Université Laval, Québec, Quebec, Canada; PROTEO-Quebec Network for Research on Protein Function, Engineering, and Applications, Québec, Quebec, Canada
| | - Imène Boudaoud
- Centre de recherche du Centre Hospitalier Universitaire (CHU) de Québec-Université Laval, Axe Oncologie, Québec, Quebec, Canada; Centre de recherche sur le cancer de l'Université Laval, Québec, Quebec, Canada
| | - Ugo Dionne
- Centre de recherche du Centre Hospitalier Universitaire (CHU) de Québec-Université Laval, Axe Oncologie, Québec, Quebec, Canada; Centre de recherche sur le cancer de l'Université Laval, Québec, Quebec, Canada; PROTEO-Quebec Network for Research on Protein Function, Engineering, and Applications, Québec, Quebec, Canada
| | - Noémie Lavoie
- Centre de recherche du Centre Hospitalier Universitaire (CHU) de Québec-Université Laval, Axe Oncologie, Québec, Quebec, Canada; Centre de recherche sur le cancer de l'Université Laval, Québec, Quebec, Canada; PROTEO-Quebec Network for Research on Protein Function, Engineering, and Applications, Québec, Quebec, Canada
| | - Steve Bilodeau
- Centre de recherche du Centre Hospitalier Universitaire (CHU) de Québec-Université Laval, Axe Oncologie, Québec, Quebec, Canada; Centre de recherche sur le cancer de l'Université Laval, Québec, Quebec, Canada; Centre de recherche en données massives de l'Université Laval, Québec, Québec, Canada; Department of Molecular Biology, Medical Biochemistry and Pathology, Faculté de Médecine, Université Laval, Québec, Quebec, Canada
| | - Frédéric Pouliot
- Centre de recherche du Centre Hospitalier Universitaire (CHU) de Québec-Université Laval, Axe Oncologie, Québec, Quebec, Canada; Centre de recherche sur le cancer de l'Université Laval, Québec, Quebec, Canada; Department of Surgery, Faculté de Médecine, Université Laval, Québec, Quebec, Canada.
| | - Nicolas Bisson
- Centre de recherche du Centre Hospitalier Universitaire (CHU) de Québec-Université Laval, Axe Oncologie, Québec, Quebec, Canada; Centre de recherche sur le cancer de l'Université Laval, Québec, Quebec, Canada; PROTEO-Quebec Network for Research on Protein Function, Engineering, and Applications, Québec, Quebec, Canada; Department of Molecular Biology, Medical Biochemistry and Pathology, Faculté de Médecine, Université Laval, Québec, Quebec, Canada.
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Silveira MA, Tav C, Bérube-Simard FA, Cuppens T, Leclercq M, Fournier É, Côté MC, Droit A, Bilodeau S. Modulating HSF1 levels impacts expression of the estrogen receptor α and antiestrogen response. Life Sci Alliance 2021; 4:4/5/e202000811. [PMID: 33593922 PMCID: PMC7893817 DOI: 10.26508/lsa.202000811] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2020] [Revised: 02/01/2021] [Accepted: 02/03/2021] [Indexed: 12/21/2022] Open
Abstract
This work shows that activation of the main cellular stress response pathway is responsible for antiestrogen resistance in breast cancer, a process that is reversible. Master transcription factors control the transcriptional program and are essential to maintain cellular functions. Among them, steroid nuclear receptors, such as the estrogen receptor α (ERα), are central to the etiology of hormone-dependent cancers which are accordingly treated with corresponding endocrine therapies. However, resistance invariably arises. Here, we show that high levels of the stress response master regulator, the heat shock factor 1 (HSF1), are associated with antiestrogen resistance in breast cancer cells. Indeed, overexpression of HSF1 leads to ERα degradation, decreased expression of ERα-activated genes, and antiestrogen resistance. Furthermore, we demonstrate that reducing HSF1 levels reinstates expression of the ERα and restores response to antiestrogens. Last, our results establish a proof of concept that inhibition of HSF1, in combination with antiestrogens, is a valid strategy to tackle resistant breast cancers. Taken together, we are proposing a mechanism where high HSF1 levels interfere with the ERα-dependent transcriptional program leading to endocrine resistance in breast cancer.
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Affiliation(s)
- Maruhen Ad Silveira
- Centre de Recherche du CHU de Québec - Université Laval, Axe Oncologie, Québec, Canada.,Centre de Recherche sur le Cancer de l'Université Laval, Québec, Canada
| | - Christophe Tav
- Centre de Recherche du CHU de Québec - Université Laval, Axe Oncologie, Québec, Canada.,Centre de Recherche sur le Cancer de l'Université Laval, Québec, Canada.,Centre de Recherche du CHU de Québec - Université Laval, Axe Endocrinologie et Néphrologie, Québec, Canada.,Centre de Recherche en Données Massives de l'Université Laval, Québec, Canada
| | - Félix-Antoine Bérube-Simard
- Centre de Recherche du CHU de Québec - Université Laval, Axe Oncologie, Québec, Canada.,Centre de Recherche sur le Cancer de l'Université Laval, Québec, Canada
| | - Tania Cuppens
- Centre de Recherche sur le Cancer de l'Université Laval, Québec, Canada.,Centre de Recherche du CHU de Québec - Université Laval, Axe Endocrinologie et Néphrologie, Québec, Canada.,Centre de Recherche en Données Massives de l'Université Laval, Québec, Canada
| | - Mickaël Leclercq
- Centre de Recherche sur le Cancer de l'Université Laval, Québec, Canada.,Centre de Recherche du CHU de Québec - Université Laval, Axe Endocrinologie et Néphrologie, Québec, Canada.,Centre de Recherche en Données Massives de l'Université Laval, Québec, Canada
| | - Éric Fournier
- Centre de Recherche du CHU de Québec - Université Laval, Axe Oncologie, Québec, Canada.,Centre de Recherche sur le Cancer de l'Université Laval, Québec, Canada.,Centre de Recherche du CHU de Québec - Université Laval, Axe Endocrinologie et Néphrologie, Québec, Canada
| | - Maxime C Côté
- Centre de Recherche du CHU de Québec - Université Laval, Axe Oncologie, Québec, Canada.,Centre de Recherche sur le Cancer de l'Université Laval, Québec, Canada
| | - Arnaud Droit
- Centre de Recherche sur le Cancer de l'Université Laval, Québec, Canada.,Centre de Recherche du CHU de Québec - Université Laval, Axe Endocrinologie et Néphrologie, Québec, Canada.,Centre de Recherche en Données Massives de l'Université Laval, Québec, Canada.,Département de Médecine Moléculaire, Faculté de Médecine, Université Laval, Québec, Canada
| | - Steve Bilodeau
- Centre de Recherche du CHU de Québec - Université Laval, Axe Oncologie, Québec, Canada .,Centre de Recherche sur le Cancer de l'Université Laval, Québec, Canada.,Centre de Recherche en Données Massives de l'Université Laval, Québec, Canada.,Département de Biologie Moléculaire, Biochimie Médicale et Pathologie, Faculté de Médecine, Université Laval, Québec, Canada
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Tav C, Tempel S, Poligny L, Tahi F. miRNAFold: a web server for fast miRNA precursor prediction in genomes. Nucleic Acids Res 2016; 44:W181-4. [PMID: 27242364 PMCID: PMC4987958 DOI: 10.1093/nar/gkw459] [Citation(s) in RCA: 50] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2016] [Accepted: 05/12/2016] [Indexed: 01/05/2023] Open
Abstract
Computational methods are required for prediction of non-coding RNAs (ncRNAs), which are involved in many biological processes, especially at post-transcriptional level. Among these ncRNAs, miRNAs have been largely studied and biologists need efficient and fast tools for their identification. In particular, ab initio methods are usually required when predicting novel miRNAs. Here we present a web server dedicated for miRNA precursors identification at a large scale in genomes. It is based on an algorithm called miRNAFold that allows predicting miRNA hairpin structures quickly with high sensitivity. miRNAFold is implemented as a web server with an intuitive and user-friendly interface, as well as a standalone version. The web server is freely available at: http://EvryRNA.ibisc.univ-evry.fr/miRNAFold.
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Affiliation(s)
- Christophe Tav
- IBISC-IBGBI, Université Evry, Genopole, 23 Boulevard de France, 91037 Evry CEDEX, France
| | - Sébastien Tempel
- IBISC-IBGBI, Université Evry, Genopole, 23 Boulevard de France, 91037 Evry CEDEX, France
| | - Laurent Poligny
- IBISC-IBGBI, Université Evry, Genopole, 23 Boulevard de France, 91037 Evry CEDEX, France
| | - Fariza Tahi
- IBISC-IBGBI, Université Evry, Genopole, 23 Boulevard de France, 91037 Evry CEDEX, France Institute of Plant Sciences Paris Saclay (IPS2), CNRS, INRA, Université Paris-Sud, Université Evry, Université Paris-Saclay, Batiment 630, 91405 Orsay, France
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Celiktas C, Tav C. A method for obtaining the pure annihilation peak of radioisotope. RADIAT MEAS 2005. [DOI: 10.1016/j.radmeas.2004.10.013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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