1
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Larivera S, Neumeier J, Meister G. Post-transcriptional gene silencing in a dynamic RNP world. Biol Chem 2023; 404:1051-1067. [PMID: 37739934 DOI: 10.1515/hsz-2023-0203] [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: 05/05/2023] [Accepted: 08/04/2023] [Indexed: 09/24/2023]
Abstract
MicroRNA (miRNA)-guided gene silencing is a key regulatory process in various organisms and linked to many human diseases. MiRNAs are processed from precursor molecules and associate with Argonaute proteins to repress the expression of complementary target mRNAs. Excellent work by numerous labs has contributed to a detailed understanding of the mechanisms of miRNA function. However, miRNA effects have mostly been analyzed and viewed as isolated events and their natural environment as part of complex RNA-protein particles (RNPs) is often neglected. RNA binding proteins (RBPs) regulate key enzymes of the miRNA processing machinery and furthermore RBPs or readers of RNA modifications may modulate miRNA activity on mRNAs. Such proteins may function similarly to miRNAs and add their own contributions to the overall expression level of a particular gene. Therefore, post-transcriptional gene regulation might be more the sum of individual regulatory events and should be viewed as part of a dynamic and complex RNP world.
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Affiliation(s)
- Simone Larivera
- Regensburg Center for Biochemistry (RCB), Laboratory for RNA Biology, University of Regensburg, D-93053, Regensburg, Germany
| | - Julia Neumeier
- Regensburg Center for Biochemistry (RCB), Laboratory for RNA Biology, University of Regensburg, D-93053, Regensburg, Germany
| | - Gunter Meister
- Regensburg Center for Biochemistry (RCB), Laboratory for RNA Biology, University of Regensburg, D-93053, Regensburg, Germany
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2
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Wang Z, Shu W, Zhao R, Liu Y, Wang H. Sodium butyrate induces ferroptosis in endometrial cancer cells via the RBM3/SLC7A11 axis. Apoptosis 2023:10.1007/s10495-023-01850-4. [PMID: 37170022 DOI: 10.1007/s10495-023-01850-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/21/2023] [Indexed: 05/13/2023]
Abstract
Ferroptosis is a form of programmed cell death with important biological functions in the progression of various diseases, and targeting ferroptosis is a new tumor treatment strategy. Studies have shown that sodium butyrate plays a tumor-suppressing role in the progression of various tumors, however, the mechanism of NaBu in endometrial cancer is unclear. Cell viability, clone formation, proliferation, migration, invasion abilities and cell cycle distribution were assessed by CCK8 assay, Clone formation ability assay, EdU incorporation, Transwell chambers and flow cytometry. The level of ferroptosis was assayed by the levels of ROS and lipid peroxidation, the ratio of GSH/GSSG and the morphology of mitochondria. Molecular mechanisms were explored by metabolome, transcriptome, RNA-pulldown and mass spectrometry. The in-vivo mechanism was validated using subcutaneous xenograft model. In this study, NaBu was identified to inhibit the progression of endometrial cancer in vitro and in vivo. Mechanistically, RBM3 has a binding relationship with SLC7A11 mRNA. NaBu indirectly downregulates the expression of SLC7A11 by promoting the expression of RBM3, thereby promoting ferroptosis in endometrial cancer cells. In conclusion, Sodium butyrate can promote the expression of RBM3 and indirectly downregulate the expression of SLC7A11 to stimulate ferroptosis, which may be a promising cancer treatment strategy.
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Affiliation(s)
- Ziwei Wang
- Department of Obstetrics and Gynecology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430022, Hubei, People's Republic of China
| | - Wan Shu
- Department of Obstetrics and Gynecology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430022, Hubei, People's Republic of China
| | - Rong Zhao
- Department of Obstetrics and Gynecology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430022, Hubei, People's Republic of China
| | - Yan Liu
- Department of Obstetrics and Gynecology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430022, Hubei, People's Republic of China.
| | - Hongbo Wang
- Department of Obstetrics and Gynecology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430022, Hubei, People's Republic of China.
- Clinical Research Center of Cancer Immunotherapy, Hubei, Wuhan, 430022, Hubei, People's Republic of China.
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3
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Kuret K, Amalietti AG, Jones DM, Capitanchik C, Ule J. Positional motif analysis reveals the extent of specificity of protein-RNA interactions observed by CLIP. Genome Biol 2022; 23:191. [PMID: 36085079 PMCID: PMC9461102 DOI: 10.1186/s13059-022-02755-2] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2021] [Accepted: 08/22/2022] [Indexed: 12/01/2022] Open
Abstract
Background Crosslinking and immunoprecipitation (CLIP) is a method used to identify in vivo RNA–protein binding sites on a transcriptome-wide scale. With the increasing amounts of available data for RNA-binding proteins (RBPs), it is important to understand to what degree the enriched motifs specify the RNA-binding profiles of RBPs in cells. Results We develop positionally enriched k-mer analysis (PEKA), a computational tool for efficient analysis of enriched motifs from individual CLIP datasets, which minimizes the impact of technical and regional genomic biases by internal data normalization. We cross-validate PEKA with mCross and show that the use of input control for background correction is not required to yield high specificity of enriched motifs. We identify motif classes with common enrichment patterns across eCLIP datasets and across RNA regions, while also observing variations in the specificity and the extent of motif enrichment across eCLIP datasets, between variant CLIP protocols, and between CLIP and in vitro binding data. Thereby, we gain insights into the contributions of technical and regional genomic biases to the enriched motifs, and find how motif enrichment features relate to the domain composition and low-complexity regions of the studied proteins. Conclusions Our study provides insights into the overall contributions of regional binding preferences, protein domains, and low-complexity regions to the specificity of protein-RNA interactions, and shows the value of cross-motif and cross-RBP comparison for data interpretation. Our results are presented for exploratory analysis via an online platform in an RBP-centric and motif-centric manner (https://imaps.goodwright.com/apps/peka/). Supplementary Information The online version contains supplementary material available at 10.1186/s13059-022-02755-2.
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Affiliation(s)
- Klara Kuret
- National Institute of Chemistry, Hajdrihova 19, SI-1001, Ljubljana, Slovenia.,Jozef Stefan International Postgraduate School, Jamova cesta 39, 1000, Ljubljana, Slovenia.,The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK
| | - Aram Gustav Amalietti
- National Institute of Chemistry, Hajdrihova 19, SI-1001, Ljubljana, Slovenia.,The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK
| | - D Marc Jones
- The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK.,UK Dementia Research Institute, King's College London, London, UK
| | - Charlotte Capitanchik
- The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK.,UK Dementia Research Institute, King's College London, London, UK
| | - Jernej Ule
- National Institute of Chemistry, Hajdrihova 19, SI-1001, Ljubljana, Slovenia. .,The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK. .,UK Dementia Research Institute, King's College London, London, UK.
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4
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Laverty KU, Jolma A, Pour SE, Zheng H, Ray D, Morris Q, Hughes TR. PRIESSTESS: interpretable, high-performing models of the sequence and structure preferences of RNA-binding proteins. Nucleic Acids Res 2022; 50:e111. [PMID: 36018788 DOI: 10.1093/nar/gkac694] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2021] [Revised: 07/22/2022] [Accepted: 08/03/2022] [Indexed: 12/23/2022] Open
Abstract
Modelling both primary sequence and secondary structure preferences for RNA binding proteins (RBPs) remains an ongoing challenge. Current models use varied RNA structure representations and can be difficult to interpret and evaluate. To address these issues, we present a universal RNA motif-finding/scanning strategy, termed PRIESSTESS (Predictive RBP-RNA InterpretablE Sequence-Structure moTif regrESSion), that can be applied to diverse RNA binding datasets. PRIESSTESS identifies dozens of enriched RNA sequence and/or structure motifs that are subsequently reduced to a set of core motifs by logistic regression with LASSO regularization. Importantly, these core motifs are easily visualized and interpreted, and provide a measure of RBP secondary structure specificity. We used PRIESSTESS to interrogate new HTR-SELEX data for 23 RBPs with diverse RNA binding modes and captured known primary sequence and secondary structure preferences for each. Moreover, when applying PRIESSTESS to 144 RBPs across 202 RNA binding datasets, 75% showed an RNA secondary structure preference but only 10% had a preference besides unpaired bases, suggesting that most RBPs simply recognize the accessibility of primary sequences.
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Affiliation(s)
- Kaitlin U Laverty
- Department of Molecular Genetics, University of Toronto, Toronto, Canada
| | - Arttu Jolma
- Department of Molecular Genetics, University of Toronto, Toronto, Canada.,Donnelly Centre, University of Toronto, Toronto, Canada
| | - Sara E Pour
- Department of Molecular Genetics, University of Toronto, Toronto, Canada
| | - Hong Zheng
- Donnelly Centre, University of Toronto, Toronto, Canada
| | - Debashish Ray
- Donnelly Centre, University of Toronto, Toronto, Canada
| | - Quaid Morris
- Department of Molecular Genetics, University of Toronto, Toronto, Canada.,Computational and Systems Biology, Memorial Sloan Kettering Cancer Center, New York, USA
| | - Timothy R Hughes
- Department of Molecular Genetics, University of Toronto, Toronto, Canada.,Donnelly Centre, University of Toronto, Toronto, Canada
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5
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Paz I, Argoetti A, Cohen N, Even N, Mandel-Gutfreund Y. RBPmap: A Tool for Mapping and Predicting the Binding Sites of RNA-Binding Proteins Considering the Motif Environment. Methods Mol Biol 2022; 2404:53-65. [PMID: 34694603 DOI: 10.1007/978-1-0716-1851-6_3] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
RNA-binding proteins (RBPs) play a key role in post-transcriptional regulation via binding to coding and non-coding RNAs. Recent development in experimental technologies, aimed to identify the targets of RBPs, has significantly broadened our knowledge on protein-RNA interactions. However, for many RBPs in many organisms and cell types, experimental RNA-binding data is not available. In this chapter we describe a computational approach, named RBPmap, available as a web service via http://rbpmap.technion.ac.il/ and as a stand-alone version for download. RBPmap was designed for mapping and predicting the binding sites of any RBP within a nucleic acid sequence, given the availability of an experimentally defined binding motif of the RBP. The algorithm searches for a sub-sequence that significantly matches the RBP motif, considering the clustering propensity of other weak matches within the motif environment. Here, we present different applications of RBPmap for discovering the involvement of RBPs and their targets in a variety of cellular processes, in health and disease states. Finally, we demonstrate the performance of RBPmap in predicting the binding targets of RBPs in large-scale RNA-binding data, reinforcing the strength of the tool in distinguishing cognate binding sites from weak motifs.
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Affiliation(s)
- Inbal Paz
- Faculty of Biology, Technion-Israel Institute of Technology, Haifa, Israel
| | - Amir Argoetti
- Faculty of Biology, Technion-Israel Institute of Technology, Haifa, Israel
| | - Noa Cohen
- Faculty of Biology, Technion-Israel Institute of Technology, Haifa, Israel
- Department of Computer Sciences, Technion-Israel Institute of Technology, Haifa, Israel
| | - Niv Even
- Faculty of Biology, Technion-Israel Institute of Technology, Haifa, Israel
- Department of Computer Sciences, Technion-Israel Institute of Technology, Haifa, Israel
| | - Yael Mandel-Gutfreund
- Faculty of Biology, Technion-Israel Institute of Technology, Haifa, Israel.
- Department of Computer Sciences, Technion-Israel Institute of Technology, Haifa, Israel.
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6
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Busa VF, Favorov AV, Fertig EJ, Leung AK. Spatial correlation statistics enable transcriptome-wide characterization of RNA structure binding. CELL REPORTS METHODS 2021; 1:100088. [PMID: 35474897 PMCID: PMC9017189 DOI: 10.1016/j.crmeth.2021.100088] [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] [Subscribe] [Scholar Register] [Received: 12/15/2020] [Revised: 06/23/2021] [Accepted: 08/30/2021] [Indexed: 11/20/2022]
Abstract
Molecular interactions at identical transcriptomic locations or at proximal but non-overlapping sites can mediate RNA modification and regulation, necessitating tools to uncover these spatial relationships. We present nearBynding, a flexible algorithm and software pipeline that models spatial correlation between transcriptome-wide tracks from diverse data types. nearBynding can process and correlate interval as well as continuous data and incorporate experimentally derived or in silico predicted transcriptomic tracks. nearBynding offers visualization functions for its statistics to identify colocalizations and adjacent features. We demonstrate the application of nearBynding to correlate RNA-binding protein (RBP) binding preferences with other RBPs, RNA structure, or RNA modification. By cross-correlating RBP binding and RNA structure data, we demonstrate that nearBynding recapitulates known RBP binding to structural motifs and provides biological insights into RBP binding preference of G-quadruplexes. nearBynding is available as an R/Bioconductor package and can run on a personal computer, making correlation of transcriptomic features broadly accessible.
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Affiliation(s)
- Veronica F. Busa
- McKusick-Nathans Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
- Department of Biochemistry and Molecular Biology, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD 21205, USA
| | - Alexander V. Favorov
- Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
- Laboratory of Systems Biology and Computational Genetics, Vavilov Institute of General Genetics, Russian Academy of Sciences, Moscow, Russia
| | - Elana J. Fertig
- McKusick-Nathans Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
- Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
- Department of Biomedical Engineering, Johns Hopkins University Whiting School of Engineering, Baltimore, MD 21205, USA
- Department of Applied Mathematics and Statistics, Johns Hopkins University Whiting School of Engineering, Baltimore, MD 21205, USA
| | - Anthony K.L. Leung
- McKusick-Nathans Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
- Department of Biochemistry and Molecular Biology, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD 21205, USA
- Department of Molecular Biology and Genetics, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
- Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
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7
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Vaz JM, Balaji S. Convolutional neural networks (CNNs): concepts and applications in pharmacogenomics. Mol Divers 2021; 25:1569-1584. [PMID: 34031788 PMCID: PMC8342355 DOI: 10.1007/s11030-021-10225-3] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2021] [Accepted: 04/21/2021] [Indexed: 12/17/2022]
Abstract
Convolutional neural networks (CNNs) have been used to extract information from various datasets of different dimensions. This approach has led to accurate interpretations in several subfields of biological research, like pharmacogenomics, addressing issues previously faced by other computational methods. With the rising attention for personalized and precision medicine, scientists and clinicians have now turned to artificial intelligence systems to provide them with solutions for therapeutics development. CNNs have already provided valuable insights into biological data transformation. Due to the rise of interest in precision and personalized medicine, in this review, we have provided a brief overview of the possibilities of implementing CNNs as an effective tool for analyzing one-dimensional biological data, such as nucleotide and protein sequences, as well as small molecular data, e.g., simplified molecular-input line-entry specification, InChI, binary fingerprints, etc., to categorize the models based on their objective and also highlight various challenges. The review is organized into specific research domains that participate in pharmacogenomics for a more comprehensive understanding. Furthermore, the future intentions of deep learning are outlined.
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Affiliation(s)
- Joel Markus Vaz
- Department of Biotechnology, Manipal Institute of Technology, Manipal Academy of Higher Education, Manipal, Karnataka, 576104, India
| | - S Balaji
- Department of Biotechnology, Manipal Institute of Technology, Manipal Academy of Higher Education, Manipal, Karnataka, 576104, India.
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8
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Guarracino A, Pepe G, Ballesio F, Adinolfi M, Pietrosanto M, Sangiovanni E, Vitale I, Ausiello G, Helmer-Citterich M. BRIO: a web server for RNA sequence and structure motif scan. Nucleic Acids Res 2021; 49:W67-W71. [PMID: 34038531 PMCID: PMC8262756 DOI: 10.1093/nar/gkab400] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2021] [Revised: 04/27/2021] [Accepted: 05/22/2021] [Indexed: 12/30/2022] Open
Abstract
The interaction between RNA and RNA-binding proteins (RBPs) has a key role in the regulation of gene expression, in RNA stability, and in many other biological processes. RBPs accomplish these functions by binding target RNA molecules through specific sequence and structure motifs. The identification of these binding motifs is therefore fundamental to improve our knowledge of the cellular processes and how they are regulated. Here, we present BRIO (BEAM RNA Interaction mOtifs), a new web server designed for the identification of sequence and structure RNA-binding motifs in one or more RNA molecules of interest. BRIO enables the user to scan over 2508 sequence motifs and 2296 secondary structure motifs identified in Homo sapiens and Mus musculus, in three different types of experiments (PAR-CLIP, eCLIP, HITS). The motifs are associated with the binding of 186 RBPs and 69 protein domains. The web server is freely available at http://brio.bio.uniroma2.it.
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Affiliation(s)
- Andrea Guarracino
- Department of Biology, University of Rome "Tor Vergata", Rome, Italy
| | - Gerardo Pepe
- Department of Biology, University of Rome "Tor Vergata", Rome, Italy
| | | | - Marta Adinolfi
- Department of Biology, University of Rome "Tor Vergata", Rome, Italy
| | - Marco Pietrosanto
- Department of Biology, University of Rome "Tor Vergata", Rome, Italy
| | - Elisa Sangiovanni
- Department of Biology, University of Rome "Tor Vergata", Rome, Italy
| | - Ilio Vitale
- IIGM - Italian Institute for Genomic Medicine, c/o IRCSS Candiolo, Italy.,Candiolo Cancer Institute, FPO - IRCCS, Candiolo, Italy
| | - Gabriele Ausiello
- Department of Biology, University of Rome "Tor Vergata", Rome, Italy
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9
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Pietrosanto M, Ausiello G, Helmer-Citterich M. Motif Discovery from CLIP Experiments. METHODS IN MOLECULAR BIOLOGY (CLIFTON, N.J.) 2021; 2284:43-50. [PMID: 33835436 DOI: 10.1007/978-1-0716-1307-8_3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Abstract
RNA primary and secondary motif discovery is an important step in the annotation and characterization of unknown interaction dynamics between RNAs and RNA-Binding Proteins, and several methods have been developed to meet the need of fast and efficient discovery of interaction motifs. Recent advances have increased the amount of data produced by experimental assays and there is no available method suitable for the analysis of all type of results. Here we present a simple workflow to help choosing the more appropriate method, depending on the starting situation, among the three algorithms that best cover the landscape of approaches. A detailed analysis is presented to highlight the need for different algorithms in different working settings. In conclusion, the proposed workflow depends on the nature of the starting data and on the availability of RNA annotations.
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Affiliation(s)
- Marco Pietrosanto
- Centre for Molecular Bioinformatics, Department of Biology, University of Rome Tor Vergata, Rome, Italy
| | - Gabriele Ausiello
- Centre for Molecular Bioinformatics, Department of Biology, University of Rome Tor Vergata, Rome, Italy
| | - Manuela Helmer-Citterich
- Centre for Molecular Bioinformatics, Department of Biology, University of Rome Tor Vergata, Rome, Italy.
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10
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Sen R, Fallmann J, Walter MEMT, Stadler PF. Are spliced ncRNA host genes distinct classes of lncRNAs? Theory Biosci 2020; 139:349-359. [PMID: 33219910 PMCID: PMC7719101 DOI: 10.1007/s12064-020-00330-6] [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: 09/13/2020] [Accepted: 11/10/2020] [Indexed: 12/03/2022]
Abstract
Many small nucleolar RNAs and many of the hairpin precursors of miRNAs are processed from long non-protein-coding host genes. In contrast to their highly conserved and heavily structured payload, the host genes feature poorly conserved sequences. Nevertheless, there is mounting evidence that the host genes have biological functions beyond their primary task of carrying a ncRNA as payload. So far, no connections between the function of the host genes and the function of their payloads have been reported. Here we investigate whether there is evidence for an association of host gene function or mechanisms with the type of payload. To assess this hypothesis we test whether the miRNA host genes (MIRHGs), snoRNA host genes (SNHGs), and other lncRNA host genes can be distinguished based on sequence and/or structure features unrelated to their payload. A positive answer would imply a functional and mechanistic correlation between host genes and their payload, provided the classification does not depend on the presence and type of the payload. A negative answer would indicate that to the extent that secondary functions are acquired, they are not strongly constrained by the prior, primary function of the payload. We find that the three classes can be distinguished reliably when the classifier is allowed to extract features from the payloads. They become virtually indistinguishable, however, as soon as only sequence and structure of parts of the host gene distal from the snoRNAs or miRNA payload is used for classification. This indicates that the functions of MIRHGs and SNHGs are largely independent of the functions of their payloads. Furthermore, there is no evidence that the MIRHGs and SNHGs form coherent classes of long non-coding RNAs distinguished by features other than their payloads.
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Affiliation(s)
- Rituparno Sen
- Bioinformatics Group, Department of Computer Science, and Interdisciplinary Center for Bioinformatics, University of Leipzig, Härtelstraße 16-18, 04107 Leipzig, Germany
| | - Jörg Fallmann
- Bioinformatics Group, Department of Computer Science, and Interdisciplinary Center for Bioinformatics, University of Leipzig, Härtelstraße 16-18, 04107 Leipzig, Germany
| | - Maria Emília M. T. Walter
- Departamento de Ciência da Computação, Instituto de Ciências Exatas, Universidade de Brasília, Brasília, Brazil
| | - Peter F. Stadler
- Bioinformatics Group, Department of Computer Science, and Interdisciplinary Center for Bioinformatics, University of Leipzig, Härtelstraße 16-18, 04107 Leipzig, Germany
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Competence Center for Scalable Data Services and Solutions, and Leipzig Research Center for Civilization Diseases, University Leipzig, Leipzig, Germany
- Max Planck Institute for Mathematics in the Sciences, Inselstraße 22, 04103 Leipzig, Germany
- Institute for Theoretical Chemistry, University of Vienna, Währingerstraße 17, 1090 Wien, Austria
- Facultad de Ciencias, Universidad National de Colombia, Sede Bogotá, Colombia
- Santa Fe Institute, 1399 Hyde Park Rd., Santa Fe, NM 87501 Mexico
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11
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Hollmann NM, Jagtap PKA, Masiewicz P, Guitart T, Simon B, Provaznik J, Stein F, Haberkant P, Sweetapple LJ, Villacorta L, Mooijman D, Benes V, Savitski MM, Gebauer F, Hennig J. Pseudo-RNA-Binding Domains Mediate RNA Structure Specificity in Upstream of N-Ras. Cell Rep 2020; 32:107930. [PMID: 32697992 PMCID: PMC7383231 DOI: 10.1016/j.celrep.2020.107930] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2020] [Revised: 06/03/2020] [Accepted: 06/29/2020] [Indexed: 12/12/2022] Open
Abstract
RNA-binding proteins (RBPs) commonly feature multiple RNA-binding domains (RBDs), which provide these proteins with a modular architecture. Accumulating evidence supports that RBP architectural modularity and adaptability define the specificity of their interactions with RNA. However, how multiple RBDs recognize their cognate single-stranded RNA (ssRNA) sequences in concert remains poorly understood. Here, we use Upstream of N-Ras (Unr) as a model system to address this question. Although reported to contain five ssRNA-binding cold-shock domains (CSDs), we demonstrate that Unr includes an additional four CSDs that do not bind RNA (pseudo-RBDs) but are involved in mediating RNA tertiary structure specificity by reducing the conformational heterogeneity of Unr. Disrupting the interactions between canonical and non-canonical CSDs impacts RNA binding, Unr-mediated translation regulation, and the Unr-dependent RNA interactome. Taken together, our studies reveal a new paradigm in protein-RNA recognition, where interactions between RBDs and pseudo-RBDs select RNA tertiary structures, influence RNP assembly, and define target specificity.
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Affiliation(s)
- Nele Merret Hollmann
- Structural and Computational Biology Unit, EMBL Heidelberg, Meyerhofstraße 1, 69117 Heidelberg, Germany; Collaboration for Joint PhD Degree between EMBL and Heidelberg University, Faculty of Biosciences, Heidelberg, Germany
| | | | - Pawel Masiewicz
- Structural and Computational Biology Unit, EMBL Heidelberg, Meyerhofstraße 1, 69117 Heidelberg, Germany
| | - Tanit Guitart
- Gene Regulation, Stem Cells and Cancer Programme, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, 08003 Barcelona, Spain
| | - Bernd Simon
- Structural and Computational Biology Unit, EMBL Heidelberg, Meyerhofstraße 1, 69117 Heidelberg, Germany
| | - Jan Provaznik
- Genomics Core Facility, EMBL Heidelberg, Meyerhofstraße 1, 69117 Heidelberg, Germany
| | - Frank Stein
- Proteomics Core Facility, EMBL Heidelberg, Meyerhofstraße 1, 69117 Heidelberg, Germany
| | - Per Haberkant
- Proteomics Core Facility, EMBL Heidelberg, Meyerhofstraße 1, 69117 Heidelberg, Germany
| | - Lara Jayne Sweetapple
- Structural and Computational Biology Unit, EMBL Heidelberg, Meyerhofstraße 1, 69117 Heidelberg, Germany
| | - Laura Villacorta
- Genomics Core Facility, EMBL Heidelberg, Meyerhofstraße 1, 69117 Heidelberg, Germany
| | - Dylan Mooijman
- Developmental Biology Unit, EMBL Heidelberg, Meyerhofstraße 1, 69117 Heidelberg, Germany
| | - Vladimir Benes
- Genomics Core Facility, EMBL Heidelberg, Meyerhofstraße 1, 69117 Heidelberg, Germany
| | - Mikhail M Savitski
- Proteomics Core Facility, EMBL Heidelberg, Meyerhofstraße 1, 69117 Heidelberg, Germany; Genome Biology Unit, EMBL Heidelberg, Meyerhofstraße 1, 69117 Heidelberg, Germany
| | - Fátima Gebauer
- Gene Regulation, Stem Cells and Cancer Programme, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, 08003 Barcelona, Spain; Universitat Pompeu Fabra (UPF), 08003 Barcelona, Spain
| | - Janosch Hennig
- Structural and Computational Biology Unit, EMBL Heidelberg, Meyerhofstraße 1, 69117 Heidelberg, Germany.
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12
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Ye X, Jankowsky E. High throughput approaches to study RNA-protein interactions in vitro. Methods 2020; 178:3-10. [PMID: 31494245 PMCID: PMC7071787 DOI: 10.1016/j.ymeth.2019.09.006] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2019] [Revised: 06/07/2019] [Accepted: 09/01/2019] [Indexed: 02/08/2023] Open
Abstract
To understand the regulation of gene expression it is critical to determine how proteins interact with and discriminate between different RNAs. In this review, we discuss experimental techniques that utilize high throughput approaches to characterize the interactions of proteins with large numbers of RNAs in vitro. We describe the underlying principles for the main methods, briefly discuss their scope and limitations, and outline how insight from the techniques contributes to our understanding of specificity for RNA-protein interactions.
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Affiliation(s)
- Xuan Ye
- Center for RNA Science and Therapeutics, School of Medicine, Case Western Reserve University, Cleveland, OH, United States
| | - Eckhard Jankowsky
- Center for RNA Science and Therapeutics, School of Medicine, Case Western Reserve University, Cleveland, OH, United States.
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13
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RNA-centric approaches to study RNA-protein interactions in vitro and in silico. Methods 2020; 178:11-18. [DOI: 10.1016/j.ymeth.2019.09.011] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2019] [Revised: 09/10/2019] [Accepted: 09/10/2019] [Indexed: 01/17/2023] Open
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14
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Adinolfi M, Pietrosanto M, Parca L, Ausiello G, Ferrè F, Helmer-Citterich M. Discovering sequence and structure landscapes in RNA interaction motifs. Nucleic Acids Res 2019; 47:4958-4969. [PMID: 31162604 PMCID: PMC6547422 DOI: 10.1093/nar/gkz250] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2018] [Revised: 02/22/2019] [Accepted: 04/09/2019] [Indexed: 12/16/2022] Open
Abstract
RNA molecules are able to bind proteins, DNA and other small or long RNAs using information at primary, secondary or tertiary structure level. Recent techniques that use cross-linking and immunoprecipitation of RNAs can detect these interactions and, if followed by high-throughput sequencing, molecules can be analysed to find recurrent elements shared by interactors, such as sequence and/or structure motifs. Many tools are able to find sequence motifs from lists of target RNAs, while others focus on structure using different approaches to find specific interaction elements. In this work, we make a systematic analysis of RBP-RNA and RNA-RNA datasets to better characterize the interaction landscape with information about multi-motifs on the same RNAs. To achieve this goal, we updated our BEAM algorithm to combine both sequence and structure information to create pairs of patterns that model motifs of interaction. This algorithm was applied to several RNA binding proteins and ncRNAs interactors, confirming already known motifs and discovering new ones. This landscape analysis on interaction variability reflects the diversity of target recognition and underlines that often both primary and secondary structure are involved in molecular recognition.
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Affiliation(s)
- Marta Adinolfi
- Centre for Molecular Bioinformatics, Department of Biology, University of Rome Tor Vergata, Via della Ricerca Scientifica snc, 00133 Rome, Italy
| | - Marco Pietrosanto
- Centre for Molecular Bioinformatics, Department of Biology, University of Rome Tor Vergata, Via della Ricerca Scientifica snc, 00133 Rome, Italy
| | - Luca Parca
- Centre for Molecular Bioinformatics, Department of Biology, University of Rome Tor Vergata, Via della Ricerca Scientifica snc, 00133 Rome, Italy
| | - Gabriele Ausiello
- Centre for Molecular Bioinformatics, Department of Biology, University of Rome Tor Vergata, Via della Ricerca Scientifica snc, 00133 Rome, Italy
| | - Fabrizio Ferrè
- Department of Pharmacy and Biotechnology (FaBiT), University of Bologna Alma Mater, Via Selmi 3, 40126 Bologna, Italy
| | - Manuela Helmer-Citterich
- Centre for Molecular Bioinformatics, Department of Biology, University of Rome Tor Vergata, Via della Ricerca Scientifica snc, 00133 Rome, Italy
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15
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Pan X, Yang Y, Xia C, Mirza AH, Shen H. Recent methodology progress of deep learning for RNA–protein interaction prediction. WILEY INTERDISCIPLINARY REVIEWS-RNA 2019; 10:e1544. [DOI: 10.1002/wrna.1544] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/28/2019] [Revised: 04/07/2019] [Accepted: 04/11/2019] [Indexed: 12/17/2022]
Affiliation(s)
- Xiaoyong Pan
- Institute of Image Processing and Pattern Recognition, Shanghai Jiao Tong University, and Key Laboratory of System Control and Information Processing Ministry of Education of China Shanghai China
- IDLab, Department for Electronics and Information Systems Ghent University Ghent Belgium
- BASF Agriculture Solution Ghent Belgium
| | - Yang Yang
- Department of Computer Science Shanghai Jiao Tong University, and Key Laboratory of Shanghai Education Commission for Intelligent Interaction and Cognitive Engineering Shanghai China
| | - Chun‐Qiu Xia
- Institute of Image Processing and Pattern Recognition, Shanghai Jiao Tong University, and Key Laboratory of System Control and Information Processing Ministry of Education of China Shanghai China
| | - Aashiq H. Mirza
- Department of Pharmacology Weill Cornell Medicine New York New York
| | - Hong‐Bin Shen
- Institute of Image Processing and Pattern Recognition, Shanghai Jiao Tong University, and Key Laboratory of System Control and Information Processing Ministry of Education of China Shanghai China
- Department of Computer Science Shanghai Jiao Tong University, and Key Laboratory of Shanghai Education Commission for Intelligent Interaction and Cognitive Engineering Shanghai China
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