1301
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Matia-González AM, Laing EE, Gerber AP. Conserved mRNA-binding proteomes in eukaryotic organisms. Nat Struct Mol Biol 2015; 22:1027-33. [PMID: 26595419 PMCID: PMC5759928 DOI: 10.1038/nsmb.3128] [Citation(s) in RCA: 128] [Impact Index Per Article: 14.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2015] [Accepted: 10/23/2015] [Indexed: 12/12/2022]
Abstract
RNA-binding proteins (RBPs) are essential for the post-transcriptional regulation of gene expression. Recent high-throughput screens have dramatically increased the number of experimentally identified RBPs; however, comprehensive identification of RBPs within living organisms is elusive. Here we describe the repertoire of 765 and 594 proteins that reproducibly interact with polyadenylated mRNAs in Saccharomyces cerevisiae and Caenorhabditis elegans, respectively. Furthermore, we report the differential association of mRBPs upon apoptosis induction in C. elegans L4 stage larvae. Strikingly, most proteins comprising mRNA-binding proteomes (mRBPomes) are evolutionarily conserved between yeast and C. elegans, including components of early metabolic pathways and the proteasome. Based on our evidence that glycolytic enzymes bind to distinct glycolytic mRNAs, we speculate that enzyme-mRNA interactions relate to an ancient mechanism for post-transcriptional coordination of metabolic pathways, perhaps established during the transition from the early RNA to the protein ‘world’.
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Affiliation(s)
- Ana M Matia-González
- Department of Microbial and Cellular Sciences, School of Biosciences and Medicine, Faculty of Health and Medical Sciences, University of Surrey, Guildford, UK
| | - Emma E Laing
- Department of Microbial and Cellular Sciences, School of Biosciences and Medicine, Faculty of Health and Medical Sciences, University of Surrey, Guildford, UK
| | - André P Gerber
- Department of Microbial and Cellular Sciences, School of Biosciences and Medicine, Faculty of Health and Medical Sciences, University of Surrey, Guildford, UK
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1302
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Reddy BPN, Shrestha S, Hart KJ, Liang X, Kemirembe K, Cui L, Lindner SE. A bioinformatic survey of RNA-binding proteins in Plasmodium. BMC Genomics 2015; 16:890. [PMID: 26525978 PMCID: PMC4630921 DOI: 10.1186/s12864-015-2092-1] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2015] [Accepted: 10/15/2015] [Indexed: 11/10/2022] Open
Abstract
Background The malaria parasites in the genus Plasmodium have a very complicated life cycle involving an invertebrate vector and a vertebrate host. RNA-binding proteins (RBPs) are critical factors involved in every aspect of the development of these parasites. However, very few RBPs have been functionally characterized to date in the human parasite Plasmodium falciparum. Methods Using different bioinformatic methods and tools we searched P. falciparum genome to list and annotate RBPs. A representative 3D models for each of the RBD domain identified in P. falciparum was created using I-TESSAR and SWISS-MODEL. Microarray and RNAseq data analysis pertaining PfRBPs was performed using MeV software. Finally, Cytoscape was used to create protein-protein interaction network for CITH-Dozi and Caf1-CCR4-Not complexes. Results We report the identification of 189 putative RBP genes belonging to 13 different families in Plasmodium, which comprise 3.5 % of all annotated genes. Almost 90 % (169/189) of these genes belong to six prominent RBP classes, namely RNA recognition motifs, DEAD/H-box RNA helicases, K homology, Zinc finger, Puf and Alba gene families. Interestingly, almost all of the identified RNA-binding helicases and KH genes have cognate homologs in model species, suggesting their evolutionary conservation. Exploration of the existing P. falciparum blood-stage transcriptomes revealed that most RBPs have peak mRNA expression levels early during the intraerythrocytic development cycle, which taper off in later stages. Nearly 27 % of RBPs have elevated expression in gametocytes, while 47 and 24 % have elevated mRNA expression in ookinete and asexual stages. Comparative interactome analyses using human and Plasmodium protein-protein interaction datasets suggest extensive conservation of the PfCITH/PfDOZI and PfCaf1-CCR4-NOT complexes. Conclusions The Plasmodium parasites possess a large number of putative RBPs belonging to most of RBP families identified so far, suggesting the presence of extensive post-transcriptional regulation in these parasites. Taken together, in silico identification of these putative RBPs provides a foundation for future functional studies aimed at defining a unique network of post-transcriptional regulation in P. falciparum. Electronic supplementary material The online version of this article (doi:10.1186/s12864-015-2092-1) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- B P Niranjan Reddy
- Department of Entomology, Center for Malaria Research, Pennsylvania State University, 501 ASI Bldg, University Park, PA, 16802, USA
| | - Sony Shrestha
- Department of Entomology, Center for Malaria Research, Pennsylvania State University, 501 ASI Bldg, University Park, PA, 16802, USA
| | - Kevin J Hart
- Department of Biochemistry and Molecular Biology, Center for Malaria Research, Pennsylvania State University, W223 Millennium Science Complex, University Park, PA, 16802, USA
| | - Xiaoying Liang
- Department of Entomology, Center for Malaria Research, Pennsylvania State University, 501 ASI Bldg, University Park, PA, 16802, USA
| | - Karen Kemirembe
- Department of Entomology, Center for Malaria Research, Pennsylvania State University, 501 ASI Bldg, University Park, PA, 16802, USA
| | - Liwang Cui
- Department of Entomology, Center for Malaria Research, Pennsylvania State University, 501 ASI Bldg, University Park, PA, 16802, USA.
| | - Scott E Lindner
- Department of Biochemistry and Molecular Biology, Center for Malaria Research, Pennsylvania State University, W223 Millennium Science Complex, University Park, PA, 16802, USA.
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1303
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The Crystal Structure of the NHL Domain in Complex with RNA Reveals the Molecular Basis of Drosophila Brain-Tumor-Mediated Gene Regulation. Cell Rep 2015; 13:1206-1220. [DOI: 10.1016/j.celrep.2015.09.068] [Citation(s) in RCA: 67] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2015] [Revised: 07/31/2015] [Accepted: 09/24/2015] [Indexed: 12/26/2022] Open
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1304
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Emerging Roles of Disordered Sequences in RNA-Binding Proteins. Trends Biochem Sci 2015; 40:662-672. [DOI: 10.1016/j.tibs.2015.08.012] [Citation(s) in RCA: 161] [Impact Index Per Article: 17.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2015] [Revised: 08/21/2015] [Accepted: 08/31/2015] [Indexed: 12/12/2022]
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1305
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Zaman U, Richter FM, Hofele R, Kramer K, Sachsenberg T, Kohlbacher O, Lenz C, Urlaub H. Dithiothreitol (DTT) Acts as a Specific, UV-inducible Cross-linker in Elucidation of Protein-RNA Interactions. Mol Cell Proteomics 2015; 14:3196-210. [PMID: 26450613 DOI: 10.1074/mcp.m115.052795] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2015] [Indexed: 11/06/2022] Open
Abstract
Protein-RNA cross-linking by UV irradiation at 254 nm wavelength has been established as an unbiased method to identify proteins in direct contact with RNA, and has been successfully applied to investigate the spatial arrangement of protein and RNA in large macromolecular assemblies, e.g. ribonucleoprotein-complex particles (RNPs). The mass spectrometric analysis of such peptide-RNA cross-links provides high resolution structural data to the point of mapping protein-RNA interactions to specific peptides or even amino acids. However, the approach suffers from the low yield of cross-linking products, which can be addressed by improving enrichment and analysis methods. In the present article, we introduce dithiothreitol (DTT) as a potent protein-RNA cross-linker. In order to evaluate the efficiency and specificity of DTT, we used two systems, a small synthetic peptide from smB protein incubated with U1 snRNA oligonucleotide and native ribonucleoprotein complexes from S. cerevisiae. Our results unambiguously show that DTT covalently participates in cysteine-uracil crosslinks, which is observable as a mass increment of 151.9966 Da (C(4)H(8)S(2)O(2)) upon mass spectrometric analysis. DTT presents advantages for cross-linking of cysteine containing regions of proteins. This is evidenced by comparison to experiments where (tris(2-carboxyethyl)phosphine) is used as reducing agent, and significantly less cross-links encompassing cysteine residues are found. We further propose insertion of DTT between the cysteine and uracil reactive sites as the most probable structure of the cross-linking products.
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Affiliation(s)
- Uzma Zaman
- From the ‡Bioanalytical Mass Spectrometry Group, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, D-37077 Göttingen, Germany; §Bioanalytics, Institute for Clinical Chemistry, University Medical Center Göttingen, Robert-Koch-Strasse 40, D-37075 Göttingen, Germany
| | - Florian M Richter
- From the ‡Bioanalytical Mass Spectrometry Group, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, D-37077 Göttingen, Germany
| | - Romina Hofele
- From the ‡Bioanalytical Mass Spectrometry Group, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, D-37077 Göttingen, Germany; §Bioanalytics, Institute for Clinical Chemistry, University Medical Center Göttingen, Robert-Koch-Strasse 40, D-37075 Göttingen, Germany
| | - Katharina Kramer
- From the ‡Bioanalytical Mass Spectrometry Group, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, D-37077 Göttingen, Germany; §Bioanalytics, Institute for Clinical Chemistry, University Medical Center Göttingen, Robert-Koch-Strasse 40, D-37075 Göttingen, Germany
| | - Timo Sachsenberg
- ¶Center for Bioinformatics, ‖Department of Computer Science, University of Tübingen, Sand 14, D-72076 Tübingen, Germany
| | - Oliver Kohlbacher
- ¶Center for Bioinformatics, ‖Department of Computer Science, University of Tübingen, Sand 14, D-72076 Tübingen, Germany; ¶¶Biomolecular Interactions, Max Planck Institute for Developmental Biology, Spemannstraße 35, D-72076 Tübingen, Germany
| | - Christof Lenz
- From the ‡Bioanalytical Mass Spectrometry Group, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, D-37077 Göttingen, Germany; §Bioanalytics, Institute for Clinical Chemistry, University Medical Center Göttingen, Robert-Koch-Strasse 40, D-37075 Göttingen, Germany
| | - Henning Urlaub
- From the ‡Bioanalytical Mass Spectrometry Group, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, D-37077 Göttingen, Germany; §Bioanalytics, Institute for Clinical Chemistry, University Medical Center Göttingen, Robert-Koch-Strasse 40, D-37075 Göttingen, Germany;
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1306
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Williams Z, Morozov P, Mihailovic A, Lin C, Puvvula P, Juranek S, Rosenwaks Z, Tuschl T. Discovery and Characterization of piRNAs in the Human Fetal Ovary. Cell Rep 2015; 13:854-863. [DOI: 10.1016/j.celrep.2015.09.030] [Citation(s) in RCA: 81] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2014] [Revised: 07/10/2015] [Accepted: 09/10/2015] [Indexed: 11/28/2022] Open
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1307
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Combinatorial Control of mRNA Fates by RNA-Binding Proteins and Non-Coding RNAs. Biomolecules 2015; 5:2207-22. [PMID: 26404389 PMCID: PMC4693235 DOI: 10.3390/biom5042207] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2015] [Revised: 09/02/2015] [Accepted: 09/08/2015] [Indexed: 02/07/2023] Open
Abstract
Post-transcriptional control of gene expression is mediated by RNA-binding proteins (RBPs) and small non-coding RNAs (e.g., microRNAs) that bind to distinct elements in their mRNA targets. Here, we review recent examples describing the synergistic and/or antagonistic effects mediated by RBPs and miRNAs to determine the localisation, stability and translation of mRNAs in mammalian cells. From these studies, it is becoming increasingly apparent that dynamic rearrangements of RNA-protein complexes could have profound implications in human cancer, in synaptic plasticity, and in cellular differentiation.
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1308
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Butler AA, Webb WM, Lubin FD. Regulatory RNAs and control of epigenetic mechanisms: expectations for cognition and cognitive dysfunction. Epigenomics 2015; 8:135-51. [PMID: 26366811 DOI: 10.2217/epi.15.79] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
The diverse functions of noncoding RNAs (ncRNAs) can influence virtually every aspect of the transcriptional process including epigenetic regulation of genes. In the CNS, regulatory RNA networks and epigenetic mechanisms have broad relevance to gene transcription changes involved in long-term memory formation and cognition. Thus, it is becoming increasingly clear that multiple classes of ncRNAs impact neuronal development, neuroplasticity, and cognition. Currently, a large gap exists in our knowledge of how ncRNAs facilitate epigenetic processes, and how this phenomenon affects cognitive function. In this review, we discuss recent findings highlighting a provocative role for ncRNAs including lncRNAs and piRNAs in the control of epigenetic mechanisms involved in cognitive function. Furthermore, we discuss the putative roles for these ncRNAs in cognitive disorders such as schizophrenia and Alzheimer's disease.
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Affiliation(s)
- Anderson A Butler
- Department of Neurobiology, University of Alabama at Birmingham, 1825 University Boulevard, Birmingham, AL 35294, USA
| | - William M Webb
- Department of Neurobiology, University of Alabama at Birmingham, 1825 University Boulevard, Birmingham, AL 35294, USA
| | - Farah D Lubin
- Department of Neurobiology, University of Alabama at Birmingham, 1825 University Boulevard, Birmingham, AL 35294, USA
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1309
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Barik A, Nithin C, Karampudi NBR, Mukherjee S, Bahadur RP. Probing binding hot spots at protein-RNA recognition sites. Nucleic Acids Res 2015; 44:e9. [PMID: 26365245 PMCID: PMC4737170 DOI: 10.1093/nar/gkv876] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2015] [Accepted: 08/23/2015] [Indexed: 01/30/2023] Open
Abstract
We use evolutionary conservation derived from structure alignment of polypeptide sequences along with structural and physicochemical attributes of protein–RNA interfaces to probe the binding hot spots at protein–RNA recognition sites. We find that the degree of conservation varies across the RNA binding proteins; some evolve rapidly compared to others. Additionally, irrespective of the structural class of the complexes, residues at the RNA binding sites are evolutionary better conserved than those at the solvent exposed surfaces. For recognitions involving duplex RNA, residues interacting with the major groove are better conserved than those interacting with the minor groove. We identify multi-interface residues participating simultaneously in protein–protein and protein–RNA interfaces in complexes where more than one polypeptide is involved in RNA recognition, and show that they are better conserved compared to any other RNA binding residues. We find that the residues at water preservation site are better conserved than those at hydrated or at dehydrated sites. Finally, we develop a Random Forests model using structural and physicochemical attributes for predicting binding hot spots. The model accurately predicts 80% of the instances of experimental ΔΔG values in a particular class, and provides a stepping-stone towards the engineering of protein–RNA recognition sites with desired affinity.
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Affiliation(s)
- Amita Barik
- Computational Structural Biology Laboratory, Department of Biotechnology, Indian Institute of Technology Kharagpur, Kharagpur-721302, India
| | - Chandran Nithin
- Computational Structural Biology Laboratory, Department of Biotechnology, Indian Institute of Technology Kharagpur, Kharagpur-721302, India
| | | | - Sunandan Mukherjee
- Computational Structural Biology Laboratory, Department of Biotechnology, Indian Institute of Technology Kharagpur, Kharagpur-721302, India
| | - Ranjit Prasad Bahadur
- Computational Structural Biology Laboratory, Department of Biotechnology, Indian Institute of Technology Kharagpur, Kharagpur-721302, India Advanced Technology Development Centre, Indian Institute of Technology Kharagpur, Kharagpur-721302, India
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1310
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Newman R, McHugh J, Turner M. RNA binding proteins as regulators of immune cell biology. Clin Exp Immunol 2015. [PMID: 26201441 DOI: 10.1111/cei.12684] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Sequence-specific RNA binding proteins (RBP) are important regulators of the immune response. RBP modulate gene expression by regulating splicing, polyadenylation, localization, translation and decay of target mRNAs. Increasing evidence suggests that RBP play critical roles in the development, activation and function of lymphocyte populations in the immune system. This review will discuss the post-transcriptional regulation of gene expression by RBP during lymphocyte development, with particular focus on the Tristetraprolin family of RBP.
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Affiliation(s)
- R Newman
- Babraham Institute, Cambridge, UK
| | - J McHugh
- Babraham Institute, Cambridge, UK
| | - M Turner
- Babraham Institute, Cambridge, UK
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1311
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Structural basis underlying CAC RNA recognition by the RRM domain of dimeric RNA-binding protein RBPMS. Q Rev Biophys 2015; 49:e1. [PMID: 26347403 PMCID: PMC4783296 DOI: 10.1017/s0033583515000207] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
RNA-binding protein with multiple splicing (designated RBPMS) is a higher
vertebrate mRNA-binding protein containing a single RNA recognition motif (RRM).
RBPMS has been shown to be involved in mRNA transport, localization and
stability, with key roles in axon guidance, smooth muscle plasticity, as well as
regulation of cancer cell proliferation and migration. We report on
structure-function studies of the RRM domain of RBPMS bound to a CAC-containing
single-stranded RNA. These results provide insights into potential topologies of
complexes formed by the RBPMS RRM domain and the tandem CAC repeat binding sites
as detected by photoactivatable-ribonucleoside-enhanced crosslinking and
immunoprecipitation. These studies establish that the RRM domain of RBPMS forms
a symmetrical dimer in the free state, with each monomer binding
sequence-specifically to all three nucleotides of a CAC segment in the RNA bound
state. Structure-guided mutations within the dimerization and RNA-binding
interfaces of RBPMS RRM on RNA complex formation resulted in both disruption of
dimerization and a decrease in RNA-binding affinity as observed by size
exclusion chromatography and isothermal titration calorimetry. As anticipated
from biochemical binding studies, over-expression of dimerization or RNA-binding
mutants of Flag-HA-tagged RBPMS were no longer able to track with stress
granules in HEK293 cells, thereby documenting the deleterious effects of such
mutations in vivo.
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1312
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Golumbeanu M, Mohammadi P, Beerenwinkel N. BMix: probabilistic modeling of occurring substitutions in PAR-CLIP data. Bioinformatics 2015; 32:976-83. [PMID: 26342229 DOI: 10.1093/bioinformatics/btv520] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2015] [Accepted: 08/18/2015] [Indexed: 11/13/2022] Open
Abstract
MOTIVATION Photoactivatable ribonucleoside-enhanced cross-linking and immunoprecipitation (PAR-CLIP) is an experimental method based on next-generation sequencing for identifying the RNA interaction sites of a given protein. The method deliberately inserts T-to-C substitutions at the RNA-protein interaction sites, which provides a second layer of evidence compared with other CLIP methods. However, the experiment includes several sources of noise which cause both low-frequency errors and spurious high-frequency alterations. Therefore, rigorous statistical analysis is required in order to separate true T-to-C base changes, following cross-linking, from noise. So far, most of the existing PAR-CLIP data analysis methods focus on discarding the low-frequency errors and rely on high-frequency substitutions to report binding sites, not taking into account the possibility of high-frequency false positive substitutions. RESULTS Here, we introduce BMix, a new probabilistic method which explicitly accounts for the sources of noise in PAR-CLIP data and distinguishes cross-link induced T-to-C substitutions from low and high-frequency erroneous alterations. We demonstrate the superior speed and accuracy of our method compared with existing approaches on both simulated and real, publicly available human datasets. AVAILABILITY AND IMPLEMENTATION The model is freely accessible within the BMix toolbox at www.cbg.bsse.ethz.ch/software/BMix, available for Matlab and R. SUPPLEMENTARY INFORMATION Supplementary data is available at Bioinformatics online. CONTACT niko.beerenwinkel@bsse.ethz.ch.
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Affiliation(s)
- Monica Golumbeanu
- Department of Biosystems Science and Engineering and SIB Swiss Institute of Bioinformatics, CH-4058 Basel, Switzerland
| | - Pejman Mohammadi
- Department of Biosystems Science and Engineering and SIB Swiss Institute of Bioinformatics, CH-4058 Basel, Switzerland
| | - Niko Beerenwinkel
- Department of Biosystems Science and Engineering and SIB Swiss Institute of Bioinformatics, CH-4058 Basel, Switzerland
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1313
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Kardos GR, Robertson GP. Therapeutic interventions to disrupt the protein synthetic machinery in melanoma. Pigment Cell Melanoma Res 2015; 28:501-19. [PMID: 26139519 PMCID: PMC4716672 DOI: 10.1111/pcmr.12391] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2015] [Accepted: 06/30/2015] [Indexed: 01/23/2023]
Abstract
Control of the protein synthetic machinery is deregulated in many cancers, including melanoma, to increase the protein production. Tumor suppressors and oncogenes play key roles in protein synthesis from the transcription of rRNA and ribosome biogenesis to mRNA translation initiation and protein synthesis. Major signaling pathways are altered in melanoma to modulate the protein synthetic machinery, thereby promoting tumor development. However, despite the importance of this process in melanoma development, involvement of the protein synthetic machinery in this cancer type is an underdeveloped area of study. Here, we review the coupling of melanoma development to deregulation of the protein synthetic machinery. We examine existing knowledge regarding RNA polymerase I inhibition and mRNA translation focusing on their inhibition for therapeutic applications in melanoma. Furthermore, the contribution of amino acid biosynthesis and involvement of ribosomal proteins are also reviewed as future therapeutic strategies to target deregulated protein production in melanoma.
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Affiliation(s)
- Gregory R. Kardos
- Department of Pharmacology, The Pennsylvania State University College of Medicine, 500 University Drive, Hershey, PA, USA, 17033
- The Melanoma and Skin Cancer Center, The Pennsylvania State University College of Medicine, 500 University Drive, Hershey, PA, USA, 17033
- The Melanoma Therapeutics Program, The Pennsylvania State University College of Medicine, 500 University Drive, Hershey, PA, USA, 17033
| | - Gavin P. Robertson
- Department of Pharmacology, The Pennsylvania State University College of Medicine, 500 University Drive, Hershey, PA, USA, 17033
- Department of Pathology, The Pennsylvania State University College of Medicine, 500 University Drive, Hershey, PA, USA, 17033
- Department of Dermatology, The Pennsylvania State University College of Medicine, 500 University Drive, Hershey, PA, USA, 17033
- Department of Surgery, The Pennsylvania State University College of Medicine, 500 University Drive, Hershey, PA, USA, 17033
- The Melanoma and Skin Cancer Center, The Pennsylvania State University College of Medicine, 500 University Drive, Hershey, PA, USA, 17033
- The Melanoma Therapeutics Program, The Pennsylvania State University College of Medicine, 500 University Drive, Hershey, PA, USA, 17033
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1314
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Nakamura S, Kahyo T, Tao H, Shibata K, Kurabe N, Yamada H, Shinmura K, Ohnishi K, Sugimura H. Novel roles for LIX1L in promoting cancer cell proliferation through ROS1-mediated LIX1L phosphorylation. Sci Rep 2015; 5:13474. [PMID: 26310847 PMCID: PMC4550850 DOI: 10.1038/srep13474] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2015] [Accepted: 07/27/2015] [Indexed: 11/25/2022] Open
Abstract
Herein, we report the characterization of Limb expression 1-like, (LIX1L), a putative RNA-binding protein (RBP) containing a double-stranded RNA binding motif, which is highly expressed in various cancer tissues. Analysis of MALDI-TOF/TOF mass spectrometry and RNA immunoprecipitation-sequencing of interacting proteins and the microRNAs (miRNAs) bound to LIX1L revealed that LIX1L interacts with proteins (RIOK1, nucleolin and PABPC4) and miRNAs (has-miRNA-520a-5p, −300, −216b, −326, −190a, −548b-3p, −7–5p and −1296) in HEK-293 cells. Moreover, the reduction of phosphorylated Tyr136 (pTyr136) in LIX1L through the homeodomain peptide, PY136, inhibited LIX1L-induced cell proliferation in vitro, and PY136 inhibited MKN45 cell proliferation in vivo. We also determined the miRNA-targeted genes and showed that was apoptosis induced through the reduction of pTyr136. Moreover, ROS1, HCK, ABL1, ABL2, JAK3, LCK and TYR03 were identified as candidate kinases responsible for the phosphorylation of Tyr136 of LIX1L. These data provide novel insights into the biological significance of LIX1L, suggesting that this protein might be an RBP, with implications for therapeutic approaches for targeting LIX1L in LIX1L-expressing cancer cells.
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Affiliation(s)
- Satoki Nakamura
- Department of Tumor Pathology, 1-20-1 Handayama, Higashi-ku, Hamamatsu, Shizuoka 431-3192, Japan
| | - Tomoaki Kahyo
- Department of Tumor Pathology, 1-20-1 Handayama, Higashi-ku, Hamamatsu, Shizuoka 431-3192, Japan
| | - Hong Tao
- Department of Tumor Pathology, 1-20-1 Handayama, Higashi-ku, Hamamatsu, Shizuoka 431-3192, Japan
| | - Kiyoshi Shibata
- Equipment Center, 1-20-1 Handayama, Higashi-ku, Hamamatsu, Shizuoka 431-3192, Japan
| | - Nobuya Kurabe
- Department of Tumor Pathology, 1-20-1 Handayama, Higashi-ku, Hamamatsu, Shizuoka 431-3192, Japan
| | - Hidetaka Yamada
- Department of Tumor Pathology, 1-20-1 Handayama, Higashi-ku, Hamamatsu, Shizuoka 431-3192, Japan
| | - Kazuya Shinmura
- Department of Tumor Pathology, 1-20-1 Handayama, Higashi-ku, Hamamatsu, Shizuoka 431-3192, Japan
| | - Kazunori Ohnishi
- Cancer Center, Hamamatsu University School of Medicine, 1-20-1 Handayama, Higashi-ku, Hamamatsu, Shizuoka 431-3192, Japan
| | - Haruhiko Sugimura
- Department of Tumor Pathology, 1-20-1 Handayama, Higashi-ku, Hamamatsu, Shizuoka 431-3192, Japan
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1315
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Kubota M, Chan D, Spitale RC. RNA structure: merging chemistry and genomics for a holistic perspective. Bioessays 2015; 37:1129-38. [PMID: 26288173 DOI: 10.1002/bies.201300146] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
The advent of deep sequencing technology has unexpectedly advanced our structural understanding of molecules composed of nucleic acids. A significant amount of progress has been made recently extrapolating the chemical methods to probe RNA structure into sequencing methods. Herein we review some of the canonical methods to analyze RNA structure, and then we outline how these have been used to probe the structure of many RNAs in parallel. The key is the transformation of structural biology problems into sequencing problems, whereby sequencing power can be interpreted to understand nucleic acid proximity, nucleic acid conformation, or nucleic acid-protein interactions. Utilizing such technologies in this way has the promise to provide novel structural insights into the mechanisms that control normal cellular physiology and provide insight into how structure could be perturbed in disease.
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Affiliation(s)
- Miles Kubota
- Department of Pharmaceutical Sciences, University of California, Irvine, Irvine, CA, USA
| | - Dalen Chan
- Department of Pharmaceutical Sciences, University of California, Irvine, Irvine, CA, USA
| | - Robert C Spitale
- Department of Pharmaceutical Sciences, University of California, Irvine, Irvine, CA, USA
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1316
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Abstract
To fully understand the regulation of gene expression, it is critical to quantitatively define whether and how RNA-binding proteins (RBPs) discriminate between alternative binding sites in RNAs. Here, we describe new methods that measure protein binding to large numbers of RNA variants, and ways to analyse and interpret data obtained by these approaches, including affinity distributions and free energy landscapes. We discuss how the new methodologies and the associated concepts enable the development of inclusive, quantitative models for RNA-protein interactions that transcend the traditional binary classification of RBPs as either specific or nonspecific.
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1317
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Ren H, Shen Y. RNA-binding residues prediction using structural features. BMC Bioinformatics 2015; 16:249. [PMID: 26254826 PMCID: PMC4529986 DOI: 10.1186/s12859-015-0691-0] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2015] [Accepted: 07/31/2015] [Indexed: 01/25/2023] Open
Abstract
Background RNA-protein complexes play an essential role in many biological processes. To explore potential functions of RNA-protein complexes, it’s important to identify RNA-binding residues in proteins. Results In this work, we propose a set of new structural features for RNA-binding residue prediction. A set of template patches are first extracted from RNA-binding interfaces. To construct structural features for a residue, we compare its surrounding patches with each template patch and use the accumulated distances as its structural features. These new features provide sufficient structural information of surrounding surface of a residue and they can be used to measure the structural similarity between the surface surrounding two residues. The new structural features, together with other sequence features, are used to predict RNA-binding residues using ensemble learning technique. Conclusions The experimental results reveal the effectiveness of the proposed structural features. In addition, the clustering results on template patches exhibit distinct structural patterns of RNA-binding sites, although the sequences of template patches in the same cluster are not conserved. We speculate that RNAs may have structure preferences when binding with proteins.
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Affiliation(s)
- Huizhu Ren
- 2011 Collaborative Innovation Center of Tianjin for Medical Epigenetics, Key Laboratory of Hormones and Development (Ministry of Health), Metabolic Diseases Hospital & Tianjin Institute of Endocrinology, Tianjin Medical University, Tianjin, 300070, China.
| | - Ying Shen
- School of Software Engineering, Tongji University, Shanghai, 201804, China. .,Key Laboratory of Intelligent Perception and Systems for High-Dimensional Information, Ministry of Education, Nanjing University of Science and Technology, Nanjing, 210094, P.R. China.
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1318
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Sharma K, Hrle A, Kramer K, Sachsenberg T, Staals RHJ, Randau L, Marchfelder A, van der Oost J, Kohlbacher O, Conti E, Urlaub H. Analysis of protein-RNA interactions in CRISPR proteins and effector complexes by UV-induced cross-linking and mass spectrometry. Methods 2015; 89:138-48. [PMID: 26071038 DOI: 10.1016/j.ymeth.2015.06.005] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2015] [Revised: 05/19/2015] [Accepted: 06/04/2015] [Indexed: 11/16/2022] Open
Abstract
Ribonucleoprotein (RNP) complexes play important roles in the cell by mediating basic cellular processes, including gene expression and its regulation. Understanding the molecular details of these processes requires the identification and characterization of protein-RNA interactions. Over the years various approaches have been used to investigate these interactions, including computational analyses to look for RNA binding domains, gel-shift mobility assays on recombinant and mutant proteins as well as co-crystallization and NMR studies for structure elucidation. Here we report a more specialized and direct approach using UV-induced cross-linking coupled with mass spectrometry. This approach permits the identification of cross-linked peptides and RNA moieties and can also pin-point exact RNA contact sites within the protein. The power of this method is illustrated by the application to different single- and multi-subunit RNP complexes belonging to the prokaryotic adaptive immune system, CRISPR-Cas (CRISPR: clustered regularly interspaced short palindromic repeats; Cas: CRISPR associated). In particular, we identified the RNA-binding sites within three Cas7 protein homologs and mapped the cross-linking results to reveal structurally conserved Cas7 - RNA binding interfaces. These results demonstrate the strong potential of UV-induced cross-linking coupled with mass spectrometry analysis to identify RNA interaction sites on the RNA binding proteins.
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Affiliation(s)
- Kundan Sharma
- Bioanalytical Mass Spectrometry, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
| | - Ajla Hrle
- Structural Cell Biology Department, Max Planck Institute for Biochemistry, Martinsried, Germany
| | - Katharina Kramer
- Bioanalytical Mass Spectrometry, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany; Plant Proteomics Group, Max Planck Institute for Plant Breeding Research, Cologne, Germany
| | - Timo Sachsenberg
- Center for Bioinformatics, University of Tübingen, Tübingen, Germany; Department of Computer Science, University of Tübingen, Tübingen, Germany
| | - Raymond H J Staals
- Laboratory of Microbiology, Department of Agrotechnology and Food Sciences, Wageningen University, Wageningen, The Netherlands
| | - Lennart Randau
- Prokaryotic Small RNA Biology, Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
| | | | - John van der Oost
- Laboratory of Microbiology, Department of Agrotechnology and Food Sciences, Wageningen University, Wageningen, The Netherlands
| | - Oliver Kohlbacher
- Center for Bioinformatics, University of Tübingen, Tübingen, Germany; Department of Computer Science, University of Tübingen, Tübingen, Germany; Quantitative Biology Center, University of Tübingen, Tübingen, Germany; Faculty of Medicine, University of Tübingen, Tübingen, Germany
| | - Elena Conti
- Structural Cell Biology Department, Max Planck Institute for Biochemistry, Martinsried, Germany
| | - Henning Urlaub
- Bioanalytical Mass Spectrometry, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany; Bioanalytics Research Group, Department of Clinical Chemistry, University Medical Center, Göttingen, Germany
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1319
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Li W, Freudenberg J, Oswald M. Principles for the organization of gene-sets. Comput Biol Chem 2015; 59 Pt B:139-49. [PMID: 26188561 DOI: 10.1016/j.compbiolchem.2015.04.005] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2015] [Accepted: 04/08/2015] [Indexed: 12/23/2022]
Abstract
A gene-set, an important concept in microarray expression analysis and systems biology, is a collection of genes and/or their products (i.e. proteins) that have some features in common. There are many different ways to construct gene-sets, but a systematic organization of these ways is lacking. Gene-sets are mainly organized ad hoc in current public-domain databases, with group header names often determined by practical reasons (such as the types of technology in obtaining the gene-sets or a balanced number of gene-sets under a header). Here we aim at providing a gene-set organization principle according to the level at which genes are connected: homology, physical map proximity, chemical interaction, biological, and phenotypic-medical levels. We also distinguish two types of connections between genes: actual connection versus sharing of a label. Actual connections denote direct biological interactions, whereas shared label connection denotes shared membership in a group. Some extensions of the framework are also addressed such as overlapping of gene-sets, modules, and the incorporation of other non-protein-coding entities such as microRNAs.
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Affiliation(s)
- Wentian Li
- The Robert S. Boas Center for Genomics and Human Genetics, The Feinstein Institute for Medical Research, North Shore LIJ Health System, Manhasset, NY, USA.
| | - Jan Freudenberg
- The Robert S. Boas Center for Genomics and Human Genetics, The Feinstein Institute for Medical Research, North Shore LIJ Health System, Manhasset, NY, USA
| | - Michaela Oswald
- The Robert S. Boas Center for Genomics and Human Genetics, The Feinstein Institute for Medical Research, North Shore LIJ Health System, Manhasset, NY, USA
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1320
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Hennig J, Sattler M. Deciphering the protein-RNA recognition code: Combining large-scale quantitative methods with structural biology. Bioessays 2015; 37:899-908. [DOI: 10.1002/bies.201500033] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Affiliation(s)
- Janosch Hennig
- Institute of Structural Biology; Helmholtz Zentrum M; ü; nchen; München Germany
- Department Chemie; Center for Integrated Protein Science Munich at Biomolecular NMR Spectroscopy; Technische Universität München; Garching Germany
| | - Michael Sattler
- Institute of Structural Biology; Helmholtz Zentrum M; ü; nchen; München Germany
- Department Chemie; Center for Integrated Protein Science Munich at Biomolecular NMR Spectroscopy; Technische Universität München; Garching Germany
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1321
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Chou MT, Han BW, Hsiao CP, Zamore PD, Weng Z, Hung JH. Tailor: a computational framework for detecting non-templated tailing of small silencing RNAs. Nucleic Acids Res 2015; 43:e109. [PMID: 26007652 PMCID: PMC4632877 DOI: 10.1093/nar/gkv537] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2015] [Accepted: 05/10/2015] [Indexed: 12/19/2022] Open
Abstract
Small silencing RNAs, including microRNAs, endogenous small interfering RNAs (endo-siRNAs) and Piwi-interacting RNAs (piRNAs), have been shown to play important roles in fine-tuning gene expression, defending virus and controlling transposons. Loss of small silencing RNAs or components in their pathways often leads to severe developmental defects, including lethality and sterility. Recently, non-templated addition of nucleotides to the 3′ end, namely tailing, was found to associate with the processing and stability of small silencing RNAs. Next Generation Sequencing has made it possible to detect such modifications at nucleotide resolution in an unprecedented throughput. Unfortunately, detecting such events from millions of short reads confounded by sequencing errors and RNA editing is still a tricky problem. Here, we developed a computational framework, Tailor, driven by an efficient and accurate aligner specifically designed for capturing the tailing events directly from the alignments without extensive post-processing. The performance of Tailor was fully tested and compared favorably with other general-purpose aligners using both simulated and real datasets for tailing analysis. Moreover, to show the broad utility of Tailor, we used Tailor to reanalyze published datasets and revealed novel findings worth further experimental validation. The source code and the executable binaries are freely available at https://github.com/jhhung/Tailor.
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Affiliation(s)
- Min-Te Chou
- Institute of Bioinformatics and Systems Biology and Department of Biological Science and Technology, National Chiao Tung University, HsinChu, Taiwan, 300, Republic of China
| | - Bo W Han
- RNA Therapeutics Institute, Howard Hughes Medical Institute, and Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Chiung-Po Hsiao
- Institute of Bioinformatics and Systems Biology and Department of Biological Science and Technology, National Chiao Tung University, HsinChu, Taiwan, 300, Republic of China
| | - Phillip D Zamore
- RNA Therapeutics Institute, Howard Hughes Medical Institute, and Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Zhiping Weng
- Program in Bioinformatics and Integrative Biology, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Jui-Hung Hung
- Institute of Bioinformatics and Systems Biology and Department of Biological Science and Technology, National Chiao Tung University, HsinChu, Taiwan, 300, Republic of China
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1322
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Piñeiro D, Fernandez-Chamorro J, Francisco-Velilla R, Martinez-Salas E. Gemin5: A Multitasking RNA-Binding Protein Involved in Translation Control. Biomolecules 2015; 5:528-44. [PMID: 25898402 PMCID: PMC4496684 DOI: 10.3390/biom5020528] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2015] [Revised: 04/01/2015] [Accepted: 04/09/2015] [Indexed: 12/31/2022] Open
Abstract
Gemin5 is a RNA-binding protein (RBP) that was first identified as a peripheral component of the survival of motor neurons (SMN) complex. This predominantly cytoplasmic protein recognises the small nuclear RNAs (snRNAs) through its WD repeat domains, allowing assembly of the SMN complex into small nuclear ribonucleoproteins (snRNPs). Additionally, the amino-terminal end of the protein has been reported to possess cap-binding capacity and to interact with the eukaryotic initiation factor 4E (eIF4E). Gemin5 was also shown to downregulate translation, to be a substrate of the picornavirus L protease and to interact with viral internal ribosome entry site (IRES) elements via a bipartite non-canonical RNA-binding site located at its carboxy-terminal end. These features link Gemin5 with translation control events. Thus, beyond its role in snRNPs biogenesis, Gemin5 appears to be a multitasking protein cooperating in various RNA-guided processes. In this review, we will summarise current knowledge of Gemin5 functions. We will discuss the involvement of the protein on translation control and propose a model to explain how the proteolysis fragments of this RBP in picornavirus-infected cells could modulate protein synthesis.
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Affiliation(s)
- David Piñeiro
- Medical Research Council Toxicology Unit, Lancaster Rd, Leicester LE1 9HN, UK.
| | - Javier Fernandez-Chamorro
- Centro de Biología Molecular Severo Ochoa, Consejo Superior de Investigaciones Científicas-Universidad Autónoma de Madrid, Nicolas Cabrera 1, Madrid 28049, Spain.
| | - Rosario Francisco-Velilla
- Centro de Biología Molecular Severo Ochoa, Consejo Superior de Investigaciones Científicas-Universidad Autónoma de Madrid, Nicolas Cabrera 1, Madrid 28049, Spain.
| | - Encarna Martinez-Salas
- Centro de Biología Molecular Severo Ochoa, Consejo Superior de Investigaciones Científicas-Universidad Autónoma de Madrid, Nicolas Cabrera 1, Madrid 28049, Spain.
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1323
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Takeuchi O. [Posttranscriptional control of inflammation by an RNase Regnase-1]. Nihon Yakurigaku Zasshi 2015; 145:129-33. [PMID: 25765494 DOI: 10.1254/fpj.145.129] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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