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      Profusion of G-quadruplexes on both subunits of metazoan ribosomes

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          Abstract

          Mammalian and bird ribosomes are nearly twice the mass of prokaryotic ribosomes in part because of their extraordinarily long rRNA tentacles. Human rRNA tentacles are not fully observable in current three-dimensional structures and their conformations remain to be fully resolved. In previous work we identified sequences that favor G-quadruplexes in silico and in vitro in rRNA tentacles of the human large ribosomal subunit. We demonstrated by experiment that these sequences form G-quadruplexes in vitro. Here, using a more recent motif definition, we report additional G-quadruplex sequences on surfaces of both subunits of the human ribosome. The revised sequence definition reveals expansive arrays of potential G-quadruplex sequences on LSU tentacles. In addition, we demonstrate by a variety of experimental methods that fragments of the small subunit rRNA form G-quadruplexes in vitro. Prior to this report rRNA sequences that form G-quadruplexes were confined to the large ribosomal subunit. Our combined results indicate that the surface of the assembled human ribosome contains numerous sequences capable of forming G-quadruplexes on both ribosomal subunits. The data suggest conversion between duplexes and G-quadruplexes in response to association with proteins, ions, or other RNAs. In some systems it seems likely that the integrated population of RNA G-quadruplexes may be dominated by rRNA, which is the most abundant cellular RNA.

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          Database resources of the National Center for Biotechnology Information

          Abstract The National Center for Biotechnology Information (NCBI) provides a large suite of online resources for biological information and data, including the GenBank® nucleic acid sequence database and the PubMed database of citations and abstracts for published life science journals. The Entrez system provides search and retrieval operations for most of these data from 39 distinct databases. The E-utilities serve as the programming interface for the Entrez system. Augmenting many of the Web applications are custom implementations of the BLAST program optimized to search specialized data sets. New resources released in the past year include PubMed Data Management, RefSeq Functional Elements, genome data download, variation services API, Magic-BLAST, QuickBLASTp, and Identical Protein Groups. Resources that were updated in the past year include the genome data viewer, a human genome resources page, Gene, virus variation, OSIRIS, and PubChem. All of these resources can be accessed through the NCBI home page at www.ncbi.nlm.nih.gov.
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            rG4-seq reveals widespread formation of G-quadruplex structures in the human transcriptome.

            We introduce RNA G-quadruplex sequencing (rG4-seq), a transcriptome-wide RNA G-quadruplex (rG4) profiling method that couples rG4-mediated reverse transcriptase stalling with next-generation sequencing. Using rG4-seq on polyadenylated-enriched HeLa RNA, we generated a global in vitro map of thousands of canonical and noncanonical rG4 structures. We characterize rG4 formation relative to cytosine content and alternative RNA structure stability, uncover rG4-dependent differences in RNA folding and show evolutionarily conserved enrichment in transcripts mediating RNA processing and stability.
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              G-quadruplexes in RNA biology.

              G-quadruplexes are noncanonical structures formed by G-rich DNA and RNA sequences that fold into a four-stranded conformation. Experimental studies and computational predictions show that RNA G-quadruplexes are present in transcripts associated with telomeres, in noncoding sequences of primary transcripts and within mature transcripts. RNA G-quadruplexes at these specific locations play important roles in key cellular functions, including telomere homeostasis and gene expression. Indeed, RNA G-quadruplexes appear as important regulators of pre-mRNA processing (splicing and polyadenylation), RNA turnover, mRNA targeting and translation. The regulatory mechanisms controlled by RNA G-quadruplexes involve the binding of protein factors that modulate G-quadruplex conformation and/or serve as a bridge to recruit additional protein regulators. In this review, we summarize the current knowledge on the role of G-quadruplexes in RNA biology with particular emphasis on the molecular mechanisms underlying their specific function in RNA metabolism occurring in physiological or pathological conditions. Copyright © 2012 John Wiley & Sons, Ltd.
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                Author and article information

                Contributors
                Role: ConceptualizationRole: InvestigationRole: SupervisionRole: ValidationRole: VisualizationRole: Writing – original draftRole: Writing – review & editing
                Role: SoftwareRole: VisualizationRole: Writing – original draft
                Role: InvestigationRole: Validation
                Role: Investigation
                Role: Investigation
                Role: ConceptualizationRole: Funding acquisitionRole: ResourcesRole: VisualizationRole: Writing – original draft
                Role: ConceptualizationRole: Funding acquisitionRole: ResourcesRole: SupervisionRole: VisualizationRole: Writing – original draftRole: Writing – review & editing
                Role: Editor
                Journal
                PLoS One
                PLoS ONE
                plos
                plosone
                PLoS ONE
                Public Library of Science (San Francisco, CA USA )
                1932-6203
                13 December 2019
                2019
                : 14
                : 12
                : e0226177
                Affiliations
                [1 ] Center for the Origin of Life, Georgia Institute of Technology, Atlanta, Georgia, United States of America
                [2 ] School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, Georgia, United States of America
                [3 ] School of Biological Sciences, Georgia Institute of Technology, Atlanta, Georgia, United States of America
                [4 ] James Graham Brown Cancer Center, University of Louisville, Louisville, Kentucky, United States of America
                Florida International University, UNITED STATES
                Author notes

                Competing Interests: The authors have declared that no competing interests exist.

                Author information
                http://orcid.org/0000-0002-9027-3824
                http://orcid.org/0000-0002-7215-4194
                Article
                PONE-D-19-27856
                10.1371/journal.pone.0226177
                6910669
                31834895
                1854f8ae-7422-4aff-9a2a-043ff903ac6a

                This is an open access article, free of all copyright, and may be freely reproduced, distributed, transmitted, modified, built upon, or otherwise used by anyone for any lawful purpose. The work is made available under the Creative Commons CC0 public domain dedication.

                History
                : 7 October 2019
                : 3 November 2019
                Page count
                Figures: 4, Tables: 2, Pages: 15
                Funding
                Funded by: funder-id http://dx.doi.org/10.13039/100000104, National Aeronautics and Space Administration;
                Award ID: 80NSSC17K0295 and 80NSSC18K1139
                Award Recipient :
                Funded by: funder-id http://dx.doi.org/10.13039/100000002, National Institutes of Health;
                Award ID: GM077422
                Award Recipient :
                Funded by LDW and JBC. Grant Numbers: LDW (80NSSC17K0295 and 80NSSC18K1139), JBC (GM077422). LDW (National Aeronautics and Space Administration). JBC (National Institute of Health and the James Graham Brown Foundation). https://www.nasa.gov/. https://www.nih.gov/. https://jgbf.org/. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.
                Categories
                Research Article
                Biology and life sciences
                Biochemistry
                Nucleic acids
                RNA
                Non-coding RNA
                Ribosomal RNA
                Biology and life sciences
                Biochemistry
                Ribosomes
                Ribosomal RNA
                Biology and life sciences
                Cell biology
                Cellular structures and organelles
                Ribosomes
                Ribosomal RNA
                Research and Analysis Methods
                Database and Informatics Methods
                Bioinformatics
                Sequence Analysis
                Sequence Motif Analysis
                Research and Analysis Methods
                Computational Techniques
                Split-Decomposition Method
                Multiple Alignment Calculation
                Biology and life sciences
                Biophysics
                Nucleic acid thermodynamics
                Genetic annealing
                RNA annealing
                Physical sciences
                Physics
                Biophysics
                Nucleic acid thermodynamics
                Genetic annealing
                RNA annealing
                Biology and life sciences
                Biochemistry
                Nucleic acids
                Nucleic acid thermodynamics
                Genetic annealing
                RNA annealing
                Biology and Life Sciences
                Biochemistry
                Ribosomes
                Biology and Life Sciences
                Cell Biology
                Cellular Structures and Organelles
                Ribosomes
                Research and Analysis Methods
                Database and Informatics Methods
                Bioinformatics
                Sequence Analysis
                Sequence Alignment
                Physical Sciences
                Materials Science
                Materials
                Oligomers
                Biology and Life Sciences
                Taxonomy
                Animal Taxonomy
                Chordata
                Computer and Information Sciences
                Data Management
                Taxonomy
                Animal Taxonomy
                Chordata
                Biology and Life Sciences
                Zoology
                Animal Taxonomy
                Chordata
                Custom metadata
                All relevant data are within the manuscript and its Supporting Information files.

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