Ribosomal frameshifting in the CCR5 mRNA is regulated by miRNAs and the NMD pathway
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Bruce A. Shapiro | Wojciech K. Kasprzak | Jonathan D. Dinman | B. Shapiro | J. Dinman | S. Musalgaonkar | W. Kasprzak | Ashton Trey Belew | Arturas Meskauskas | Sharmishtha Musalgaonkar | Vivek M. Advani | Sergey O. Sulima | A. T. Belew | A. Meskauskas | A. Meškauskas
[1] J. Dinman,et al. Single-molecule measurements of the CCR5 mRNA unfolding pathways. , 2014, Biophysical journal.
[2] Christopher D. Brown,et al. A conserved eEF2 coding variant in SCA26 leads to loss of translational fidelity and increased susceptibility to proteostatic insult. , 2012, Human molecular genetics.
[3] J. Dinman,et al. Yeast telomere maintenance is globally controlled by programmed ribosomal frameshifting and the nonsense-mediated mRNA decay pathway , 2013, Translation.
[4] J. Dinman,et al. Torsional restraint: a new twist on frameshifting pseudoknots , 2005, Nucleic acids research.
[5] Stein Aerts,et al. Exome sequencing identifies mutation in CNOT3 and ribosomal genes RPL5 and RPL10 in T-cell acute lymphoblastic leukemia , 2012, Nature Genetics.
[6] J. Guhaniyogi,et al. Regulation of mRNA stability in mammalian cells. , 2001, Gene.
[7] Barry Moore,et al. A Functional –1 Ribosomal Frameshift Signal in the Human Paraneoplastic Ma3 Gene* , 2006, Journal of Biological Chemistry.
[8] T. Darden,et al. A smooth particle mesh Ewald method , 1995 .
[9] I. Brierley,et al. Characterization of the frameshift signal of Edr, a mammalian example of programmed −1 ribosomal frameshifting , 2005, Nucleic acids research.
[10] R. Wickner,et al. Ribosomal frameshifting efficiency and gag/gag-pol ratio are critical for yeast M1 double-stranded RNA virus propagation , 1992, Journal of virology.
[11] Nicholas T. Ingolia,et al. The translational landscape of mTOR signalling steers cancer initiation and metastasis , 2012, Nature.
[12] W. Gilbert,et al. Chemical probes for higher-order structure in RNA. , 1980, Proceedings of the National Academy of Sciences of the United States of America.
[13] P. Kelly,et al. Release factor RF-3 GTPase activity acts in disassembly of the ribosome termination complex. , 1998, RNA.
[14] Edmund K. Burke,et al. RNA FRABASE 2.0: an advanced web-accessible database with the capacity to search the three-dimensional fragments within RNA structures , 2010, BMC Bioinformatics.
[15] G. M. Wilson,et al. Chapter 3. Assays of adenylate uridylate-rich element-mediated mRNA decay in cells. , 2008, Methods in enzymology.
[16] Dennis B. Troup,et al. NCBI GEO: archive for high-throughput functional genomic data , 2008, Nucleic Acids Res..
[17] O Gascuel,et al. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. , 1997, Molecular biology and evolution.
[18] Y. Zhang,et al. Sequence evolution of the CCR5 chemokine receptor gene in primates. , 1999, Molecular biology and evolution.
[19] D. W. Staple,et al. Solution structure and thermodynamic investigation of the HIV-1 frameshift inducing element. , 2005, Journal of molecular biology.
[20] Stefan Aachen,et al. Recoding Expansion Of Decoding Rules Enriches Gene Expression , 2016 .
[21] V. Kim,et al. Human UPF1 Participates in Small RNA-Induced mRNA Downregulation , 2009, Molecular and Cellular Biology.
[22] O. Gascuel,et al. New algorithms and methods to estimate maximum-likelihood phylogenies: assessing the performance of PhyML 3.0. , 2010, Systematic biology.
[23] Junmei Wang,et al. How well does a restrained electrostatic potential (RESP) model perform in calculating conformational energies of organic and biological molecules? , 2000, J. Comput. Chem..
[24] Davide Ruggero,et al. rRNA pseudouridylation defects affect ribosomal ligand binding and translational fidelity from yeast to human cells. , 2011, Molecular cell.
[25] Ali Nahvi,et al. A Parsimonious Model for Gene Regulation by miRNAs , 2011, Science.
[26] Jonathan D Dinman,et al. PRFdb: A database of computationally predicted eukaryotic programmed -1 ribosomal frameshift signals , 2008, BMC Genomics.
[27] Michael Legge,et al. Mammalian Gene PEG10 Expresses Two Reading Frames by High Efficiency –1 Frameshifting in Embryonic-associated Tissues* , 2007, Journal of Biological Chemistry.
[28] Richard A. Moore,et al. The Completion of the Mammalian Gene Collection (mgc) Recommended Citation , 2022 .
[29] Virginia Litwin,et al. HIV-1 entry into CD4+ cells is mediated by the chemokine receptor CC-CKR-5 , 1996, Nature.
[30] Mario Roederer,et al. Massive infection and loss of memory CD4+ T cells in multiple tissues during acute SIV infection , 2005, Nature.
[31] M. Woodside,et al. Programmed −1 frameshifting efficiency correlates with RNA pseudoknot conformational plasticity, not resistance to mechanical unfolding , 2012, Proceedings of the National Academy of Sciences.
[32] J. F. Atkins,et al. Recoding : expansion of decoding rules enriches gene expression , 2010 .
[33] K. Weeks,et al. Selective 2′-hydroxyl acylation analyzed by primer extension (SHAPE): quantitative RNA structure analysis at single nucleotide resolution , 2006, Nature Protocols.
[34] J. Dinman. Mechanisms and implications of programmed translational frameshifting , 2012, Wiley interdisciplinary reviews. RNA.
[35] A. Lund,et al. Isolation of microRNA targets using biotinylated synthetic microRNAs. , 2007, Methods.
[36] J. Dinman,et al. Endogenous ribosomal frameshift signals operate as mRNA destabilizing elements through at least two molecular pathways in yeast , 2010, Nucleic acids research.
[37] O. Gascuel,et al. SeaView version 4: A multiplatform graphical user interface for sequence alignment and phylogenetic tree building. , 2010, Molecular biology and evolution.
[38] N. Shankar,et al. An equilibrium-dependent retroviral mRNA switch regulates translational recoding , 2011, Nature.
[39] J. Dinman,et al. Systematic analysis of bicistronic reporter assay data , 2004, Nucleic acids research.
[40] Arlen W. Johnson,et al. Bypass of the pre-60S ribosomal quality control as a pathway to oncogenesis , 2014, Proceedings of the National Academy of Sciences.
[41] Nicholas T. Ingolia,et al. Mammalian microRNAs predominantly act to decrease target mRNA levels , 2010, Nature.
[42] H. Berendsen,et al. Molecular dynamics with coupling to an external bath , 1984 .
[43] Steven L Salzberg,et al. Fast gapped-read alignment with Bowtie 2 , 2012, Nature Methods.
[44] B. Chesebro,et al. Effects of CCR5 and CD4 Cell Surface Concentrations on Infections by Macrophagetropic Isolates of Human Immunodeficiency Virus Type 1 , 1998, Journal of Virology.
[45] J. Thompson,et al. CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. , 1994, Nucleic acids research.
[46] J. Maizel,et al. RNA2D3D: A program for Generating, Viewing, and Comparing 3-Dimensional Models of RNA , 2008, Journal of biomolecular structure & dynamics.
[47] J. F. Atkins,et al. A dual-luciferase reporter system for studying recoding signals. , 1998, RNA.
[48] J. Dinman,et al. Mutants That Affect Recoding , 2010 .
[49] Jacek Blazewicz,et al. Automated 3D structure composition for large RNAs , 2012, Nucleic acids research.