Genes adopt non-optimal codon usage to generate cell cycle-dependent oscillations in protein levels
暂无分享,去创建一个
Milana Frenkel-Morgenstern | Lars Juhl Jensen | Tamar Danon | Thomas Christian | Lydia Cohen | Takao Igarashi | L. Jensen | M. Frenkel-Morgenstern | L. Cohen | T. Danon | Ya-Ming Hou | Ya-Ming Hou | T. Christian | T. Igarashi | Lydia Cohen | Lars Juhl Jensen | Ya-Ming Hou | Tamar Danon | Takao Igarashi
[1] Marco Thiel,et al. The Dynamics of Supply and Demand in mRNA Translation , 2011, PLoS Comput. Biol..
[2] E. Phizicky,et al. The yeast rapid tRNA decay pathway primarily monitors the structural integrity of the acceptor and T-stems of mature tRNA. , 2011, Genes & development.
[3] Y. Pilpel,et al. Determinants of translation efficiency and accuracy , 2011, Molecular systems biology.
[4] J. Plotkin,et al. Synonymous but not the same: the causes and consequences of codon bias , 2011, Nature Reviews Genetics.
[5] M. Ibba,et al. New Roles for Codon Usage , 2010, Science.
[6] Y. Pilpel,et al. An Evolutionarily Conserved Mechanism for Controlling the Efficiency of Protein Translation , 2010, Cell.
[7] Nicol N. Schraudolph,et al. A Role for Codon Order in Translation Dynamics , 2010, Cell.
[8] Søren Brunak,et al. Cyclebase.org: version 2.0, an updated comprehensive, multi-species repository of cell cycle experiments and derived analysis results , 2009, Nucleic Acids Res..
[9] Attila Csikász-Nagy,et al. Computational systems biology of the cell cycle , 2009, Briefings Bioinform..
[10] Martijn A. Huynen,et al. Clustering of Codons with Rare Cognate tRNAs in Human Genes Suggests an Extra Level of Expression Regulation , 2009, PLoS genetics.
[11] A. Hinnebusch,et al. Regulation of Translation Initiation in Eukaryotes: Mechanisms and Biological Targets , 2009, Cell.
[12] Reinhard Wolf,et al. Coding-Sequence Determinants of Gene Expression in Escherichia coli , 2009 .
[13] R. Milo,et al. Dynamic Proteomics of Individual Cancer Cells in Response to a Drug , 2008, Science.
[14] Claus O. Wilke,et al. Mistranslation-Induced Protein Misfolding as a Dominant Constraint on Coding-Sequence Evolution , 2008, Cell.
[15] C. Francklyn,et al. Methods for kinetic and thermodynamic analysis of aminoacyl-tRNA synthetases. , 2008, Methods.
[16] Søren Brunak,et al. Cyclebase.org—a comprehensive multi-organism online database of cell-cycle experiments , 2007, Nucleic Acids Res..
[17] Jürg Bähler,et al. Chapter 5 Translational Control of Gene Expression , 2008 .
[18] Jürg Bähler,et al. Translational control of gene expression from transcripts to transcriptomes. , 2008, International review of cell and molecular biology.
[19] Tsutomu Suzuki,et al. Wobble Inosine tRNA Modification Is Essential to Cell Cycle Progression in G1/S and G2/M Transitions in Fission Yeast* , 2007, Journal of Biological Chemistry.
[20] Uri Alon,et al. Generation of a fluorescently labeled endogenous protein library in living human cells , 2007, Nature Protocols.
[21] Lippincott-Schwartz,et al. Supporting Online Material Materials and Methods Som Text Figs. S1 to S8 Table S1 Movies S1 to S3 a " Silent " Polymorphism in the Mdr1 Gene Changes Substrate Specificity Corrected 30 November 2007; See Last Page , 2022 .
[22] Tao Pan,et al. Tissue-Specific Differences in Human Transfer RNA Expression , 2006, PLoS genetics.
[23] T. Pan,et al. Diversity of tRNA genes in eukaryotes , 2006, Nucleic acids research.
[24] R. Milo,et al. Variability and memory of protein levels in human cells , 2006, Nature.
[25] P. Bork,et al. Co-evolution of transcriptional and post-translational cell-cycle regulation , 2006, Nature.
[26] Yan Wang,et al. Genome-wide functional analysis of human cell-cycle regulators , 2006, Proceedings of the National Academy of Sciences.
[27] Anne E Carpenter,et al. Dynamic proteomics in individual human cells uncovers widespread cell-cycle dependence of nuclear proteins , 2006, Nature Methods.
[28] C. Wilke,et al. A single determinant dominates the rate of yeast protein evolution. , 2006, Molecular biology and evolution.
[29] Yizhar Lavner,et al. The action of selection on codon bias in the human genome is related to frequency, complexity, and chronology of amino acids , 2006, BMC Genomics.
[30] John SantaLucia,et al. Nearest-neighbor thermodynamics of deoxyinosine pairs in DNA duplexes , 2005, Nucleic acids research.
[31] Peter Schattner,et al. The tRNAscan-SE, snoscan and snoGPS web servers for the detection of tRNAs and snoRNAs , 2005, Nucleic Acids Res..
[32] J. Elf,et al. Selective charging of tRNA isoacceptors induced by amino‐acid starvation , 2005, EMBO reports.
[33] Yizhar Lavner,et al. Codon bias as a factor in regulating expression via translation rate in the human genome. , 2005, Gene.
[34] Blake C Meyers,et al. Effects of gene expression on molecular evolution in Arabidopsis thaliana and Arabidopsis lyrata. , 2004, Molecular biology and evolution.
[35] J. M. Comeron,et al. Selective and Mutational Patterns Associated With Gene Expression in Humans , 2004, Genetics.
[36] Dieter Söll,et al. Aminoacyl-tRNAs: setting the limits of the genetic code. , 2004, Genes & development.
[37] G. Heijne,et al. The tRNA cycle and its relation to the rate of protein synthesis , 2004, European Biophysics Journal.
[38] Edward N Trifonov,et al. Distribution of Rare Triplets Along mRNA and Their Relation to Protein Folding , 2002, Journal of biomolecular structure & dynamics.
[39] C. Francklyn,et al. Aminoacyl-tRNA synthetases: versatile players in the changing theater of translation. , 2002, RNA.
[40] Arkady B. Khodursky,et al. Global analysis of mRNA decay and abundance in Escherichia coli at single-gene resolution using two-color fluorescent DNA microarrays , 2002, Proceedings of the National Academy of Sciences of the United States of America.
[41] C. Ball,et al. Identification of genes periodically expressed in the human cell cycle and their expression in tumors. , 2002, Molecular biology of the cell.
[42] International Human Genome Sequencing Consortium. Initial sequencing and analysis of the human genome , 2001, Nature.
[43] K. H. Wolfe,et al. Relationship of codon bias to mRNA concentration and protein length in Saccharomyces cerevisiae , 2000, Yeast.
[44] L. Duret,et al. tRNA gene number and codon usage in the C. elegans genome are co-adapted for optimal translation of highly expressed genes. , 2000, Trends in genetics : TIG.
[45] G. Blobel,et al. Cell Cycle–Regulated Attachment of the Ubiquitin-Related Protein Sumo to the Yeast Septins , 1999, The Journal of cell biology.
[46] B. Futcher,et al. A Sampling of the Yeast Proteome , 1999, Molecular and Cellular Biology.
[47] S. Kanaya,et al. Studies of codon usage and tRNA genes of 18 unicellular organisms and quantification of Bacillus subtilis tRNAs: gene expression level and species-specific diversity of codon usage based on multivariate analysis. , 1999, Gene.
[48] L. Duret,et al. Expression pattern and, surprisingly, gene length shape codon usage in Caenorhabditis, Drosophila, and Arabidopsis. , 1999, Proceedings of the National Academy of Sciences of the United States of America.
[49] H. Akashi,et al. Translational selection and molecular evolution. , 1998, Current opinion in genetics & development.
[50] Michael Ruogu Zhang,et al. Comprehensive identification of cell cycle-regulated genes of the yeast Saccharomyces cerevisiae by microarray hybridization. , 1998, Molecular biology of the cell.
[51] Ronald W. Davis,et al. A genome-wide transcriptional analysis of the mitotic cell cycle. , 1998, Molecular cell.
[52] A. Pavesi,et al. Transfer RNA gene redundancy and translational selection in Saccharomyces cerevisiae. , 1997, Journal of molecular biology.
[53] S. Eddy,et al. tRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence. , 1997, Nucleic acids research.
[54] J. Ebel,et al. Cell cycle variations of dinucleoside polyphosphates in synchronized cultures of mammalian cells , 1987, Molecular and cellular biology.
[55] G. von Heijne,et al. Translation rate modification by preferential codon usage: intragenic position effects. , 1987, Journal of Theoretical Biology.
[56] Paul M. Sharp,et al. Codon usage in yeast: cluster analysis clearly differentiates highly and lowly expressed genes , 1986, Nucleic Acids Res..
[57] T. Ikemura. Codon usage and tRNA content in unicellular and multicellular organisms. , 1985, Molecular biology and evolution.
[58] M. Gouy,et al. Codon usage in bacteria: correlation with gene expressivity. , 1982, Nucleic acids research.
[59] T. Ikemura. Correlation between the abundance of yeast transfer RNAs and the occurrence of the respective codons in protein genes. Differences in synonymous codon choice patterns of yeast and Escherichia coli with reference to the abundance of isoaccepting transfer RNAs. , 1982, Journal of molecular biology.
[60] W. Fiers,et al. Preferential codon usage in prokaryotic genes: the optimal codon-anticodon interaction energy and the selective codon usage in efficiently expressed genes. , 1982, Gene.
[61] W. Reith,et al. Organization and sequence analysis of a cluster of repetitive DNA elements from Xenopus laevis. , 1981, Journal of molecular biology.
[62] T. Ikemura. Correlation between the abundance of Escherichia coli transfer RNAs and the occurrence of the respective codons in its protein genes: a proposal for a synonymous codon choice that is optimal for the E. coli translational system. , 1981, Journal of molecular biology.
[63] Manolo Gouy,et al. Codon catalog usage is a genome strategy modulated for gene expressivity , 1981, Nucleic Acids Res..
[64] F. Crick. Codon--anticodon pairing: the wobble hypothesis. , 1966, Journal of molecular biology.