Insights into RNA structure and function from genome-wide studies
暂无分享,去创建一个
[1] P. Walter,et al. Ribosome pausing and stacking during translation of a eukaryotic mRNA. , 1988, The EMBO journal.
[2] J. van Duin,et al. Secondary structure of the central region of bacteriophage MS2 RNA. Conservation and biological significance. , 1990, Journal of molecular biology.
[3] R. Panniers. Translational control during heat shock. , 1994, Biochimie.
[4] S. Beaucage,et al. Current Protocols in Nucleic Acid Chemistry , 1999 .
[5] W. Sundquist,et al. Biological Crystallography Structures of the Hiv-1 Capsid Protein Dimerization Domain at 2.6 a Ê Resolution , 2022 .
[6] M. Ares,et al. Use of dimethyl sulfate to probe RNA structure in vivo. , 2000, Methods in enzymology.
[7] D. Botstein,et al. Genomic expression programs in the response of yeast cells to environmental changes. , 2000, Molecular biology of the cell.
[8] D. Engelke,et al. Probing RNA Structure with Chemical Reagents and Enzymes , 2000, Current protocols in nucleic acid chemistry.
[9] Robert H Singer,et al. Asymmetric sorting of ash1p in yeast results from inhibition of translation by localization elements in the mRNA. , 2002, Molecular cell.
[10] Michael Zuker,et al. Mfold web server for nucleic acid folding and hybridization prediction , 2003, Nucleic Acids Res..
[11] E. O’Shea,et al. Global analysis of protein expression in yeast , 2003, Nature.
[12] C. Burge,et al. Widespread selection for local RNA secondary structure in coding regions of bacterial genes. , 2003, Genome research.
[13] John D. Storey,et al. Genome-wide analysis of mRNA translation profiles in Saccharomyces cerevisiae , 2003, Proceedings of the National Academy of Sciences of the United States of America.
[14] Ivo L. Hofacker,et al. Vienna RNA secondary structure server , 2003, Nucleic Acids Res..
[15] D. Turner,et al. Incorporating chemical modification constraints into a dynamic programming algorithm for prediction of RNA secondary structure. , 2004, Proceedings of the National Academy of Sciences of the United States of America.
[16] M. Kozak,et al. Regulation of translation via mRNA structure in prokaryotes and eukaryotes. , 2005, Gene.
[17] K. Weeks,et al. RNA structure analysis at single nucleotide resolution by selective 2'-hydroxyl acylation and primer extension (SHAPE). , 2005, Journal of the American Chemical Society.
[18] István Miklós,et al. Statistical evidence for conserved, local secondary structure in the coding regions of eukaryotic mRNAs and pre-mRNAs , 2005, Nucleic acids research.
[19] P. Clote,et al. Structural RNA has lower folding energy than random RNA of the same dinucleotide frequency. , 2005, RNA.
[20] K. Shokat,et al. Human Catechol-O-Methyltransferase Haplotypes Modulate Protein Expression by Altering mRNA Secondary Structure , 2006, Science.
[21] F. Narberhaus,et al. Molecular basis for temperature sensing by an RNA thermometer , 2006, The EMBO journal.
[22] J. Derisi,et al. Single-cell proteomic analysis of S. cerevisiae reveals the architecture of biological noise , 2006, Nature.
[23] W. Sundquist,et al. Implications for viral capsid assembly from crystal structures of HIV-1 Gag(1-278) and CA(N)(133-278). , 2006, Biochemistry.
[24] Aleksey Y. Ogurtsov,et al. A periodic pattern of mRNA secondary structure created by the genetic code , 2006, Nucleic acids research.
[25] K. Weeks,et al. A fast-acting reagent for accurate analysis of RNA secondary and tertiary structure by SHAPE chemistry. , 2007, Journal of the American Chemical Society.
[26] R. Russell,et al. DMS footprinting of structured RNAs and RNA–protein complexes , 2007, Nature Protocols.
[27] Manolis Kellis,et al. Evolution, biogenesis, expression, and target predictions of a substantially expanded set of Drosophila microRNAs. , 2007, Genome research.
[28] Michael Kertesz,et al. The role of site accessibility in microRNA target recognition , 2007, Nature Genetics.
[29] P. Tomançak,et al. Global Analysis of mRNA Localization Reveals a Prominent Role in Organizing Cellular Architecture and Function , 2007, Cell.
[30] T. Rapoport,et al. The Signal Sequence Coding Region Promotes Nuclear Export of mRNA , 2007, PLoS biology.
[31] B. Williams,et al. The response of mammalian cells to double-stranded RNA. , 2007, Cytokine & growth factor reviews.
[32] J. Derisi,et al. Cis-acting determinants of asymmetric, cytoplasmic RNA transport. , 2007, RNA.
[33] Magdalena A. Jonikas,et al. Distinct contribution of electrostatics, initial conformational ensemble, and macromolecular stability in RNA folding , 2007, Proceedings of the National Academy of Sciences.
[34] Jeffrey Wilusz,et al. The highways and byways of mRNA decay , 2007, Nature Reviews Molecular Cell Biology.
[35] T. Adilakshmi,et al. Concurrent nucleation of 16S folding and induced fit in 30S ribosome assembly , 2008, Nature.
[36] R. Lister,et al. A link between RNA metabolism and silencing affecting Arabidopsis development. , 2008, Developmental cell.
[37] S. Luo,et al. Global identification of microRNA–target RNA pairs by parallel analysis of RNA ends , 2008, Nature Biotechnology.
[38] Ignacio Tinoco,et al. Following translation by single ribosomes one codon at a time , 2008, Nature.
[39] D. Bartel,et al. Endogenous siRNA and miRNA Targets Identified by Sequencing of the Arabidopsis Degradome , 2008, Current Biology.
[40] Magdalena A. Jonikas,et al. Structural inference of native and partially folded RNA by high-throughput contact mapping , 2008, Proceedings of the National Academy of Sciences.
[41] D. Bartel. MicroRNAs: Target Recognition and Regulatory Functions , 2009, Cell.
[42] K. Martin,et al. mRNA Localization: Gene Expression in the Spatial Dimension , 2009, Cell.
[43] Kristen K. Dang,et al. Architecture and Secondary Structure of an Entire HIV-1 RNA Genome , 2009, Nature.
[44] Eric Westhof,et al. The Dynamic Landscapes of RNA Architecture , 2009, Cell.
[45] Nicholas T. Ingolia,et al. Genome-Wide Analysis in Vivo of Translation with Nucleotide Resolution Using Ribosome Profiling , 2009, Science.
[46] S. Bullock,et al. Egalitarian is a selective RNA-binding protein linking mRNA localization signals to the dynein motor. , 2009, Genes & development.
[47] C. Holt,et al. Subcellular mRNA Localization in Animal Cells and Why It Matters , 2009, Science.
[48] A. Mele,et al. Ago HITS-CLIP decodes miRNA-mRNA interaction maps , 2009, Nature.
[49] Phillip A Sharp,et al. The Centrality of RNA , 2009, Cell.
[50] F. Bonneau,et al. The Yeast Exosome Functions as a Macromolecular Cage to Channel RNA Substrates for Degradation , 2009, Cell.
[51] David Tollervey,et al. Coding-Sequence Determinants of Gene Expression in Escherichia coli , 2009, Science.
[52] A. Komar,et al. A pause for thought along the co-translational folding pathway. , 2009, Trends in biochemical sciences.
[53] J Andrew Berglund,et al. Role of RNA structure in regulating pre-mRNA splicing. , 2010, Trends in biochemical sciences.
[54] D. Ish-Horowicz,et al. A′-form RNA helices drive microtubule-based mRNA transport in Drosophila , 2010, Nature Structural &Molecular Biology.
[55] R. Montange,et al. Free state conformational sampling of the SAM-I riboswitch aptamer domain. , 2010, Structure.
[56] Alain Laederach,et al. Disease-Associated Mutations That Alter the RNA Structural Ensemble , 2010, PLoS genetics.
[57] Gene W. Yeo,et al. Comprehensive discovery of endogenous Argonaute binding sites in Caenorhabditis elegans , 2010, Nature Structural &Molecular Biology.
[58] D. Haussler,et al. FragSeq: transcriptome-wide RNA structure probing using high-throughput sequencing , 2010, Nature Methods.
[59] Eytan Ruppin,et al. Translation efficiency is determined by both codon bias and folding energy , 2010, Proceedings of the National Academy of Sciences.
[60] Tong Zhou,et al. A Universal Trend of Reduced mRNA Stability near the Translation-Initiation Site in Prokaryotes and Eukaryotes , 2010, PLoS Comput. Biol..
[61] K. Weeks. Advances in RNA structure analysis by chemical probing. , 2010, Current opinion in structural biology.
[62] Howard Y. Chang,et al. Genome-wide measurement of RNA secondary structure in yeast , 2010, Nature.
[63] P. Ryvkin,et al. Genome-Wide Double-Stranded RNA Sequencing Reveals the Functional Significance of Base-Paired RNAs in Arabidopsis , 2010, PLoS genetics.
[64] R. Bock,et al. Local Absence of Secondary Structure Permits Translation of mRNAs that Lack Ribosome-Binding Sites , 2011, PLoS genetics.
[65] Cole Trapnell,et al. Multiplexed RNA structure characterization with selective 2′-hydroxyl acylation analyzed by primer extension sequencing (SHAPE-Seq) , 2011, Proceedings of the National Academy of Sciences.
[66] Cole Trapnell,et al. Modeling and automation of sequencing-based characterization of RNA structure , 2011, Proceedings of the National Academy of Sciences.
[67] C Joel McManus,et al. RNA structure and the mechanisms of alternative splicing. , 2011, Current opinion in genetics & development.
[68] Hui Zhou,et al. starBase: a database for exploring microRNA–mRNA interaction maps from Argonaute CLIP-Seq and Degradome-Seq data , 2010, Nucleic Acids Res..
[69] E. Eyras,et al. Deciphering 3'ss selection in the yeast genome reveals an RNA thermosensor that mediates alternative splicing. , 2011, Molecular cell.
[70] Rhiju Das,et al. A two-dimensional mutate-and-map strategy for non-coding RNA structure. , 2011, Nature chemistry.
[71] A. Gasch,et al. Molecular Systems Biology Peer Review Process File a Dynamic Model of Proteome Changes Reveals New Roles for Transcript Alteration in Yeast Transaction Report , 2022 .
[72] Howard Y. Chang,et al. Understanding the transcriptome through RNA structure , 2011, Nature Reviews Genetics.
[73] Patrick Xuechun Zhao,et al. Computational analysis of miRNA targets in plants: current status and challenges , 2011, Briefings Bioinform..
[74] Tamir Tuller,et al. Strong association between mRNA folding strength and protein abundance in S. cerevisiae , 2012, EMBO reports.
[75] Robert Tibshirani,et al. Genome-wide measurement of RNA folding energies. , 2012, Molecular cell.
[76] F. Narberhaus,et al. Bacterial RNA thermometers: molecular zippers and switches , 2012, Nature Reviews Microbiology.
[77] Paul Ryvkin,et al. Global analysis of RNA secondary structure in two metazoans. , 2012, Cell reports.
[78] K. Weeks,et al. SHAPE-directed discovery of potent shRNA inhibitors of HIV-1. , 2012, Molecular therapy : the journal of the American Society of Gene Therapy.
[79] Javier G. Magadán,et al. Monitoring cotranslational protein folding in mammalian cells at codon resolution , 2012, Proceedings of the National Academy of Sciences.
[80] Tamir Tuller,et al. Determinants of Translation Elongation Speed and Ribosomal Profiling Biases in Mouse Embryonic Stem Cells , 2012, PLoS Comput. Biol..
[81] B. Gregory,et al. PRMD: an integrated database for plant RNA modifications , 2012, Plant Cell.
[82] K. Weeks,et al. The genetic code as expressed through relationships between mRNA structure and protein function , 2013, FEBS Letters.
[83] J. Doudna,et al. Molecular mechanisms of RNA interference. , 2013, Annual review of biophysics.
[84] Sriram Kosuri,et al. Causes and Effects of N-Terminal Codon Bias in Bacterial Genes , 2013, Science.
[85] Chang-Shung Tung,et al. Rise of the RNA machines: exploring the structure of long non-coding RNAs. , 2013, Journal of molecular biology.
[86] P. Stadler,et al. Widespread purifying selection on RNA structure in mammals , 2013, Nucleic acids research.
[87] K. Weeks,et al. The cellular environment stabilizes adenine riboswitch RNA structure. , 2013, Biochemistry.
[88] J. Kjems,et al. An Unusual Topological Structure of the HIV-1 Rev Response Element , 2013, Cell.
[89] Yuanhui Mao,et al. Universally increased mRNA stability downstream of the translation initiation site in eukaryotes and prokaryotes. , 2013, Gene.
[90] Michael P Snyder,et al. SeqFold: Genome-scale reconstruction of RNA secondary structure integrating high-throughput sequencing data , 2013, Genome research.
[91] B. Gregory,et al. Genomic era analyses of RNA secondary structure and RNA-binding proteins reveal their significance to post-transcriptional regulation in plants. , 2013, Plant science : an international journal of experimental plant biology.
[92] Yiliang Ding,et al. Determination of in vivo RNA structure in low-abundance transcripts , 2013, Nature Communications.
[93] J. Plotkin,et al. Rate-Limiting Steps in Yeast Protein Translation , 2013, Cell.
[94] N. Blüthgen,et al. Molecular Systems Biology 9; Article number 675; doi:10.1038/msb.2013.32 Citation: Molecular Systems Biology 9:675 , 2022 .
[95] J. Mattick,et al. Structure and function of long noncoding RNAs in epigenetic regulation , 2013, Nature Structural &Molecular Biology.
[96] B. Gregory,et al. Arabidopsis mRNA secondary structure correlates with protein function and domains , 2013, Plant signaling & behavior.
[97] Howard Y. Chang,et al. RNA SHAPE analysis in living cells. , 2013, Nature chemical biology.
[98] Lukasz Jan Kielpinski,et al. Massive parallel-sequencing-based hydroxyl radical probing of RNA accessibility , 2014, Nucleic acids research.
[99] Minjae Lee,et al. RNA design rules from a massive open laboratory , 2014, Proceedings of the National Academy of Sciences.
[100] Manolis Kellis,et al. Genome-wide probing of RNA structure reveals active unfolding of mRNA structures in vivo , 2013, Nature.
[101] Hui Zhou,et al. starBase v2.0: decoding miRNA-ceRNA, miRNA-ncRNA and protein–RNA interaction networks from large-scale CLIP-Seq data , 2013, Nucleic Acids Res..
[102] Nathan D. Berkowitz,et al. Improved genome-wide mapping of uncapped and cleaved transcripts in eukaryotes--GMUCT 2.0. , 2014, Methods.
[103] Rhiju Das,et al. Massively parallel RNA chemical mapping with a reduced bias MAP-seq protocol. , 2013, Methods in molecular biology.
[104] Y. Zhang,et al. In vivo genome-wide profiling of RNA secondary structure reveals novel regulatory features , 2013, Nature.
[105] Qiangfeng Cliff Zhang,et al. Landscape and variation of RNA secondary structure across the human transcriptome , 2014, Nature.
[106] K. Huth. Transport , 2015, Canadian Medical Association Journal.