Comparative Visualization of the RNA Suboptimal Conformational Ensemble In Vivo

[1]  Claude E. Shannon,et al.  Prediction and Entropy of Printed English , 1951 .

[2]  W. Torgerson Multidimensional scaling: I. Theory and method , 1952 .

[3]  D. Defays,et al.  An Efficient Algorithm for a Complete Link Method , 1977, Comput. J..

[4]  J. Lawrence,et al.  Intracellular localization of messenger RNAs for cytoskeletal proteins , 1986, Cell.

[5]  W. Marzluff,et al.  The stem-loop structure at the 3' end of histone mRNA is necessary and sufficient for regulation of histone mRNA stability , 1987, Molecular and cellular biology.

[6]  Bruce A. Shapiro,et al.  An algorithm for comparing multiple RNA secondary structures , 1988, Comput. Appl. Biosci..

[7]  D. Schümperli,et al.  Regulation of histone mRNA in the unperturbed cell cycle: evidence suggesting control at two posttranscriptional steps , 1991, Molecular and cellular biology.

[8]  W. Marzluff,et al.  The histone mRNA 3' end is required for localization of histone mRNA to polyribosomes. , 1992, Nucleic acids research.

[9]  A. R. Srinivasan,et al.  The nucleic acid database. A comprehensive relational database of three-dimensional structures of nucleic acids. , 1992, Biophysical journal.

[10]  R. Singer,et al.  Sequences responsible for intracellular localization of beta-actin messenger RNA also affect cell phenotype , 1994, The Journal of cell biology.

[11]  M. Hentze,et al.  Starting at the Beginning, Middle, and End: Translation Initiation in Eukaryotes , 1997, Cell.

[12]  R. Singer,et al.  Characterization of a beta-actin mRNA zipcode-binding protein , 1997, Molecular and cellular biology.

[13]  H. Stanley,et al.  Discrete molecular dynamics studies of the folding of a protein-like model. , 1998, Folding & design.

[14]  J. Sabina,et al.  Expanded sequence dependence of thermodynamic parameters improves prediction of RNA secondary structure. , 1999, Journal of molecular biology.

[15]  T. Steitz,et al.  The complete atomic structure of the large ribosomal subunit at 2.4 A resolution. , 2000, Science.

[16]  C. Vonrhein,et al.  Structure of the 30S ribosomal subunit , 2000, Nature.

[17]  Elena Rivas,et al.  Noncoding RNA gene detection using comparative sequence analysis , 2001, BMC Bioinformatics.

[18]  Frank Schluenzen,et al.  High Resolution Structure of the Large Ribosomal Subunit from a Mesophilic Eubacterium , 2001, Cell.

[19]  X. Zhuang,et al.  Exploring the folding landscape of a structured RNA , 2001, Proceedings of the National Academy of Sciences of the United States of America.

[20]  J. C. Wu,et al.  RNA folding pathway functional intermediates: their prediction and analysis. , 2001, Journal of molecular biology.

[21]  D. Ecker,et al.  RNAMotif, an RNA secondary structure definition and search algorithm. , 2001, Nucleic acids research.

[22]  D. Turner,et al.  Experimentally derived nearest-neighbor parameters for the stability of RNA three- and four-way multibranch loops. , 2002, Biochemistry.

[23]  M. Chance,et al.  Probing the structural dynamics of nucleic acids by quantitative time-resolved and equilibrium hydroxyl radical "footprinting". , 2002, Current opinion in structural biology.

[24]  V. Ramakrishnan,et al.  Ribosome Structure and the Mechanism of Translation , 2002, Cell.

[25]  Rhiju Das,et al.  The fastest global events in RNA folding: electrostatic relaxation and tertiary collapse of the Tetrahymena ribozyme. , 2003, Journal of molecular biology.

[26]  Robert Giegerich,et al.  Abstract shapes of RNA. , 2004, Nucleic acids research.

[27]  A. Serganov,et al.  Structural basis for discriminative regulation of gene expression by adenine- and guanine-sensing mRNAs. , 2004, Chemistry & biology.

[28]  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.

[29]  Ye Ding,et al.  Sfold web server for statistical folding and rational design of nucleic acids , 2004, Nucleic Acids Res..

[30]  C. Lawrence,et al.  RNA secondary structure prediction by centroids in a Boltzmann weighted ensemble. , 2005, RNA.

[31]  Harry F Noller,et al.  RNA Structure: Reading the Ribosome , 2005, Science.

[32]  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.

[33]  M. Buckle,et al.  Real-time characterization of intermediates in the pathway to open complex formation by Escherichia coli RNA polymerase at the T7A1 promoter. , 2005, Proceedings of the National Academy of Sciences of the United States of America.

[34]  Xiaowei Zhuang,et al.  Single-molecule RNA folding. , 2005, Accounts of chemical research.

[35]  D. Thirumalai,et al.  RNA and protein folding: common themes and variations. , 2005, Biochemistry.

[36]  J. Condeelis,et al.  Spatial regulation of β-actin translation by Src-dependent phosphorylation of ZBP1 , 2005, Nature.

[37]  D. Lilley,et al.  Folding of the adenine riboswitch. , 2006, Chemistry & biology.

[38]  K. Weeks,et al.  Selective 2′-hydroxyl acylation analyzed by primer extension (SHAPE): quantitative RNA structure analysis at single nucleotide resolution , 2006, Nature Protocols.

[39]  C. Lawrence,et al.  Clustering of RNA secondary structures with application to messenger RNAs. , 2006, Journal of molecular biology.

[40]  David H Mathews,et al.  Revolutions in RNA secondary structure prediction. , 2006, Journal of molecular biology.

[41]  Robert Giegerich,et al.  RNAshapes: an integrated RNA analysis package based on abstract shapes. , 2006, Bioinformatics.

[42]  M. Brenowitz,et al.  Fast Fenton footprinting: a laboratory-based method for the time-resolved analysis of DNA, RNA and proteins , 2006, Nucleic acids research.

[43]  Peter Clote,et al.  Computing the Partition Function and Sampling for Saturated Secondary Structures of RNA, with Respect to the Turner Energy Model , 2007, J. Comput. Biol..

[44]  John D. Hunter,et al.  Matplotlib: A 2D Graphics Environment , 2007, Computing in Science & Engineering.

[45]  D. Lafontaine,et al.  Core requirements of the adenine riboswitch aptamer for ligand binding. , 2007, RNA.

[46]  Y. Ponty Efficient sampling of RNA secondary structures from the Boltzmann ensemble of low-energy , 2007, Journal of mathematical biology.

[47]  A. Laederach,et al.  Energy barriers, pathways, and dynamics during folding of large, multidomain RNAs. , 2008, Current opinion in chemical biology.

[48]  Seema Chauhan,et al.  Tertiary interactions determine the accuracy of RNA folding. , 2008, Journal of the American Chemical Society.

[49]  F. Ding,et al.  Ab initio RNA folding by discrete molecular dynamics: from structure prediction to folding mechanisms. , 2008, RNA.

[50]  Morgan C. Giddings,et al.  Influence of nucleotide identity on ribose 2'-hydroxyl reactivity in RNA. , 2009, RNA.

[51]  D. Lafontaine,et al.  Molecular basis of RNA-mediated gene regulation on the adenine riboswitch by single-molecule approaches. , 2009, Methods in molecular biology.

[52]  Kiyoshi Asai,et al.  Prediction of RNA secondary structure using generalized centroid estimators , 2009, Bioinform..

[53]  Sean R Eddy,et al.  A new generation of homology search tools based on probabilistic inference. , 2009, Genome informatics. International Conference on Genome Informatics.

[54]  D. Mathews,et al.  Accurate SHAPE-directed RNA structure determination , 2009, Proceedings of the National Academy of Sciences.

[55]  A. Yonath Hibernating Bears , Antibiotics , and the Evolving Ribosome ( Nobel Lecture ) * * , 2010 .

[56]  A. Laederach,et al.  Evaluation of the information content of RNA structure mapping data for secondary structure prediction. , 2010, RNA.

[57]  Daniel Herschlag,et al.  Multiple Native States Reveal Persistent Ruggedness of an RNA Folding Landscape , 2010, Nature.

[58]  A. Yonath Polar bears, antibiotics, and the evolving ribosome (Nobel Lecture). , 2010, Angewandte Chemie.

[59]  Alain Laederach,et al.  Disease-Associated Mutations That Alter the RNA Structural Ensemble , 2010, PLoS genetics.

[60]  S. Almo,et al.  ZBP1 recognition of beta-actin zipcode induces RNA looping. , 2010, Genes & development.

[61]  T. Irving,et al.  Multistage collapse of a bacterial ribozyme observed by time-resolved small-angle X-ray scattering. , 2010, Journal of the American Chemical Society.

[62]  Patricia Bouchard,et al.  Riboswitch structure: an internal residue mimicking the purine ligand , 2009, Nucleic acids research.

[63]  Russ B Altman,et al.  RNA molecules with conserved catalytic cores but variable peripheries fold along unique energetically optimized pathways. , 2011, RNA.

[64]  Rhiju Das,et al.  A two-dimensional mutate-and-map strategy for non-coding RNA structure. , 2011, Nature chemistry.

[65]  Rick Russell,et al.  The Azoarcus Group I Intron Ribozyme Misfolds and Is Accelerated for Refolding by ATP-dependent RNA Chaperone Proteins* , 2011, The Journal of Biological Chemistry.

[66]  Francesca Fanelli,et al.  Wordom: A User-Friendly Program for the Analysis of Molecular Structures, Trajectories, and Free Energy Surfaces , 2010, J. Comput. Chem..

[67]  F. Ding,et al.  Discrete molecular dynamics , 2012 .

[68]  É. Massé,et al.  Comparative Study between Transcriptionally- and Translationally-Acting Adenine Riboswitches Reveals Key Differences in Riboswitch Regulatory Mechanisms , 2011, PLoS genetics.

[69]  Rhiju Das,et al.  A mutate-and-map strategy accurately infers the base pairs of a 35-nucleotide model RNA. , 2011, RNA.

[70]  K. Weeks,et al.  The mechanisms of RNA SHAPE chemistry. , 2012, Journal of the American Chemical Society.

[71]  Feng Ding,et al.  Discrete molecular dynamics: an efficient and versatile simulation method for fine protein characterization. , 2012, The journal of physical chemistry. B.

[72]  Julius B. Lucks,et al.  An RNA Mapping DataBase for curating RNA structure mapping experiments , 2012, Bioinform..

[73]  F. Ding,et al.  DMD: An Efficient And Versatile Simulation Method For Fine Protein Characterization , 2012 .

[74]  S. Almo,et al.  Spatial arrangement of an RNA zipcode identifies mRNAs under post-transcriptional control. , 2012, Genes & development.

[75]  Alain Laederach,et al.  Structural effects of linkage disequilibrium on the transcriptome. , 2012, RNA.

[76]  Alain Laederach,et al.  Evaluating our ability to predict the structural disruption of RNA by SNPs , 2012, BMC Genomics.

[77]  Jiasheng Wang,et al.  ACTB in cancer. , 2013, Clinica chimica acta; international journal of clinical chemistry.

[78]  Michael C. Hout,et al.  Multidimensional Scaling , 2003, Encyclopedic Dictionary of Archaeology.

[79]  Joshua S. Martin,et al.  Evolutionary Evidence for Alternative Structure in RNA Sequence Co-variation , 2013, PLoS Comput. Biol..

[80]  Howard Y. Chang,et al.  RNA SHAPE analysis in living cells. , 2013, Nature chemical biology.

[81]  Steven Busan,et al.  RNA motif discovery by SHAPE and mutational profiling (SHAPE-MaP) , 2014, Nature Methods.

[82]  John D. Westbrook,et al.  The Nucleic Acid Database: new features and capabilities , 2013, Nucleic Acids Res..

[83]  K. Weeks,et al.  Multiple conformations are a conserved and regulatory feature of the RB1 5′ UTR , 2015, RNA.

[84]  A. Ferré-D’Amaré,et al.  Synthesis and applications of RNAs with position-selective labeling and mosaic composition , 2015, Nature.

[85]  Rhiju Das,et al.  Consistent global structures of complex RNA states through multidimensional chemical mapping , 2015, eLife.

[86]  Alain Laederach,et al.  The potential of the riboSNitch in personalized medicine , 2015, Wiley interdisciplinary reviews. RNA.

[87]  Christopher A. Lavender,et al.  In-cell SHAPE reveals that free 30S ribosome subunits are in the inactive state , 2015, Proceedings of the National Academy of Sciences.

[88]  D. Herschlag,et al.  From static to dynamic: the need for structural ensembles and a predictive model of RNA folding and function. , 2015, Current opinion in structural biology.

[89]  K. Weeks,et al.  Detection of RNA-Protein Interactions in Living Cells with SHAPE. , 2015, Biochemistry.

[90]  Pablo Cordero,et al.  Rich RNA Structure Landscapes Revealed by Mutate-and-Map Analysis , 2015, PLoS Comput. Biol..

[91]  N. Perrone-Bizzozero,et al.  Different motif requirements for the localization zipcode element of β-actin mRNA binding by HuD and ZBP1 , 2015, Nucleic acids research.

[92]  Kaoru Inoue,et al.  SHAPE reveals transcript-wide interactions, complex structural domains, and protein interactions across the Xist lncRNA in living cells , 2016, Proceedings of the National Academy of Sciences.

[93]  D. Herschlag,et al.  RNA Structural Modules Control the Rate and Pathway of RNA Folding and Assembly. , 2016, Journal of molecular biology.

[94]  A. Laederach,et al.  Transcending the prediction paradigm: novel applications of SHAPE to RNA function and evolution , 2016, Wiley interdisciplinary reviews. RNA.