RNA structure drives interaction with proteins

[1]  P. Avner,et al.  Phase separation drives X-chromosome inactivation: a hypothesis , 2019, Nature Structural & Molecular Biology.

[2]  G. Tartaglia,et al.  An Integrative Study of Protein-RNA Condensates Identifies Scaffolding RNAs and Reveals Players in Fragile X-Associated Tremor/Ataxia Syndrome , 2018, Cell reports.

[3]  P. Roepstorff,et al.  Analysis of the Effect of Intestinal Ischemia and Reperfusion on the Rat Neutrophils Proteome , 2018, Front. Mol. Biosci..

[4]  Alexandros Armaos,et al.  RNAct: Protein–RNA interaction predictions for model organisms with supporting experimental data , 2018, Nucleic Acids Res..

[5]  R. Parker,et al.  Emerging Roles for Intermolecular RNA-RNA Interactions in RNP Assemblies , 2018, Cell.

[6]  P. Tomançak,et al.  RNA buffers the phase separation behavior of prion-like RNA binding proteins , 2018, Science.

[7]  Alexandros Armaos,et al.  A Method for RNA Structure Prediction Shows Evidence for Structure in lncRNAs , 2018, bioRxiv.

[8]  Hugh C. Woolfenden,et al.  Rice In Vivo RNA Structurome Reveals RNA Secondary Structure Conservation and Divergence in Plants , 2018, Molecular plant.

[9]  C Joel McManus,et al.  Structural analyses of NEAT1 lncRNAs suggest long-range RNA interactions that may contribute to paraspeckle architecture , 2018, Nucleic acids research.

[10]  R. Pappu,et al.  Phase separation of a yeast prion protein promotes cellular fitness , 2018, Science.

[11]  Lionel Spinelli,et al.  Protein complex scaffolding predicted as a prevalent function of long non-coding RNAs , 2017, Nucleic acids research.

[12]  E. Tolosa,et al.  Discovering the 3′ UTR-mediated regulation of alpha-synuclein , 2017, Nucleic acids research.

[13]  Davide Cirillo,et al.  omiXcore: a web server for prediction of protein interactions with large RNA , 2017, Bioinform..

[14]  Jan Gorodkin,et al.  The identification and functional annotation of RNA structures conserved in vertebrates , 2017, Genome research.

[15]  A. Hyman,et al.  An aberrant phase transition of stress granules triggered by misfolded protein and prevented by chaperone function , 2017, The EMBO journal.

[16]  P. Avner,et al.  Quantitative predictions of protein interactions with long noncoding RNAs , 2016, Nature Methods.

[17]  G. Tartaglia,et al.  A high-throughput approach to profile RNA structure , 2016, Nucleic acids research.

[18]  S. Eddy,et al.  A statistical test for conserved RNA structure shows lack of evidence for structure in lncRNAs , 2016, Nature Methods.

[19]  Gene W. Yeo,et al.  SONAR Discovers RNA-Binding Proteins from Analysis of Large-Scale Protein-Protein Interactomes. , 2016, Molecular cell.

[20]  R. Kingston,et al.  Structural, super-resolution microscopy analysis of paraspeckle nuclear body organization , 2016, The Journal of cell biology.

[21]  G. Leo,et al.  A Surveillance Function of the HSPB8-BAG3-HSP70 Chaperone Complex Ensures Stress Granule Integrity and Dynamism. , 2016, Molecular cell.

[22]  C. Livi,et al.  Advances in the characterization of RNA‐binding proteins , 2016, Wiley interdisciplinary reviews. RNA.

[23]  J. Valpuesta,et al.  Clathrin Coat Disassembly Illuminates the Mechanisms of Hsp70 Force Generation , 2016, Nature Structural &Molecular Biology.

[24]  Ben Lehner,et al.  A Concentration-Dependent Liquid Phase Separation Can Cause Toxicity upon Increased Protein Expression , 2016, Cell reports.

[25]  B. Gregory,et al.  The Conservation and Function of RNA Secondary Structure in Plants. , 2016, Annual review of plant biology.

[26]  Gene W. Yeo,et al.  Robust transcriptome-wide discovery of RNA binding protein binding sites with enhanced CLIP (eCLIP) , 2016, Nature Methods.

[27]  C. Livi,et al.  Protein aggregation, structural disorder and RNA-binding ability: a new approach for physico-chemical and gene ontology classification of multiple datasets , 2015, BMC Genomics.

[28]  D. Cirillo,et al.  Neurodegeneration and Cancer: Where the Disorder Prevails , 2015, Scientific Reports.

[29]  Jianzhi Zhang,et al.  Human long noncoding RNAs are substantially less folded than messenger RNAs. , 2015, Molecular biology and evolution.

[30]  V. Ramakrishnan,et al.  The Ribosome Emerges from a Black Box , 2014, Cell.

[31]  S. Gerstberger,et al.  A census of human RNA-binding proteins , 2014, Nature Reviews Genetics.

[32]  M. Madan Babu,et al.  A million peptide motifs for the molecular biologist. , 2014, Molecular cell.

[33]  R. Parker,et al.  Principles and properties of eukaryotic mRNPs. , 2014, Molecular cell.

[34]  Petr Klus,et al.  The cleverSuite approach for protein characterization: predictions of structural properties, solubility, chaperone requirements and RNA-binding abilities , 2014, Bioinform..

[35]  Qiangfeng Cliff Zhang,et al.  Landscape and variation of RNA secondary structure across the human transcriptome , 2014, Nature.

[36]  Carmen Maria Livi,et al.  Constitutive patterns of gene expression regulated by RNA-binding proteins , 2014, Genome Biology.

[37]  H. Madhani.  snRNA Catalysts in the Spliceosome’s Ancient Core , 2013, Cell.

[38]  Manolis Kellis,et al.  Genome-wide probing of RNA structure reveals active unfolding of mRNA structures in vivo , 2013, Nature.

[39]  Q. Morris,et al.  Finding the target sites of RNA-binding proteins , 2013, Wiley interdisciplinary reviews. RNA.

[40]  Carmen Maria Livi,et al.  Principles of self-organization in biological pathways: a hypothesis on the autogenous association of alpha-synuclein , 2013, Nucleic acids research.

[41]  Petr Klus,et al.  catRAPID omics: a web server for large-scale prediction of protein–RNA interactions , 2013, Bioinform..

[42]  Jörg Gsponer,et al.  On the Importance of Polar Interactions for Complexes Containing Intrinsically Disordered Proteins , 2013, PLoS Comput. Biol..

[43]  Yujin E. Kim,et al.  Molecular chaperone functions in protein folding and proteostasis. , 2013, Annual review of biochemistry.

[44]  M. Gill,et al.  Development of Strategies for SNP Detection in RNA-Seq Data: Application to Lymphoblastoid Cell Lines and Evaluation Using 1000 Genomes Data , 2013, PloS one.

[45]  Michael P Snyder,et al.  SeqFold: Genome-scale reconstruction of RNA secondary structure integrating high-throughput sequencing data , 2013, Genome research.

[46]  M. Babu,et al.  Cellular Strategies for Regulating Functional and Nonfunctional Protein Aggregation , 2012, Cell reports.

[47]  Howard Y. Chang,et al.  Identification of proteins binding coding and non-coding human RNAs using protein microarrays , 2012, BMC Genomics.

[48]  Nadav S. Bar,et al.  Landscape of transcription in human cells , 2012, Nature.

[49]  Jimin Pei,et al.  Cell-free Formation of RNA Granules: Bound RNAs Identify Features and Components of Cellular Assemblies , 2012, Cell.

[50]  Jimin Pei,et al.  Cell-free Formation of RNA Granules: Low Complexity Sequence Domains Form Dynamic Fibers within Hydrogels , 2012, Cell.

[51]  A. Wakamatsu,et al.  Genome-wide determination of RNA stability reveals hundreds of short-lived noncoding transcripts in mammals , 2012, Genome research.

[52]  Reza Salavati,et al.  Systematic Discovery of Structural Elements Governing Mammalian mRNA Stability , 2012, Nature.

[53]  J. Perona,et al.  Kinetics of tRNA Folding Monitored by Aminoacylation , 2012, RNA.

[54]  Vasant Honavar,et al.  Predicting RNA-Protein Interactions Using Only Sequence Information , 2011, BMC Bioinformatics.

[55]  Federico Agostini,et al.  Predicting protein associations with long noncoding RNAs , 2011, Nature Methods.

[56]  Michele Vendruscolo,et al.  Proteome-level interplay between folding and aggregation propensities of proteins. , 2010, Journal of molecular biology.

[57]  B. Blencowe,et al.  The nuclear-retained noncoding RNA MALAT1 regulates alternative splicing by modulating SR splicing factor phosphorylation. , 2010, Molecular cell.

[58]  Howard Y. Chang,et al.  Genome-wide measurement of RNA secondary structure in yeast , 2010, Nature.

[59]  C. Dobson,et al.  Physicochemical determinants of chaperone requirements. , 2010, Journal of molecular biology.

[60]  E. Sontheimer,et al.  Origins and Mechanisms of miRNAs and siRNAs , 2009, Cell.

[61]  B. Seong,et al.  RNA-mediated chaperone type for de novo protein folding , 2009, RNA biology.

[62]  James C. Carrington,et al.  Specialization and evolution of endogenous small RNA pathways , 2007, Nature Reviews Genetics.

[63]  Gabriele Varani,et al.  RNA is rarely at a loss for companions; as soon as RNA , 2008 .

[64]  Adam Godzik,et al.  Cd-hit: a fast program for clustering and comparing large sets of protein or nucleotide sequences , 2006, Bioinform..

[65]  Laurent Lestrade,et al.  snoRNA-LBME-db, a comprehensive database of human H/ACA and C/D box snoRNAs , 2005, Nucleic Acids Res..

[66]  P. Stadler,et al.  The effect of RNA secondary structures on RNA-ligand binding and the modifier RNA mechanism: a quantitative model. , 2005, Gene.

[67]  A. Barabasi,et al.  Lethality and centrality in protein networks , 2001, Nature.

[68]  M. Clemens,et al.  Detection of double-stranded RNA-protein interactions by methylene blue-mediated photo-crosslinking. , 1996, RNA.

[69]  D. Koshland.  The Key–Lock Theory and the Induced Fit Theory , 1995 .

[70]  Eka Swadiansa.  The hypothesis , 1990 .

[71]  Piero Carninci,et al.  Discovery and functional analysis of lncRNAs: Methodologies to investigate an uncharacterized transcriptome. , 2016, Biochimica et biophysica acta.

[72]  Jeroen Krijgsveld,et al.  Comprehensive Identification of RNA-Binding Proteins by RNA Interactome Capture. , 2016, Methods in molecular biology.

[73]  Robert H Singer,et al.  Structural basis for the coevolution of a viral RNA–protein complex , 2008, Nature Structural &Molecular Biology.

[74]  The FANTOM Consortium and the RIKEN Genome Exploration Team,et al.  Analysis of the mouse transcriptome based on functional annotation of 60,770 full-length cDNAs , 2002 .

[75]  O. Strausz,et al.  Kinetics of the , 1967 .