Multi-disciplinary methods to define RNA-protein interactions and regulatory networks.

[1]  A. Klug,et al.  Correlation between structural transformation and cleavage of the major head protein of T4 bacteriophage , 1976, Cell.

[2]  Characterization of heterogeneous nuclear RNA-protein complexes in vivo with monoclonal antibodies. , 1984, Molecular and cellular biology.

[3]  P. Sharp,et al.  Identification and purification of a 62,000-dalton protein that binds specifically to the polypyrimidine tract of introns. , 1989, Genes & development.

[4]  M. Wickens,et al.  Purification of RNA and RNA-protein complexes by an R17 coat protein affinity method. , 1990, Nucleic acids research.

[5]  J. G. Patton,et al.  Characterization and molecular cloning of polypyrimidine tract-binding protein: a component of a complex necessary for pre-mRNA splicing. , 1991, Genes & development.

[6]  K. Williams,et al.  Identification of amino acid residues at interface of protein-nucleic acid complexes by photochemical cross-linking. , 1991, Methods in enzymology.

[7]  G. Dreyfuss,et al.  Primary structure and binding activity of the hnRNP U protein: binding RNA through RGG box. , 1992, The EMBO journal.

[8]  R. Darnell,et al.  The neuronal RNA binding protein Nova-1 recognizes specific RNA targets in vitro and in vivo , 1997, Molecular and cellular biology.

[9]  R. Singer,et al.  Localization of ASH1 mRNA particles in living yeast. , 1998, Molecular cell.

[10]  S K Burley,et al.  Crystal structures of Nova-1 and Nova-2 K-homology RNA-binding domains. , 1999, Structure.

[11]  S. Kostka,et al.  A General Approach for Identification of RNA-Protein Cross-linking Sites within Native Human Spliceosomal Small Nuclear Ribonucleoproteins (snRNPs) , 2000, The Journal of Biological Chemistry.

[12]  S K Burley,et al.  The tetranucleotide UCAY directs the specific recognition of RNA by the Nova K-homology 3 domain. , 2000, Proceedings of the National Academy of Sciences of the United States of America.

[13]  E. K. White,et al.  PUM2, a novel murine puf protein, and its consensus RNA-binding site. , 2001, RNA.

[14]  P. Zamore,et al.  Crystal structure of a Pumilio homology domain. , 2001, Molecular cell.

[15]  Hanno Steen,et al.  Analysis of protein-nucleic acid interactions by photochemical cross-linking and mass spectrometry. , 2002, Mass spectrometry reviews.

[16]  Phillip D. Zamore,et al.  Modular Recognition of RNA by a Human Pumilio-Homology Domain , 2002, Cell.

[17]  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.

[18]  R. Reed,et al.  Purification of Functional RNA‐Protein Complexes using MS2‐MBP , 2003, Current protocols in molecular biology.

[19]  Juan Valcárcel,et al.  Building specificity with nonspecific RNA-binding proteins , 2005, Nature Structural &Molecular Biology.

[20]  S. Eddy,et al.  Kissing complex RNAs mediate interaction between the Fragile-X mental retardation protein KH2 domain and brain polyribosomes. , 2005, Genes & development.

[21]  N. Windbichler,et al.  Isolation of specific RNA-binding proteins using the streptomycin-binding RNA aptamer , 2006, Nature Protocols.

[22]  Daniel Herschlag,et al.  Genome-wide identification of mRNAs associated with the translational regulator PUMILIO in Drosophila melanogaster. , 2006, Proceedings of the National Academy of Sciences of the United States of America.

[23]  Tommi Kajander,et al.  Fragile X mental retardation syndrome: structure of the KH1-KH2 domains of fragile X mental retardation protein. , 2007, Structure.

[24]  A. Krogh,et al.  Molecular Composition of IMP1 Ribonucleoprotein Granules*S , 2007, Molecular & Cellular Proteomics.

[25]  Tyson A. Clark,et al.  HITS-CLIP yields genome-wide insights into brain alternative RNA processing , 2008, Nature.

[26]  Shalini Sharma Isolation of a sequence-specific RNA binding protein, polypyrimidine tract binding protein, using RNA affinity chromatography. , 2008, Methods in molecular biology.

[27]  D. Engelke,et al.  RNA affinity tags for the rapid purification and investigation of RNAs and RNA-protein complexes. , 2008, Methods in molecular biology.

[28]  P. Sharp,et al.  Proliferating Cells Express mRNAs with Shortened 3' Untranslated Regions and Fewer MicroRNA Target Sites , 2008, Science.

[29]  C. Mayr,et al.  Widespread Shortening of 3′UTRs by Alternative Cleavage and Polyadenylation Activates Oncogenes in Cancer Cells , 2009, Cell.

[30]  Sanjay Tyagi,et al.  Imaging intracellular RNA distribution and dynamics in living cells , 2009, Nature Methods.

[31]  Nicholas T. Ingolia,et al.  Genome-Wide Analysis in Vivo of Translation with Nucleotide Resolution Using Ribosome Profiling , 2009, Science.

[32]  Matthias Mann,et al.  Unbiased RNA–protein interaction screen by quantitative proteomics , 2009, Proceedings of the National Academy of Sciences.

[33]  David Tollervey,et al.  Identification of protein binding sites on U3 snoRNA and pre-rRNA by UV cross-linking and high-throughput analysis of cDNAs , 2009, Proceedings of the National Academy of Sciences.

[34]  Scott B. Dewell,et al.  Transcriptome-wide Identification of RNA-Binding Protein and MicroRNA Target Sites by PAR-CLIP , 2010, Cell.

[35]  Kotb Abdelmohsen,et al.  Posttranscriptional regulation of cancer traits by HuR , 2010, Wiley interdisciplinary reviews. RNA.

[36]  Fatima Al-Shahrour,et al.  Musashi-2 regulates normal hematopoiesis and promotes aggressive myeloid leukemia , 2010, Nature Medicine.

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

[38]  Michael Briese,et al.  iCLIP Predicts the Dual Splicing Effects of TIA-RNA Interactions , 2010, PLoS biology.

[39]  Nicholas T. Ingolia,et al.  Mammalian microRNAs predominantly act to decrease target mRNA levels , 2010, Nature.

[40]  N. Mukherjee,et al.  Systematic analysis of posttranscriptional gene expression , 2010, Wiley interdisciplinary reviews. Systems biology and medicine.

[41]  Toshiro K. Ohsumi,et al.  Genome-wide identification of polycomb-associated RNAs by RIP-seq. , 2010, Molecular cell.

[42]  Takahiro Ito,et al.  Regulation of myeloid leukemia by the cell fate determinant Musashi , 2010, Nature.

[43]  J. Ule,et al.  iCLIP reveals the function of hnRNP particles in splicing at individual nucleotide resolution , 2010, Nature Structural &Molecular Biology.

[44]  Nicholas T. Ingolia,et al.  Ribosome Profiling of Mouse Embryonic Stem Cells Reveals the Complexity and Dynamics of Mammalian Proteomes , 2011, Cell.

[45]  D. Bartel,et al.  Formation, Regulation and Evolution of Caenorhabditis elegans 3′UTRs , 2010, Nature.

[46]  R. Abagyan,et al.  Protein-RNA and protein-protein recognition by dual KH1/2 domains of the neuronal splicing factor Nova-1. , 2011, Structure.

[47]  Uwe Ohler,et al.  Integrative regulatory mapping indicates that the RNA-binding protein HuR couples pre-mRNA processing and mRNA stability. , 2011, Molecular cell.

[48]  Lan Huang,et al.  Quantitative Profiling of In Vivo-assembled RNA-Protein Complexes Using a Novel Integrated Proteomic Approach* , 2011, Molecular & Cellular Proteomics.

[49]  T. Glisovic,et al.  Structure of a Key Intermediate of the SMN Complex Reveals Gemin2's Crucial Function in snRNP Assembly , 2011, Cell.

[50]  Norman E. Davey,et al.  Insights into RNA Biology from an Atlas of Mammalian mRNA-Binding Proteins , 2012, Cell.

[51]  Larry N. Singh,et al.  U1 snRNP Determines mRNA Length and Regulates Isoform Expression , 2012, Cell.

[52]  Stefan Hüttelmaier,et al.  Insulin-like growth factor 2 mRNA-binding proteins (IGF2BPs): post-transcriptional drivers of cancer progression? , 2012, Cellular and Molecular Life Sciences.

[53]  Uwe Ohler,et al.  FMR1 targets distinct mRNA sequence elements to regulate protein expression , 2012, Nature.

[54]  Richard Bonneau,et al.  The mRNA-bound proteome and its global occupancy profile on protein-coding transcripts. , 2012, Molecular cell.

[55]  Matthias Mann,et al.  Quantitative mass spectrometry and PAR-CLIP to identify RNA-protein interactions , 2012, Nucleic acids research.

[56]  R. Gregory,et al.  How does Lin28 let-7 control development and disease? , 2012, Trends in cell biology.

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

[58]  P. Northcott,et al.  The RNA-binding protein Musashi1 affects medulloblastoma growth via a network of cancer-related genes and is an indicator of poor prognosis. , 2012, The American journal of pathology.

[59]  Thomas Tuschl,et al.  Identification of RNA–protein interaction networks using PAR‐CLIP , 2012, Wiley interdisciplinary reviews. RNA.