human Argonaute proteins Identifying mRNA sequence elements for target recognition by Material

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[1]  D. Bartel MicroRNAs: Target Recognition and Regulatory Functions , 2009, Cell.

[2]  Quaid Morris,et al.  Predicting in vivo binding sites of RNA-binding proteins using mRNA secondary structure. , 2010, RNA.

[3]  W. Filipowicz,et al.  Tethering of human Ago proteins to mRNA mimics the miRNA-mediated repression of protein synthesis. , 2004, RNA.

[4]  Peter F. Stadler,et al.  Local RNA base pairing probabilities in large sequences , 2006, Bioinform..

[5]  Brendan J. Frey,et al.  A compendium of RNA-binding motifs for decoding gene regulation , 2013, Nature.

[6]  G. Hannon,et al.  The Structure of Human Argonaute-2 in Complex with miR-20a , 2012, Cell.

[7]  Wei Yang,et al.  Mechanism of MicroRNA-Target Interaction: Molecular Dynamics Simulations and Thermodynamics Analysis , 2010, PLoS Comput. Biol..

[8]  Gregory J. Hannon,et al.  Sorting of Small RNAs into Arabidopsis Argonaute Complexes Is Directed by the 5′ Terminal Nucleotide , 2008, Cell.

[9]  Lourdes Peña Castillo,et al.  Rapid and systematic analysis of the RNA recognition specificities of RNA-binding proteins , 2009, Nature Biotechnology.

[10]  D. Patel,et al.  Structural basis for overhang-specific small interfering RNA recognition by the PAZ domain , 2004, Nature.

[11]  J. M. Thomson,et al.  Argonaute2 Is the Catalytic Engine of Mammalian RNAi , 2004, Science.

[12]  W. Wooster,et al.  Crystal structure of , 2005 .

[13]  Timothy L. Bailey,et al.  Discriminative motif discovery in DNA and protein sequences using the DEME algorithm , 2007, BMC Bioinformatics.

[14]  M. Zavolan,et al.  Molecular characterization of human Argonaute-containing ribonucleoprotein complexes and their bound target mRNAs. , 2008, RNA.

[15]  N. Sonenberg,et al.  Structural basis for 5′-nucleotide base-specific recognition of guide RNA by human AGO2 , 2010, Nature.

[16]  T. Tuschl,et al.  Structure of an argonaute silencing complex with a seed-containing guide DNA and target RNA duplex , 2008, Nature.

[17]  M. Kiebler,et al.  Faculty Opinions recommendation of Argonaute HITS-CLIP decodes microRNA-mRNA interaction maps. , 2009 .

[18]  R. Darnell,et al.  Mapping in vivo protein-RNA interactions at single-nucleotide resolution from HITS-CLIP data , 2011, Nature Biotechnology.

[19]  Ali Nahvi,et al.  A Parsimonious Model for Gene Regulation by miRNAs , 2011, Science.

[20]  D. Tollervey,et al.  Mapping the Human miRNA Interactome by CLASH Reveals Frequent Noncanonical Binding , 2013, Cell.

[21]  G. Meister,et al.  The Argonaute protein family , 2008, Genome Biology.

[22]  M. Zavolan,et al.  A quantitative analysis of CLIP methods for identifying binding sites of RNA-binding proteins , 2011, Nature Methods.

[23]  Stefan L Ameres,et al.  The impact of target site accessibility on the design of effective siRNAs , 2008, Nature Biotechnology.

[24]  Gunter Meister,et al.  Argonaute proteins: mediators of RNA silencing. , 2007, Molecular cell.

[25]  G. Hannon,et al.  Crystal Structure of Argonaute and Its Implications for RISC Slicer Activity , 2004, Science.

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

[27]  Michael Sattler,et al.  Nucleic acid 3′-end recognition by the Argonaute2 PAZ domain , 2004, Nature Structural &Molecular Biology.

[28]  Terrence S. Furey,et al.  The UCSC Table Browser data retrieval tool , 2004, Nucleic Acids Res..

[29]  D. Haussler,et al.  Evolutionarily conserved elements in vertebrate, insect, worm, and yeast genomes. , 2005, Genome research.

[30]  D. Barford,et al.  Structural insights into mRNA recognition from a PIWI domain–siRNA guide complex , 2005, Nature.

[31]  L. Lim,et al.  MicroRNA targeting specificity in mammals: determinants beyond seed pairing. , 2007, Molecular cell.