Thomas Tuschl

Summary

Affiliation: The Rockefeller University
Country: USA

Publications

  1. pmc miRNA in situ hybridization in formaldehyde and EDC-fixed tissues
    John T G Pena
    Howard Hughes Medical Institute, Laboratory of RNA Molecular Biology, The Rockefeller University, 1230 York Avenue, Box 186, New York, New York 10065, USA
    Nat Methods 6:139-41. 2009
  2. pmc RNA targets of wild-type and mutant FET family proteins
    Jessica I Hoell
    Howard Hughes Medical Institute, Laboratory of RNA Molecular Biology, The Rockefeller University, New York, New York, USA
    Nat Struct Mol Biol 18:1428-31. 2011
  3. pmc MicroRNAs miR-26a, miR-26b, and miR-29b accelerate osteogenic differentiation of unrestricted somatic stem cells from human cord blood
    Hans Ingo Trompeter
    University Düsseldorf, Medical Faculty, Institute for Transplantation Diagnostics and Cell Therapeutics ITZ, Dusseldorf, Germany
    BMC Genomics 14:111. 2013
  4. pmc Genome-wide annotation and analysis of zebra finch microRNA repertoire reveal sex-biased expression
    Guan Zheng Luo
    State Kay Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
    BMC Genomics 13:727. 2012
  5. pmc Identification of clustered microRNAs using an ab initio prediction method
    Alain Sewer
    Biozentrum, Universitat Basel, Basel, Switzerland
    BMC Bioinformatics 6:267. 2005
  6. ncbi request reprint The small RNA profile during Drosophila melanogaster development
    Alexei A Aravin
    Department of Animal Molecular Genetics, Institute of Molecular Genetics, Kurchatov sq 2, 123182, Moscow, Russia
    Dev Cell 5:337-50. 2003
  7. ncbi request reprint Identification and characterization of small RNAs involved in RNA silencing
    Alexei Aravin
    Laboratory of RNA Molecular Biology, The Rockefeller University, New York, NY 10021, USA
    FEBS Lett 579:5830-40. 2005
  8. pmc Structure of an argonaute silencing complex with a seed-containing guide DNA and target RNA duplex
    Yanli Wang
    Structural Biology Program, Memorial Sloan Kettering Cancer Center, New York, New York 10065, USA
    Nature 456:921-6. 2008
  9. ncbi request reprint Identification of novel argonaute-associated proteins
    Gunter Meister
    Laboratory of RNA Molecular Biology, The Rockefeller University, 1230 York Avenue, Box 186, New York, New York 10021, USA
    Curr Biol 15:2149-55. 2005
  10. pmc Structural and functional insights into 5'-ppp RNA pattern recognition by the innate immune receptor RIG-I
    Yanli Wang
    Structural Biology Program, Memorial Sloan Kettering Cancer Center, New York, New York, USA
    Nat Struct Mol Biol 17:781-7. 2010

Detail Information

Publications86

  1. pmc miRNA in situ hybridization in formaldehyde and EDC-fixed tissues
    John T G Pena
    Howard Hughes Medical Institute, Laboratory of RNA Molecular Biology, The Rockefeller University, 1230 York Avenue, Box 186, New York, New York 10065, USA
    Nat Methods 6:139-41. 2009
    ..We determined optimal hybridization parameters for 130 locked nucleic acid probes by recording nucleic acid melting temperature during ISH...
  2. pmc RNA targets of wild-type and mutant FET family proteins
    Jessica I Hoell
    Howard Hughes Medical Institute, Laboratory of RNA Molecular Biology, The Rockefeller University, New York, New York, USA
    Nat Struct Mol Biol 18:1428-31. 2011
    ..FET members showed similar binding profiles, whereas FUS mutants showed a drastically altered binding pattern, consistent with changes in subcellular localization...
  3. pmc MicroRNAs miR-26a, miR-26b, and miR-29b accelerate osteogenic differentiation of unrestricted somatic stem cells from human cord blood
    Hans Ingo Trompeter
    University Düsseldorf, Medical Faculty, Institute for Transplantation Diagnostics and Cell Therapeutics ITZ, Dusseldorf, Germany
    BMC Genomics 14:111. 2013
    ..Here we analyzed the functional impact of miRNAs on the osteogenic differentiation in USSC...
  4. pmc Genome-wide annotation and analysis of zebra finch microRNA repertoire reveal sex-biased expression
    Guan Zheng Luo
    State Kay Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
    BMC Genomics 13:727. 2012
    ....
  5. pmc Identification of clustered microRNAs using an ab initio prediction method
    Alain Sewer
    Biozentrum, Universitat Basel, Basel, Switzerland
    BMC Bioinformatics 6:267. 2005
    ..Bioinformatics approaches have proved to be very useful toward this goal by guiding the experimental investigations...
  6. ncbi request reprint The small RNA profile during Drosophila melanogaster development
    Alexei A Aravin
    Department of Animal Molecular Genetics, Institute of Molecular Genetics, Kurchatov sq 2, 123182, Moscow, Russia
    Dev Cell 5:337-50. 2003
    ..rasiRNAs are most abundant in testes and early embryos, where regulation of transposon activity is critical and dramatic changes in heterochromatin structure occur...
  7. ncbi request reprint Identification and characterization of small RNAs involved in RNA silencing
    Alexei Aravin
    Laboratory of RNA Molecular Biology, The Rockefeller University, New York, NY 10021, USA
    FEBS Lett 579:5830-40. 2005
    ..The identification and characterization of small RNAs and their expression patterns is important for elucidating gene regulatory networks...
  8. pmc Structure of an argonaute silencing complex with a seed-containing guide DNA and target RNA duplex
    Yanli Wang
    Structural Biology Program, Memorial Sloan Kettering Cancer Center, New York, New York 10065, USA
    Nature 456:921-6. 2008
    ..Consistent with the geometry of the ternary complex, bulges residing in the seed segments of the target, but not the guide strand, were better accommodated and their complexes were catalytically active...
  9. ncbi request reprint Identification of novel argonaute-associated proteins
    Gunter Meister
    Laboratory of RNA Molecular Biology, The Rockefeller University, 1230 York Avenue, Box 186, New York, New York 10021, USA
    Curr Biol 15:2149-55. 2005
    ..The new proteins localize, similar to Ago proteins, to mRNA-degrading cytoplasmic P bodies, and they are functionally required to mediate miRNA-guided mRNA cleavage...
  10. pmc Structural and functional insights into 5'-ppp RNA pattern recognition by the innate immune receptor RIG-I
    Yanli Wang
    Structural Biology Program, Memorial Sloan Kettering Cancer Center, New York, New York, USA
    Nat Struct Mol Biol 17:781-7. 2010
    ....
  11. pmc RNA-ligase-dependent biases in miRNA representation in deep-sequenced small RNA cDNA libraries
    Markus Hafner
    Howard Hughes Medical Institute, Laboratory for RNA Molecular Biology, The Rockefeller University, New York, New York 10065, USA
    RNA 17:1697-712. 2011
    ....
  12. ncbi request reprint Crystal structure of A. aeolicus argonaute, a site-specific DNA-guided endoribonuclease, provides insights into RISC-mediated mRNA cleavage
    Yu Ren Yuan
    Structural Biology Program, Memorial Sloan Kettering Cancer Center, New York, New York 10021, USA
    Mol Cell 19:405-19. 2005
    ..We propose a four-step Ago-mediated catalytic cleavage cycle model, which provides distinct perspectives into the mechanism of guide strand-mediated mRNA cleavage within the RISC...
  13. ncbi request reprint Human Argonaute2 mediates RNA cleavage targeted by miRNAs and siRNAs
    Gunter Meister
    Laboratory of RNA Molecular Biology, The Rockefeller University, 1230 York Avenue, Box 186, New York, NY 10021, USA
    Mol Cell 15:185-97. 2004
    ..The specific role of Ago2 in guiding target RNA cleavage was confirmed independently by siRNA-based depletion of individual Ago members in combination with a sensitive positive-readout reporter assay...
  14. pmc DGCR8-dependent microRNA biogenesis is essential for skin development
    Rui Yi
    Howard Hughes Medical Institute, Laboratory of Mammalian Cell Biology and Development, and Laboratory of RNA Molecular Biology, The Rockefeller University, New York, NY 10065, USA
    Proc Natl Acad Sci U S A 106:498-502. 2009
    ..Our results underscore a specific importance of microRNAs in controlling mammalian skin development...
  15. pmc Multicolor microRNA FISH effectively differentiates tumor types
    Neil Renwick
    Howard Hughes Medical Institute, Laboratory of RNA Molecular Biology, The Rockefeller University, New York, New York 10065, USA
    J Clin Invest 123:2694-702. 2013
    ..Our study establishes a reliable miRNA FISH technique for parallel visualization of differentially expressed miRNAs in FFPE tumor tissues...
  16. pmc A mammalian microRNA expression atlas based on small RNA library sequencing
    Pablo Landgraf
    Howard Hughes Medical Institute, Laboratory of RNA Molecular Biology, Box 186, The Rockefeller University, New York, NY 10021, USA
    Cell 129:1401-14. 2007
    ..We also propose a subclassification scheme for miRNAs for assisting future experimental and computational functional analyses...
  17. pmc Deep sequencing of small RNAs specifically associated with Arabidopsis AGO1 and AGO4 uncovers new AGO functions
    Huan Wang
    Laboratory of Plant Molecular Biology, The Rockefeller University, New York, NY 10065, USA
    Plant J 67:292-304. 2011
    ....
  18. ncbi request reprint Antisense-mediated depletion reveals essential and specific functions of microRNAs in Drosophila development
    Dan Leaman
    Laboratory of Developmental Neurogenetics, Rockefeller University, 1230 York Ave, New York, New York 10021, USA
    Cell 121:1097-108. 2005
    ..Our findings demonstrate that microRNAs act as specific and essential regulators in a wide range of developmental processes...
  19. ncbi request reprint A potential protein-RNA recognition event along the RISC-loading pathway from the structure of A. aeolicus Argonaute with externally bound siRNA
    Yu Ren Yuan
    Structural Biology Program, Memorial Sloan Kettering Cancer Center, New York, New York 10021, USA
    Structure 14:1557-65. 2006
    ..The structure and biochemical data together provide insights into a protein-RNA recognition event potentially associated with the RISC-loading pathway...
  20. pmc MicroRNA-mediated down-regulation of PRDM1/Blimp-1 in Hodgkin/Reed-Sternberg cells: a potential pathogenetic lesion in Hodgkin lymphomas
    Kui Nie
    Department of Pathology and Laboratory Medicine, Joan and Sanford I Weill Medical College of Cornell University, New York, New York 10021, USA
    Am J Pathol 173:242-52. 2008
    ....
  21. doi request reprint Structure of the guide-strand-containing argonaute silencing complex
    Yanli Wang
    Structural Biology Program, Memorial Sloan Kettering Cancer Center, New York, New York 10065, USA
    Nature 456:209-13. 2008
    ....
  22. pmc Molecular characterization of human Argonaute-containing ribonucleoprotein complexes and their bound target mRNAs
    Markus Landthaler
    Laboratory of RNA Molecular Biology, Howard Hughes Medical Institute, The Rockefeller University, New York, New York 10065, USA
    RNA 14:2580-96. 2008
    ..Our results further demonstrate that we have developed an effective biochemical approach to identify physiologically relevant human miRNA targets...
  23. pmc A Drosophila pasha mutant distinguishes the canonical microRNA and mirtron pathways
    Raquel Martin
    Department of Developmental Biology, 1017 Rockefeller Research Laboratories, Sloan Kettering Institute, New York, New York 10065, USA
    Mol Cell Biol 29:861-70. 2009
    ..These data suggest limitations to somatic clonal analysis of miRNA pathway components...
  24. ncbi request reprint The human DiGeorge syndrome critical region gene 8 and Its D. melanogaster homolog are required for miRNA biogenesis
    Markus Landthaler
    Laboratory of RNA Molecular Biology, The Rockefeller University, 1230 York Avenue, Box 186, New York, NY 10021, USA
    Curr Biol 14:2162-7. 2004
    ..Our results suggest that DGCR8 and Drosha interact in human cells and reside in a functional pri-miRNA processing complex...
  25. pmc Strand-specific 5'-O-methylation of siRNA duplexes controls guide strand selection and targeting specificity
    Po Yu Chen
    Laboratory of RNA Molecular Biology, Howard Hughes Medical Institute, The Rockefeller University, New York, New York 10021, USA
    RNA 14:263-74. 2008
    ..We conclude that asymmetric 5' modification of siRNA duplexes can be useful for controlling targeting specificity...
  26. pmc Identification of mRNAs bound and regulated by human LIN28 proteins and molecular requirements for RNA recognition
    Markus Hafner
    Howard Hughes Medical Institute and Laboratory for RNA Molecular Biology, The Rockefeller University, New York, New York 10065, USA
    RNA 19:613-26. 2013
    ....
  27. pmc FMRP targets distinct mRNA sequence elements to regulate protein expression
    Manuel Ascano
    Howard Hughes Medical Institute, Laboratory of RNA Molecular Biology, The Rockefeller University, New York, New York 10065, USA
    Nature 492:382-6. 2012
    ..As the importance of signalling pathways in both FXS and ASD is becoming increasingly apparent, our results provide a ranked list of genes as basis for the pursuit of new therapeutic targets for these neurological disorders...
  28. pmc Specificity, duplex degradation and subcellular localization of antagomirs
    Jan Krutzfeldt
    Laboratory of Metabolic Diseases, The Rockefeller University, 1230 York Avenue, New York, NY 10021, USA
    Nucleic Acids Res 35:2885-92. 2007
    ..Our data further validate the effectiveness of antagomirs in vivo and should facilitate future studies to silence miRNAs for functional analysis and in clinically relevant settings...
  29. pmc Identification of microRNAs and other small regulatory RNAs using cDNA library sequencing
    Markus Hafner
    Howard Hughes Medical Institute, Laboratory of RNA Molecular Biology, The Rockefeller University, 1230 York Avenue, Box 186, New York, NY 10065, USA
    Methods 44:3-12. 2008
    ..This protocol includes the use of new deep sequencing methods (454/Roche and Solexa) to facilitate the characterization of diverse sequence pools of small RNAs...
  30. pmc Human MicroRNA targets
    Bino John
    Computational Biology Center, Memorial Sloan Kettering Cancer Center, New York, New York, USA
    PLoS Biol 2:e363. 2004
    ..microrna.org. Our analysis suggests that miRNA genes, which are about 1% of all human genes, regulate protein production for 10% or more of all human genes...
  31. pmc A role for neuronal piRNAs in the epigenetic control of memory-related synaptic plasticity
    Priyamvada Rajasethupathy
    Department of Neuroscience, Columbia University, New York, NY 10032, USA
    Cell 149:693-707. 2012
    ..These findings provide a small RNA-mediated gene regulatory mechanism for establishing stable long-term changes in neurons for the persistence of memory...
  32. ncbi request reprint Identification of microRNAs of the herpesvirus family
    Sebastien Pfeffer
    Laboratory of RNA Molecular Biology, The Rockefeller University, 1230 York Avenue, Box 186, New York, New York 10021, USA
    Nat Methods 2:269-76. 2005
    ..Generally, we predicted miRNAs in several large DNA viruses, and we could neither predict nor experimentally identify miRNAs in the genomes of small RNA viruses or retroviruses...
  33. pmc Bioinformatic analysis of barcoded cDNA libraries for small RNA profiling by next-generation sequencing
    Thalia A Farazi
    Howard Hughes Medical Institute, Laboratory of RNA Molecular Biology, The Rockefeller University, 1230 York Avenue, Box 186, New York, NY 10065, USA
    Methods 58:171-87. 2012
    ....
  34. pmc Barcoded cDNA library preparation for small RNA profiling by next-generation sequencing
    Markus Hafner
    Laboratory of RNA Molecular Biology, Howard Hughes Medical Institute, The Rockefeller University, 1230 York Avenue, Box 186, NY 10065, USA
    Methods 58:164-70. 2012
    ..Here we present a step-by-step protocol for generating barcoded small RNA cDNA libraries compatible with Illumina HiSeq sequencing, thereby facilitating miRNA and other small RNA profiling of large sample collections...
  35. pmc Nucleation, propagation and cleavage of target RNAs in Ago silencing complexes
    Yanli Wang
    Structural Biology Program, Memorial Sloan Kettering Cancer Center, New York, New York 10065, USA
    Nature 461:754-61. 2009
    ..Cleavage assays on targets of various lengths supported this model, and sugar-phosphate-backbone-modified target strands showed the importance of structural and catalytic divalent metal ions observed in the crystal structures...
  36. pmc Multimeric assembly and biochemical characterization of the Trax-translin endonuclease complex
    Yuan Tian
    Structural Biology Program, Memorial Sloan Kettering Cancer Center, New York, New York, USA Graduate Program in Neuroscience, Weill Medical College of Cornell University, New York, New York, USA
    Nat Struct Mol Biol 18:658-64. 2011
    ..Truncated C3PO, like full-length C3PO, shows endoRNase activity that leaves 3'-hydroxyl-cleaved ends. We have measured the catalytic activity of C3PO and shown it to cleave almost stoichiometric amounts of substrate per second...
  37. pmc Genome-wide identification of microRNA targets in human ES cells reveals a role for miR-302 in modulating BMP response
    Inna Lipchina
    Developmental Biology Program, Memorial Sloan Kettering Cancer Center, New York 10065, USA
    Genes Dev 25:2173-86. 2011
    ..This study broadens our understanding of microRNA function in hESCs and is a valuable resource for future studies in this area...
  38. doi request reprint Structure-function analysis of STING activation by c[G(2',5')pA(3',5')p] and targeting by antiviral DMXAA
    Pu Gao
    Structural Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
    Cell 154:748-62. 2013
    ..Our structural and functional analysis highlights the unexpected versatility of STING in the recognition of natural and synthetic ligands within a small-molecule pocket created by the dimerization of STING...
  39. ncbi request reprint Silencing of microRNAs in vivo with 'antagomirs'
    Jan Krutzfeldt
    Laboratory of Metabolic Diseases, The Rockefeller University, 1230 York Avenue, New York, New York 10021, USA
    Nature 438:685-9. 2005
    ..Our findings show that antagomirs are powerful tools to silence specific miRNAs in vivo and may represent a therapeutic strategy for silencing miRNAs in disease...
  40. ncbi request reprint Identification of virus-encoded microRNAs
    Sebastien Pfeffer
    Laboratory of RNA Molecular Biology, The Rockefeller University, 1230 York Avenue, Box 186, New York, NY 10021, USA
    Science 304:734-6. 2004
    ..Given that miRNAs function in RNA silencing pathways either by targeting messenger RNAs for degradation or by repressing translation, we identified viral regulators of host and/or viral gene expression...
  41. ncbi request reprint PAR-CLIP (Photoactivatable Ribonucleoside-Enhanced Crosslinking and Immunoprecipitation): a step-by-step protocol to the transcriptome-wide identification of binding sites of RNA-binding proteins
    Jessica Spitzer
    Howard Hughes Medical Institute, Laboratory of RNA Molecular Biology, The Rockefeller University, New York, NY, USA these authors contributed equally to this work
    Methods Enzymol 539:113-61. 2014
    ....
  42. pmc FOXO1 is an essential regulator of pluripotency in human embryonic stem cells
    Xin Zhang
    Department of Developmental and Regenerative Biology, Mount Sinai School of Medicine, New York, New York 10029, USA
    Nat Cell Biol 13:1092-9. 2011
    ..These findings have critical implications for stem cell biology, development, longevity and reprogramming, with potentially important ramifications for therapy...
  43. pmc MicroRNAs in human cancer
    Thalia A Farazi
    Howard Hughes Medical Institute, The Rockefeller University, New York, NY 10065, USA
    Adv Exp Med Biol 774:1-20. 2013
    ..Given the critical role miRNAs play in tumorigenesis processes and their disease specific expression, they hold potential as therapeutic targets and novel biomarkers...
  44. pmc Transcriptome-wide identification of RNA-binding protein and microRNA target sites by PAR-CLIP
    Markus Hafner
    Howard Hughes Medical Institute, Laboratory of RNA Molecular Biology, The Rockefeller University, 1230 York Avenue, Box 186, New York, NY 10065, USA
    Cell 141:129-41. 2010
    ..The precise mapping of binding sites across the transcriptome will be critical to the interpretation of the rapidly emerging data on genetic variation between individuals and how these variations contribute to complex genetic diseases...
  45. pmc The developmental miRNA profiles of zebrafish as determined by small RNA cloning
    Po Yu Chen
    Laboratory of RNA Molecular Biology, The Rockefeller University, New York, New York 10021, USA
    Genes Dev 19:1288-93. 2005
    ..Computational predictions of zebrafish miRNA targets are provided that take into account the depth of evolutionary conservation. Besides miRNAs, we identified a prominent class of repeat-associated small interfering RNAs (rasiRNAs)...
  46. pmc Characterization of small RNAs in Aplysia reveals a role for miR-124 in constraining synaptic plasticity through CREB
    Priyamvada Rajasethupathy
    Department of Neuroscience, Columbia University, New York, NY 10032, USA
    Neuron 63:803-17. 2009
    ..We therefore present direct evidence that a modulatory neurotransmitter important for learning can regulate the levels of small RNAs and present a role for miR-124 in long-term plasticity of synapses in the mature nervous system...
  47. ncbi request reprint A pancreatic islet-specific microRNA regulates insulin secretion
    Matthew N Poy
    Laboratory of Metabolic Diseases and Laboratory of RNA Molecular Biology, The Rockefeller University, 1230 York Avenue, New York, New York 10021, USA
    Nature 432:226-30. 2004
    ..Thus, miR-375 is a regulator of insulin secretion and may thereby constitute a novel pharmacological target for the treatment of diabetes...
  48. pmc Eukaryote-specific insertion elements control human ARGONAUTE slicer activity
    Kotaro Nakanishi
    Structural Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
    Cell Rep 3:1893-900. 2013
    ..Evolutionary amino acid changes to hAGO1 were readily reversible, suggesting that loading of guide RNA and pairing of seed-based miRNA and target RNA constrain its sequence drift. ..
  49. pmc Identification of RNA-protein interaction networks using PAR-CLIP
    Manuel Ascano
    Laboratory of RNA Molecular Biology, Howard Hughes Medical Institute, The Rockefeller University, New York, NY, USA
    Wiley Interdiscip Rev RNA 3:159-77. 2012
    ....
  50. pmc Cellular cofactors affecting hepatitis C virus infection and replication
    Glenn Randall
    Laboratory of Virology and Infectious Disease, Center for the Study of Hepatitis C, and Howard Hughes Medical Institute, Laboratory of RNA Molecular Biology, The Rockefeller University, New York, NY 10021, USA
    Proc Natl Acad Sci U S A 104:12884-9. 2007
    ..Our data define 26 host genes that modulate HCV infection and indicate that the requirement for functional RNAi for HCV replication is dominant over any antiviral activity this pathway may exert against HCV...
  51. pmc Comprehensive profiling of circulating microRNA via small RNA sequencing of cDNA libraries reveals biomarker potential and limitations
    Zev Williams
    Weill Cornell Medical Center, New York, NY 10021, USA
    Proc Natl Acad Sci U S A 110:4255-60. 2013
    ..These deep sequencing profiles, which may serve as a model for tumor or disease detection, allow us to define the repertoire of miRNA abundance in the circulation and potential uses as biomarkers...
  52. pmc Cucumber mosaic virus-encoded 2b suppressor inhibits Arabidopsis Argonaute1 cleavage activity to counter plant defense
    Xiuren Zhang
    Laboratory of Plant Molecular Biology, Rockefeller University, New York, New York 10021, USA
    Genes Dev 20:3255-68. 2006
    ..These findings provide insight on the molecular arms race between host antiviral RNA silencing and virus counterdefense...
  53. doi request reprint The growing catalog of small RNAs and their association with distinct Argonaute/Piwi family members
    Thalia A Farazi
    Howard Hughes Medical Institute, Laboratory of RNA Molecular Biology, The Rockefeller University, 1230 York Avenue, Box 186, New York, NY 10065, USA
    Development 135:1201-14. 2008
    ..Based on the known relationship of Argonaute/Piwi proteins with distinct classes of small RNAs, we can now predict how many new classes of small RNAs or silencing processes remain to be discovered...
  54. ncbi request reprint A novel class of small RNAs bind to MILI protein in mouse testes
    Alexei Aravin
    Howard Hughes Medical Institute, Laboratory of RNA Molecular Biology, The Rockefeller University, 1230 York Avenue, Box 186, New York, New York 10021, USA
    Nature 442:203-7. 2006
    ..The identification of this new class of small RNAs provides an important starting point to determine the molecular function of Piwi proteins in mammalian spermatogenesis...
  55. ncbi request reprint Structural basis for 5'-end-specific recognition of guide RNA by the A. fulgidus Piwi protein
    Jin Biao Ma
    Structural Biology Program, Memorial Sloan Kettering Cancer Center, New York, New York 10021, USA
    Nature 434:666-70. 2005
    ....
  56. pmc A genome-wide view of the expression and processing patterns of Thermus thermophilus HB8 CRISPR RNAs
    Stefan Juranek
    Howard Hughes Medical Institute, Laboratory of RNA Molecular Biology, The Rockefeller University, New York, New York 10065, USA
    RNA 18:783-94. 2012
    ..These observations are consistent with the operation of multiple crRNA processing systems within a bacterial strain...
  57. pmc MicroRNA sequence profiles of human kidney allografts with or without tubulointerstitial fibrosis
    Iddo Z Ben-Dov
    Howard Hughes Medical Institute, Laboratory for RNA Molecular Biology, The Rockefeller University, New York, NY, USA
    Transplantation 94:1086-94. 2012
    ..Small-RNA sequencing provides information on total miRNA abundance and specific miRNA expression and allows analysis of differential expression based on read counts...
  58. pmc Genome-wide identification of miRNA targets by PAR-CLIP
    Markus Hafner
    Laboratory of RNA Molecular Biology, Howard Hughes Medical Institute, The Rockefeller University, New York, NY, USA
    Methods 58:94-105. 2012
    ....
  59. pmc RISC is a 5' phosphomonoester-producing RNA endonuclease
    Javier Martinez
    Laboratory of RNA Molecular Biology, The Rockefeller University, New York, NY 10021, USA
    Genes Dev 18:975-80. 2004
    ..Mutational analysis of the target RNA revealed that mismatches across from the 5' or the 3' end of the siRNA had little effect and that substrate RNAs as short as 15 nucleotides were cleaved by RISC...
  60. pmc A comprehensive analysis of the effects of the deaminase AID on the transcriptome and methylome of activated B cells
    Eric L Fritz
    Laboratory of Lymphocyte Biology, The Rockefeller University, New York, New York, USA
    Nat Immunol 14:749-55. 2013
    ..Thus, despite evidence of its additional activities in other systems, antibody diversification seems to be the sole physiological function of AID in activated B cells...
  61. pmc MicroRNA-155 is a negative regulator of activation-induced cytidine deaminase
    Grace Teng
    Laboratory of Lymphocyte Biology, The Rockefeller University, 1230 York Avenue, New York, NY 10065, USA
    Immunity 28:621-9. 2008
    ..Thus, miR-155, which has recently been shown to play important roles in regulating the germinal-center reaction, does so in part by directly downmodulating AID expression...
  62. doi request reprint Cloning of small RNA molecules
    Sebastien Pfeffer
    The Rockefeller University, New York, New York, USA
    Curr Protoc Mol Biol . 2005
    ..The ligation products are reverse transcribed and PCR-amplified. It is recommended to directionally concatamerize the relatively short PCR products before cloning in order to increase the number of RNA sequences obtained per clone...
  63. ncbi request reprint Mechanisms of gene silencing by double-stranded RNA
    Gunter Meister
    Laboratory of RNA Molecular Biology, The Rockefeller University, 1230 York Avenue, Box 186, New York, New York 10021, USA
    Nature 431:343-9. 2004
    ..These short dsRNAs guide RNA silencing by specific and distinct mechanisms. Many components of the RNA silencing machinery still need to be identified and characterized, but a more complete understanding of the process is imminent...
  64. pmc The PTEN-regulating microRNA miR-26a is amplified in high-grade glioma and facilitates gliomagenesis in vivo
    Jason T Huse
    Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York 10021, USA
    Genes Dev 23:1327-37. 2009
    ..Our results document a new epigenetic mechanism for PTEN regulation in glioma and further highlight dysregulation of Akt signaling as crucial to the development of these tumors...
  65. pmc Repeat-associated siRNAs cause chromatin silencing of retrotransposons in the Drosophila melanogaster germline
    Mikhail S Klenov
    Department of Molecular Genetics of Cell, Institute of Molecular Genetics, Russian Academy of Sciences, Moscow 123182, Russia
    Nucleic Acids Res 35:5430-8. 2007
    ..Our results provide evidence that germinal Piwi-associated short RNAs induce chromatin modifications of their targets...
  66. ncbi request reprint Gene silencing with siRNA duplexes composed of target-mRNA-complementary and partially palindromic or partially complementary single-stranded siRNAs
    Markus Hossbach
    Department of Cellular Biochemistry, Max Planck Institute for Biophysical Chemistry, Gottingen, Germany
    RNA Biol 3:82-9. 2006
    ..Such siRNA duplexes may offer advantages regarding production costs and specificity of gene silencing...
  67. pmc Elevated expression of the miR-17-92 polycistron and miR-21 in hepadnavirus-associated hepatocellular carcinoma contributes to the malignant phenotype
    Erin Connolly
    Marion Bessin Liver Research Center, Department of Medicine, Albert Einstein College of Medicine, Bronx, New York 10461, USA
    Am J Pathol 173:856-64. 2008
    ..The combination of assays presented here supports a role for these miRNAs in the maintenance of the malignant transformation of hepatocytes...
  68. ncbi request reprint Single-stranded antisense siRNAs guide target RNA cleavage in RNAi
    Javier Martinez
    Department of Cellular Biochemistry, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, D 37077, Gottingen, Germany
    Cell 110:563-74. 2002
    ..Single-stranded antisense siRNAs are also effectively silencing genes in HeLa cells, especially when 5'-phosphorylated, and expand the repertoire of RNA reagents suitable for gene targeting...
  69. ncbi request reprint Quantitative technologies establish a novel microRNA profile of chronic lymphocytic leukemia
    Valerio Fulci
    Dipartimento di Biotecnologie Cellulari ed Ematologia, Sezione di Genetica Molecolare, Universita di Roma La Sapienza, Rome, Italy
    Blood 109:4944-51. 2007
    ..In summary, the results of this study offer for the first time a comprehensive and quantitative profile of miRNA expression in CLL and their healthy counterpart, suggesting that miRNAs could play a primary role in the disease itself...
  70. ncbi request reprint Analysis of gene function in somatic mammalian cells using small interfering RNAs
    Sayda M Elbashir
    Department of Cellular Biochemistry, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, D 37077 Gottingen, Germany
    Methods 26:199-213. 2002
    ..Because of the robustness of the siRNA knockdown technology, genomewide analysis of human gene function in cultured cells has now become possible...
  71. pmc Sequence-specific inhibition of microRNA- and siRNA-induced RNA silencing
    Gunter Meister
    Laboratory of RNA Molecular Biology, The Rockefeller University, New York, New York 10021, USA
    RNA 10:544-50. 2004
    ..Here we show that 2'-O-methyl oligoribonucleotides, but not 2'-deoxyoligonucleotides specifically inactivate the RNAi activity associated with miRNA-protein complexes in human cell extracts as well as in cultured human cells...
  72. ncbi request reprint Sequence, chemical, and structural variation of small interfering RNAs and short hairpin RNAs and the effect on mammalian gene silencing
    Jens Harborth
    Department of Biochemistry and Cell Biology, Max Planck Institute for Biophysical Chemistry, D 37077 Gottingen, Germany
    Antisense Nucleic Acid Drug Dev 13:83-105. 2003
    ....
  73. pmc MicroRNA targets in Drosophila
    Anton J Enright
    Computational Biology Center, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY 10021, USA
    Genome Biol 5:R1. 2003
    ..Application to the D. melanogaster, Drosophila pseudoobscura and Anopheles gambiae genomes identifies several hundred target genes potentially regulated by one or more known miRNAs...
  74. ncbi request reprint RNA interference by osmotic lysis of pinosomes: liposome-independent transfection of siRNAs into mammalian cells
    Jens Gruber
    Max Planck Institute for Biophysical Chemistry, Goettingen, Germany
    Biotechniques 37:96-102. 2004
    ..The new procedure avoids certain technical problems encountered with commercial transfection reagents while yielding silencing efficiencies that are comparable to those obtained with liposome-mediated siRNA transfection...
  75. ncbi request reprint On the art of identifying effective and specific siRNAs
    Yi Pei
    Howard Hughes Medical Institute, Laboratory of RNA Molecular Biology, The Rockefeller University, 1230 York Avenue, Box 186, New York, New York 10021, USA
    Nat Methods 3:670-6. 2006
    ..Though these methods facilitate selection of functional siRNAs, they do not yet alleviate the need for experimental validation. This perspective provides a practical guide based on current wisdom for selecting siRNAs...
  76. ncbi request reprint Identification of tissue-specific microRNAs from mouse
    Mariana Lagos-Quintana
    Department of Cellular Biochemistry, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, D 37077 Gottingen, Germany
    Curr Biol 12:735-9. 2002
    ..Finally, a miRNA was identified that appears to be the fruitfly and mammalian ortholog of C. elegans lin-4 stRNA...
  77. ncbi request reprint Expanding small RNA interference
    Thomas Tuschl
    Nat Biotechnol 20:446-8. 2002
  78. ncbi request reprint siRNAs: applications in functional genomics and potential as therapeutics
    Yair Dorsett
    Laboratory of RNA Molecular Biology, Rockefeller University, 1230 York Avenue, Box 186, New York, New York 10021, USA
    Nat Rev Drug Discov 3:318-29. 2004
  79. pmc The human 18S U11/U12 snRNP contains a set of novel proteins not found in the U2-dependent spliceosome
    Cindy L Will
    Department of Cellular Biochemistry, Max Planck Institute of Biophysical Chemistry, D 37077 Gottingen, Germany
    RNA 10:929-41. 2004
    ..The presence of unique U11/U12 snRNP proteins in the U12-type spliceosome provides insight into potential evolutionary relationships between the major and minor spliceosome...
  80. ncbi request reprint Functional genomics: RNA sets the standard
    Thomas Tuschl
    Nature 421:220-1. 2003
  81. pmc Clustering and conservation patterns of human microRNAs
    Yael Altuvia
    Department of Molecular Genetics and Biotechnology, Faculty of Medicine, The Hebrew University PO Box 12272, Jerusalem 91120, Israel
    Nucleic Acids Res 33:2697-706. 2005
    ..This suggests that the clustering of miRNA genes is higher than currently acknowledged, alluding to its evolutionary and functional implications...
  82. pmc New microRNAs from mouse and human
    Mariana Lagos-Quintana
    Department of Cellular Biochemistry, Max Planck Institute for Biophysical Chemistry, Am Fassberg 121, D 37077 Gottingen, Germany
    RNA 9:175-9. 2003
    ..A comprehensive collection of miRNAs is important for assisting bioinformatics target mRNA identification and comprehensive genome annotation...
  83. ncbi request reprint Small interfering RNAs: a revolutionary tool for the analysis of gene function and gene therapy
    Thomas Tuschl
    Department of Cellular Biochemistry, Max Planck Institute for Biophysical Chemistry, D 37077 Goettingen, Germany
    Mol Interv 2:158-67. 2002
  84. pmc A uniform system for microRNA annotation
    Victor Ambros
    Dartmouth Medical School Department of Genetics, Hanover, New Hampshire 03755, USA
    RNA 9:277-9. 2003
    ..Finally, an online clearinghouse for miRNA gene name assignments is provided by the Rfam database of RNA families...
  85. pmc siRNA Selection Server: an automated siRNA oligonucleotide prediction server
    Bingbing Yuan
    Whitehead Institute for Biomedical Research, Bioinformatics and Research Computing, Nine Cambridge Center, Cambridge, MA 02142, USA
    Nucleic Acids Res 32:W130-4. 2004
    ....