Research Topics
Genomes and GenesSpecies | Thomas TuschlSummaryAffiliation: The Rockefeller University Country: USA Publications
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Detail Information
Publications
Identification of clustered microRNAs using an ab initio prediction methodAlain 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...
The small RNA profile during Drosophila melanogaster developmentAlexei 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...- Identification and characterization of small RNAs involved in RNA silencingAlexei 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... - Repeat-associated siRNAs cause chromatin silencing of retrotransposons in the Drosophila melanogaster germlineMikhail 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... - 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... - Gene silencing with siRNA duplexes composed of target-mRNA-complementary and partially palindromic or partially complementary single-stranded siRNAsMarkus Hossbach
Department of Cellular Biochemistry, Max-Planck-Institute for Biophysical Chemistry, , Germany
RNA Biol 3:82-9. 2006..Such siRNA duplexes may offer advantages regarding production costs and specificity of gene silencing... - Cellular cofactors affecting hepatitis C virus infection and replicationGlenn 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... - Human MicroRNA targetsBino 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... - A pancreatic islet-specific microRNA regulates insulin secretionMatthew 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... - The human DiGeorge syndrome critical region gene 8 and Its D. melanogaster homolog are required for miRNA biogenesisMarkus 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... - Identification of microRNAs of the herpesvirus familySebastien 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... - A mammalian microRNA expression atlas based on small RNA library sequencingPablo 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... - Identification of novel argonaute-associated proteinsGunter 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... - Quantitative technologies establish a novel microRNA profile of chronic lymphocytic leukemiaValerio 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... - Antisense-mediated depletion reveals essential and specific functions of microRNAs in Drosophila developmentDan 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... - Elevated expression of the miR-17-92 polycistron and miR-21 in hepadnavirus-associated hepatocellular carcinoma contributes to the malignant phenotypeErin 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... - A potential protein-RNA recognition event along the RISC-loading pathway from the structure of A. aeolicus Argonaute with externally bound siRNAYu 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... - Human Argonaute2 mediates RNA cleavage targeted by miRNAs and siRNAsGunter 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... - Sequence, chemical, and structural variation of small interfering RNAs and short hairpin RNAs and the effect on mammalian gene silencingJens Harborth
Department of Biochemistry and Cell Biology, Max-Planck-Institute for Biophysical Chemistry, , Germany
Antisense Nucleic Acid Drug Dev 13:83-105. 2003.... - RNA interference by osmotic lysis of pinosomes: liposome-independent transfection of siRNAs into mammalian cellsJens 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... - Single-stranded antisense siRNAs guide target RNA cleavage in RNAiJavier 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... - Analysis of gene function in somatic mammalian cells using small interfering RNAsSayda M Elbashir
Department of Cellular Biochemistry, Max-Planck-Institute for Biophysical Chemistry, Am Fassberg 11, , 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... - MicroRNA targets in DrosophilaAnton 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... - Sequence-specific inhibition of microRNA- and siRNA-induced RNA silencingGunter 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... - MicroRNA-mediated down-regulation of PRDM1/Blimp-1 in Hodgkin/Reed-Sternberg cells: a potential pathogenetic lesion in Hodgkin lymphomasKui 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.... - Identification of microRNAs and other small regulatory RNAs using cDNA library sequencingMarkus 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... - RISC is a 5' phosphomonoester-producing RNA endonucleaseJavier 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... - Identification of virus-encoded microRNAsSebastien 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... 
The growing catalog of small RNAs and their association with distinct Argonaute/Piwi family membersThalia 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...- MicroRNA-155 is a negative regulator of activation-induced cytidine deaminaseGrace 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... - Strand-specific 5'-O-methylation of siRNA duplexes controls guide strand selection and targeting specificityPo 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... - Specificity, duplex degradation and subcellular localization of antagomirsJan 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... - Cloning of small RNA moleculesSebastien 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... - Cucumber mosaic virus-encoded 2b suppressor inhibits Arabidopsis Argonaute1 cleavage activity to counter plant defenseXiuren 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... - On the art of identifying effective and specific siRNAsYi 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... - Identification of tissue-specific microRNAs from mouseMariana Lagos-Quintana
Department of Cellular Biochemistry, Max-Planck-Institute for Biophysical Chemistry, Am Fassberg 11, , 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... - Functional genomics: RNA sets the standardThomas Tuschl
Nature 421:220-1. 2003 - New microRNAs from mouse and humanMariana Lagos-Quintana
Department of Cellular Biochemistry, Max-Planck-Institute for Biophysical Chemistry, Am Fassberg 121, , Germany
RNA 9:175-9. 2003..A comprehensive collection of miRNAs is important for assisting bioinformatics target mRNA identification and comprehensive genome annotation... - Small interfering RNAs: a revolutionary tool for the analysis of gene function and gene therapyThomas Tuschl
Department of Cellular Biochemistry, Max-Planck-Institute for Biophysical Chemistry, D-37077 Goettingen, Germany
Mol Interv 2:158-67. 2002 - siRNAs: applications in functional genomics and potential as therapeuticsYair 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 - The human 18S U11/U12 snRNP contains a set of novel proteins not found in the U2-dependent spliceosomeCindy L Will
Department of Cellular Biochemistry, Max Planck Institute of Biophysical Chemistry, , 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... - siRNA Selection Server: an automated siRNA oligonucleotide prediction serverBingbing Yuan
Whitehead Institute for Biomedical Research, Bioinformatics and Research Computing, Nine Cambridge Center, Cambridge, MA 02142, USA
Nucleic Acids Res 32:W130-4. 2004.... - Mechanisms of gene silencing by double-stranded RNAGunter 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... - A uniform system for microRNA annotationVictor 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... - Clustering and conservation patterns of human microRNAsYael 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... - The developmental miRNA profiles of zebrafish as determined by small RNA cloningPo 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)... - Structural basis for 5'-end-specific recognition of guide RNA by the A. fulgidus Piwi proteinJin Biao Ma
Structural Biology Program, Memorial Sloan Kettering Cancer Center, New York, New York 10021, USA
Nature 434:666-70. 2005.... - A novel class of small RNAs bind to MILI protein in mouse testesAlexei 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... - Expanding small RNA interferenceThomas Tuschl
Nat Biotechnol 20:446-8. 2002