David Bartel

Summary

Affiliation: Massachusetts Institute of Technology
Country: USA

Publications

  1. ncbi request reprint Vertebrate microRNA genes
    Lee P Lim
    Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
    Science 299:1540. 2003
  2. pmc The Drosophila hairpin RNA pathway generates endogenous short interfering RNAs
    Katsutomo Okamura
    Sloan Kettering Institute, Department of Developmental Biology, 521 Rockefeller Research Laboratories, 1275 York Avenue, Box 252, New York, New York 10065, USA
    Nature 453:803-6. 2008
  3. pmc Mammalian microRNAs predominantly act to decrease target mRNA levels
    Huili Guo
    Whitehead Institute for Biomedical Research, Cambridge, Massachusetts 02142, USA
    Nature 466:835-40. 2010
  4. pmc Allelic imbalance sequencing reveals that single-nucleotide polymorphisms frequently alter microRNA-directed repression
    Jinkuk Kim
    Whitehead Institute for Biomedical Research, Cambridge, Massachusetts, USA
    Nat Biotechnol 27:472-7. 2009
  5. pmc Weak seed-pairing stability and high target-site abundance decrease the proficiency of lsy-6 and other microRNAs
    David M Garcia
    Whitehead Institute for Biomedical Research, Cambridge, Massachusetts, USA
    Nat Struct Mol Biol 18:1139-46. 2011
  6. pmc The structural basis of RNA-catalyzed RNA polymerization
    David M Shechner
    Whitehead Institute for Biomedical Research, Cambridge, Massachusetts, USA
    Nat Struct Mol Biol 18:1036-42. 2011
  7. pmc Formation, regulation and evolution of Caenorhabditis elegans 3'UTRs
    Calvin H Jan
    Whitehead Institute for Biomedical Research, Cambridge, Massachusetts 02142, USA
    Nature 469:97-101. 2011
  8. ncbi request reprint Micromanagers of gene expression: the potentially widespread influence of metazoan microRNAs
    David P Bartel
    Whitehead Institute for Biomedical Research, Nine Cambridge Center, Cambridge, Massachusetts 02142, USA
    Nat Rev Genet 5:396-400. 2004
  9. ncbi request reprint MicroRNAs: genomics, biogenesis, mechanism, and function
    David P Bartel
    Whitehead Institute for Biomedical Research, 9 Cambridge Center, Cambridge, MA 02142, USA
    Cell 116:281-97. 2004
  10. ncbi request reprint Constructing an RNA world
    D P Bartel
    Whitehead Institute for Biomedical Research and Dept of Biology, MIT, 9 Cambridge Center, Cambridge, MA 02142, USA
    Trends Cell Biol 9:M9-M13. 1999

Research Grants

  1. RNA CONFORMATION AND CATALYSIS
    David Bartel; Fiscal Year: 2001
  2. The Roles of MicroRNAs in Plant Development
    David Bartel; Fiscal Year: 2007
  3. RNA CONFORMATION AND CATALYSIS
    David Bartel; Fiscal Year: 2006
  4. MicroRNA genes and their functions
    David P Bartel; Fiscal Year: 2010
  5. MicroRNA genes and their functions
    David Bartel; Fiscal Year: 2005
  6. MicroRNA genes and their functions
    David Bartel; Fiscal Year: 2004
  7. RNA CONFORMATION AND CATALYSIS
    David Bartel; Fiscal Year: 2003
  8. MicroRNA genes and their functions
    David Bartel; Fiscal Year: 2002
  9. RNA CONFORMATION AND CATALYSIS
    David Bartel; Fiscal Year: 2002
  10. MicroRNA genes and their functions
    David Bartel; Fiscal Year: 2003

Detail Information

Publications79

  1. ncbi request reprint Vertebrate microRNA genes
    Lee P Lim
    Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
    Science 299:1540. 2003
  2. pmc The Drosophila hairpin RNA pathway generates endogenous short interfering RNAs
    Katsutomo Okamura
    Sloan Kettering Institute, Department of Developmental Biology, 521 Rockefeller Research Laboratories, 1275 York Avenue, Box 252, New York, New York 10065, USA
    Nature 453:803-6. 2008
    ..These novel regulatory RNAs reveal unexpected complexity in the sorting of small RNAs, and open a window onto the biological usage of endogenous RNA interference in Drosophila...
  3. pmc Mammalian microRNAs predominantly act to decrease target mRNA levels
    Huili Guo
    Whitehead Institute for Biomedical Research, Cambridge, Massachusetts 02142, USA
    Nature 466:835-40. 2010
    ..These results show that changes in mRNA levels closely reflect the impact of miRNAs on gene expression and indicate that destabilization of target mRNAs is the predominant reason for reduced protein output...
  4. pmc Allelic imbalance sequencing reveals that single-nucleotide polymorphisms frequently alter microRNA-directed repression
    Jinkuk Kim
    Whitehead Institute for Biomedical Research, Cambridge, Massachusetts, USA
    Nat Biotechnol 27:472-7. 2009
    ..Extrapolating these results to the other broadly conserved miRNAs suggests that when comparing two mouse strains (or two human individuals), polymorphic miRNA sites cause expression of many genes (often hundreds) to differ...
  5. pmc Weak seed-pairing stability and high target-site abundance decrease the proficiency of lsy-6 and other microRNAs
    David M Garcia
    Whitehead Institute for Biomedical Research, Cambridge, Massachusetts, USA
    Nat Struct Mol Biol 18:1139-46. 2011
    ..We propose that siRNAs designed to have both weaker SPS and higher TA will have fewer off-targets without compromised on-target activity...
  6. pmc The structural basis of RNA-catalyzed RNA polymerization
    David M Shechner
    Whitehead Institute for Biomedical Research, Cambridge, Massachusetts, USA
    Nat Struct Mol Biol 18:1036-42. 2011
    ..Thus artificial ribozymes can use complex catalytic strategies that differ markedly from those of analogous biological enzymes...
  7. pmc Formation, regulation and evolution of Caenorhabditis elegans 3'UTRs
    Calvin H Jan
    Whitehead Institute for Biomedical Research, Cambridge, Massachusetts 02142, USA
    Nature 469:97-101. 2011
    ..These findings reveal the influence of cleavage and polyadenylation on the evolution of genome architecture and provide resources for studying post-transcriptional gene regulation...
  8. ncbi request reprint Micromanagers of gene expression: the potentially widespread influence of metazoan microRNAs
    David P Bartel
    Whitehead Institute for Biomedical Research, Nine Cambridge Center, Cambridge, Massachusetts 02142, USA
    Nat Rev Genet 5:396-400. 2004
  9. ncbi request reprint MicroRNAs: genomics, biogenesis, mechanism, and function
    David P Bartel
    Whitehead Institute for Biomedical Research, 9 Cambridge Center, Cambridge, MA 02142, USA
    Cell 116:281-97. 2004
    ..Although they escaped notice until relatively recently, miRNAs comprise one of the more abundant classes of gene regulatory molecules in multicellular organisms and likely influence the output of many protein-coding genes...
  10. ncbi request reprint Constructing an RNA world
    D P Bartel
    Whitehead Institute for Biomedical Research and Dept of Biology, MIT, 9 Cambridge Center, Cambridge, MA 02142, USA
    Trends Cell Biol 9:M9-M13. 1999
    ..Filling these gaps would place the hypothesis on much firmer ground and provide components for building minimal forms of RNA-based cellular life...
  11. pmc MicroRNAs: target recognition and regulatory functions
    David P Bartel
    Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
    Cell 136:215-33. 2009
    ..This review outlines the current understanding of miRNA target recognition in animals and discusses the widespread impact of miRNAs on both the expression and evolution of protein-coding genes...
  12. pmc The microRNAs of Caenorhabditis elegans
    Lee P Lim
    Department of Biology, Massachusetts Institute of Technology, Cambridge 02139, USA
    Genes Dev 17:991-1008. 2003
    ..Our census of the worm miRNAs and their expression patterns helps define this class of noncoding RNAs, lays the groundwork for functional studies, and provides the tools for more comprehensive analyses of miRNA genes in other species...
  13. ncbi request reprint Small RNAs correspond to centromere heterochromatic repeats
    Brenda J Reinhart
    Whitehead Institute for Biomedical Research and Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02142, USA
    Science 297:1831. 2002
  14. pmc Patterns of flanking sequence conservation and a characteristic upstream motif for microRNA gene identification
    Uwe Ohler
    Department of Biology, Massachusetts Institute of Technology, Cambridge 02142, USA
    RNA 10:1309-22. 2004
    ..The improved analysis supports our previous assertion that miRNA gene identification is nearing completion in C. elegans with apparently no more than 20 miRNA genes now remaining to be identified...
  15. ncbi request reprint Large-scale sequencing reveals 21U-RNAs and additional microRNAs and endogenous siRNAs in C. elegans
    J Graham Ruby
    Whitehead Institute for Biomedical Research, 9 Cambridge Center, Cambridge, MA 02142, USA
    Cell 127:1193-207. 2006
    ..The motif is conserved in other nematodes, presumably because of its importance for producing these diverse, autonomously expressed, small RNAs (dasRNAs)...
  16. pmc A single Hox locus in Drosophila produces functional microRNAs from opposite DNA strands
    Alexander Stark
    Broad Institute of Massachussetts Institute of Technology and Harvard University, Cambridge, Massachusetts 02141, USA
    Genes Dev 22:8-13. 2008
    ..We also report sense/antisense miRNAs in mouse and find antisense transcripts close to many miRNAs in both flies and mammals, suggesting that additional sense/antisense pairs exist...
  17. pmc MicroRNAs in plants
    Brenda J Reinhart
    Whitehead Institute for Biomedical Research, and Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts 02142, USA
    Genes Dev 16:1616-26. 2002
    ..The previously described roles of CARPEL FACTORY in the development of Arabidopsis embryos, leaves, and floral meristems suggest that the miRNAs could play regulatory roles in the development of plants as well as animals...
  18. pmc Discovery of functional elements in 12 Drosophila genomes using evolutionary signatures
    Alexander Stark
    The Broad Institute, Massachusetts Institute of Technology and Harvard University, Cambridge, Massachusetts 02140, USA
    Nature 450:219-32. 2007
    ..We also study how discovery power scales with the divergence and number of species compared, and we provide general guidelines for comparative studies...
  19. ncbi request reprint Prediction of plant microRNA targets
    Matthew W Rhoades
    Whitehead Institute for Biomedical Research, 9 Cambridge Center, MA 02142, USA
    Cell 110:513-20. 2002
    ..The targeting of developmental transcription factors suggests that many plant miRNAs function during cellular differentiation to clear key regulatory transcripts from daughter cell lineages...
  20. ncbi request reprint The widespread impact of mammalian MicroRNAs on mRNA repression and evolution
    Kyle Kai How Farh
    Whitehead Institute for Biomedical Research, Department of Biology, Massachusetts Institute of Technology, and Howard Hughes Medical Institute, 9 Cambridge Center, Cambridge, MA 02142, USA
    Science 310:1817-21. 2005
    ....
  21. ncbi request reprint A two-hit trigger for siRNA biogenesis in plants
    Michael J Axtell
    Howard Hughes Medical Institute, Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA
    Cell 127:565-77. 2006
    ..Therefore, two "hits,"--often, but not always, two cleavage events--constitute a conserved trigger for siRNA biogenesis, a finding with implications for recognition and silencing of aberrant RNA...
  22. pmc The impact of microRNAs on protein output
    Daehyun Baek
    Whitehead Institute for Biomedical Research, 9 Cambridge Center, Cambridge, Massachusetts 02142, USA
    Nature 455:64-71. 2008
    ..The impact of microRNAs on the proteome indicated that for most interactions microRNAs act as rheostats to make fine-scale adjustments to protein output...
  23. pmc A diverse and evolutionarily fluid set of microRNAs in Arabidopsis thaliana
    Ramya Rajagopalan
    Howard Hughes Medical Institute, Department of Biology, Massachusetts Institute of Technology, Whitehead Institute for Biomedical Research, Cambridge, Massachusetts 02142, USA
    Genes Dev 20:3407-25. 2006
    ....
  24. pmc Evolution, biogenesis, expression, and target predictions of a substantially expanded set of Drosophila microRNAs
    J Graham Ruby
    Whitehead Institute for Biomedical Research, Cambridge, Massachusetts 02142, USA
    Genome Res 17:1850-64. 2007
    ....
  25. pmc Most Caenorhabditis elegans microRNAs are individually not essential for development or viability
    Eric A Miska
    Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
    PLoS Genet 3:e215. 2007
    ..This study represents the first comprehensive genetic analysis of miRNA function in any organism and provides a unique, permanent resource for the systematic study of miRNAs...
  26. pmc Early origins and evolution of microRNAs and Piwi-interacting RNAs in animals
    Andrew Grimson
    Whitehead Institute for Biomedical Research, 9 Cambridge Center, Cambridge, Massachusetts 02142, USA
    Nature 455:1193-7. 2008
    ..Nonetheless, miRNAs and piRNAs have been available as classes of riboregulators to shape gene expression throughout the evolution and radiation of animal phyla...
  27. ncbi request reprint Computational identification of plant microRNAs and their targets, including a stress-induced miRNA
    Matthew W Jones-Rhoades
    Whitehead Institute for Biomedical Research and Department of Biology, Massachusetts Institute of Technology, 9 Cambridge Center, Cambridge, MA 02142, USA
    Mol Cell 14:787-99. 2004
    ..The expression of miR395, the sulfurylase-targeting miRNA, increases upon sulfate starvation, showing that miRNAs can be induced by environmental stress...
  28. ncbi request reprint MicroRNA regulation of NAC-domain targets is required for proper formation and separation of adjacent embryonic, vegetative, and floral organs
    Allison C Mallory
    Whitehead Institute for Biomedical Research, 9 Cambridge Center, Cambridge, MA 02142 USA
    Curr Biol 14:1035-46. 2004
    ..Here, we identify a developmental role for miR164-directed regulation of NAC-domain genes, which encode a family of transcription factors that includes CUP-SHAPED COTYLEDON1 (CUC1) and CUC2...
  29. pmc Control of developmental regulators by Polycomb in human embryonic stem cells
    Tong Ihn Lee
    Whitehead Institute for Biomedical Research, 9 Cambridge Center, Cambridge, MA 02142, USA
    Cell 125:301-13. 2006
    ..These results indicate that PRC2 occupies a special set of developmental genes in ES cells that must be repressed to maintain pluripotency and that are poised for activation during ES cell differentiation...
  30. pmc MicroRNAs in the Hox network: an apparent link to posterior prevalence
    Soraya Yekta
    Whitehead Institute for Biomedical Research, Cambridge, Massachusetts 02142, USA
    Nat Rev Genet 9:789-96. 2008
    ..In this way, miRNA-mediated regulation seems to recapitulate interactions at other levels of gene expression, some more ancestral, within a network under stabilizing selection...
  31. pmc Connecting microRNA genes to the core transcriptional regulatory circuitry of embryonic stem cells
    Alexander Marson
    Whitehead Institute for Biomedical Research, 9 Cambridge Center, Cambridge, MA 02142, USA
    Cell 134:521-33. 2008
    ..These data reveal how key ES cell transcription factors promote the ES cell miRNA expression program and integrate miRNAs into the regulatory circuitry controlling ES cell identity...
  32. ncbi request reprint Prediction of mammalian microRNA targets
    Benjamin P Lewis
    Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
    Cell 115:787-98. 2003
    ..The predicted regulatory targets of mammalian miRNAs were enriched for genes involved in transcriptional regulation but also encompassed an unexpectedly broad range of other functions...
  33. ncbi request reprint Censors of the genome
    Nelson C Lau
    Massachusetts Institute of Technology, USA
    Sci Am 289:34-41. 2003
  34. ncbi request reprint MicroRNA-directed cleavage of HOXB8 mRNA
    Soraya Yekta
    Whitehead Institute for Biomedical Research, Nine Cambridge Center, Cambridge, MA 02142, USA
    Science 304:594-6. 2004
    ....
  35. pmc Disrupting the pairing between let-7 and Hmga2 enhances oncogenic transformation
    Christine Mayr
    Howard Hughes Medical Institute and Department of Biology, Massachusetts Institute of Technology, and Whitehead Institute for Biomedical Research, 9 Cambridge Center, Cambridge, MA 02142, USA
    Science 315:1576-9. 2007
    ..Thus, losing miRNA-directed repression of an oncogene provides a mechanism for tumorigenesis, and disrupting a single miRNA-target interaction can produce an observable phenotype in mammalian cells...
  36. pmc Intronic microRNA precursors that bypass Drosha processing
    J Graham Ruby
    Whitehead Institute for Biomedical Research, 9 Cambridge Center, Cambridge, Massachusetts 02142, USA
    Nature 448:83-6. 2007
    ..This suggests that other lineages with many similarly sized introns probably also have mirtrons, and that the mirtron pathway could have provided an early avenue for the emergence of miRNAs before the advent of Drosha...
  37. pmc MicroRNA targeting specificity in mammals: determinants beyond seed pairing
    Andrew Grimson
    Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
    Mol Cell 27:91-105. 2007
    ..Because it predicts site efficacy without recourse to evolutionary conservation, the model also identifies effective nonconserved sites and siRNA off-targets...
  38. pmc MicroRNA control of PHABULOSA in leaf development: importance of pairing to the microRNA 5' region
    Allison C Mallory
    Whitehead Institute for Biomedical Research, Cambridge, MA 02142 1479, USA
    EMBO J 23:3356-64. 2004
    ....
  39. pmc miR-150, a microRNA expressed in mature B and T cells, blocks early B cell development when expressed prematurely
    Beiyan Zhou
    Whitehead Institute for Biomedical Research, Nine Cambridge Center, Cambridge, MA 02142, USA
    Proc Natl Acad Sci U S A 104:7080-5. 2007
    ..Our results indicate that miR-150 most likely down-regulates mRNAs that are important for pre- and pro-B cell formation or function, and its ectopic expression in these cells blocks further development of B cells...
  40. pmc RNAi in budding yeast
    Ines A Drinnenberg
    Whitehead Institute for Biomedical Research, 9 Cambridge Center, Cambridge, MA 02142, USA
    Science 326:544-50. 2009
    ..These results identify a previously unknown class of Dicer proteins, bring the tool of RNAi to the study of budding yeasts, and bring the tools of budding yeast to the study of RNAi...
  41. pmc Coherent but overlapping expression of microRNAs and their targets during vertebrate development
    Alena Shkumatava
    Whitehead Institute of Biomedical Research and Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts 01142, USA
    Genes Dev 23:466-81. 2009
    ..However, for most targets expression was lower in miRNA-expressing cells than in the rest of the embryo, indicating that miRNAs usually operate in concert with the other regulatory machinery of the cell...
  42. pmc MicroRNAs prevent precocious gene expression and enable pattern formation during plant embryogenesis
    Michael D Nodine
    Whitehead Institute for Biomedical Research, Cambridge, Massachusetts 02142, USA
    Genes Dev 24:2678-92. 2010
    ..We propose that, by preventing precocious expression of differentiation-promoting transcription factors, miRNAs enable proper embryonic patterning...
  43. pmc Mammalian microRNAs: experimental evaluation of novel and previously annotated genes
    H Rosaria Chiang
    Whitehead Institute for Biomedical Research, Cambridge, Massachusetts 02142, USA
    Genes Dev 24:992-1009. 2010
    ....
  44. ncbi request reprint MicroRNAs modulate hematopoietic lineage differentiation
    Chang Zheng Chen
    Whitehead Institute for Biomedical Research, Nine Cambridge Center, Cambridge, MA 02142, USA
    Science 303:83-6. 2004
    ..Our results indicate that microRNAs are components of the molecular circuitry that controls mouse hematopoiesis and suggest that other microRNAs have similar regulatory roles during other facets of vertebrate development...
  45. pmc A ribozyme that ligates RNA to protein
    Scott Baskerville
    Whitehead Institute for Biomedical Research and Department of Biology, Massachusetts Institute of Technology, 9 Cambridge Center, Cambridge, MA 02142, USA
    Proc Natl Acad Sci U S A 99:9154-9. 2002
    ....
  46. pmc Improved polymerase ribozyme efficiency on hydrophobic assemblies
    ULRICH F MULLER
    Whitehead Institute for Biomedical Research, Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts 02142, USA
    RNA 14:552-62. 2008
    ..We discuss how, during the origin of life, micellar ribozyme aggregates could have acted as precursors to membrane-encapsulated life forms...
  47. pmc Expanding the microRNA targeting code: functional sites with centered pairing
    Chanseok Shin
    Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA
    Mol Cell 38:789-802. 2010
    ..This expanded repertoire of cleavage targets and the identification of the centered site type help explain why central regions of many miRNAs are evolutionarily conserved...
  48. pmc Antiquity of microRNAs and their targets in land plants
    Michael J Axtell
    Whitehead Institute for Biomedical Research, Cambridge, Massachusetts 02142, USA
    Plant Cell 17:1658-73. 2005
    ..Therefore, several individual miRNA regulatory circuits have ancient origins and have remained intact throughout the evolution and diversification of plants...
  49. pmc Most mammalian mRNAs are conserved targets of microRNAs
    Robin C Friedman
    Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
    Genome Res 19:92-105. 2009
    ..Our expanded set of target predictions (including conserved 3'-compensatory sites), are available at the TargetScan website, which displays the P(CT) for each site and each predicted target...
  50. ncbi request reprint Crystal structure of the catalytic core of an RNA-polymerase ribozyme
    David M Shechner
    Whitehead Institute for Biomedical Research and Howard Hughes Medical Institute, 9 Cambridge Center, Cambridge, MA 02142, USA
    Science 326:1271-5. 2009
    ..A cytosine nucleobase and two backbone phosphates abut the ligation junction; their location suggests a model for catalysis resembling that of proteinaceous polymerases...
  51. pmc A class I ligase ribozyme with reduced Mg2+ dependence: Selection, sequence analysis, and identification of functional tertiary interactions
    Sarah C Bagby
    Whitehead Institute for Biomedical Research, Cambridge, Massachusetts 02142, USA
    RNA 15:2129-46. 2009
    ....
  52. pmc MicroRNA-directed regulation of Arabidopsis AUXIN RESPONSE FACTOR17 is essential for proper development and modulates expression of early auxin response genes
    Allison C Mallory
    Whitehead Institute for Biomedical Research, Cambridge, Massachusetts 02142, USA
    Plant Cell 17:1360-75. 2005
    ....
  53. ncbi request reprint Processivity of ribozyme-catalyzed RNA polymerization
    Michael S Lawrence
    Whitehead Institute for Biomedical Research and Department of Biology, Massachusetts Institute of Technology, 9 Cambridge Center, Cambridge, Massachusetts 02142, USA
    Biochemistry 42:8748-55. 2003
    ..This finding contributes to the understanding of one of the more sophisticated activities yet to be generated de novo in the laboratory and sheds light on the parameters to be targeted for further optimization...
  54. ncbi request reprint Metal ion requirements for structure and catalysis of an RNA ligase ribozyme
    Margaret E Glasner
    Whitehead Institute for Biomedical Research and Department of Biology, Massachusetts Institute of Technology, 9 Cambridge Center, Cambridge, MA 02142, USA
    Biochemistry 41:8103-12. 2002
    ..Ligation rates of the prefolded ribozyme were directly measured and proceed at 800 min(-1) at pH 9.0...
  55. pmc The three-dimensional architecture of the class I ligase ribozyme
    Nicholas H Bergman
    Whitehead Institute for Biomedical Research and Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts 02142, USA
    RNA 10:176-84. 2004
    ..The predictive value of the model was tested and supported by a photo-cross-linking experiment...
  56. pmc New ligase-derived RNA polymerase ribozymes
    Michael S Lawrence
    Whitehead Institute for Biomedical Research Biology Department, Massachusetts Institute of Technology, Cambridge, MA 02142, USA
    RNA 11:1173-80. 2005
    ..Because each of them is a new potential starting point for further in vitro evolution and engineering, together they substantially enrich the set of candidates from which an RNA replicase ribozyme might eventually emerge...
  57. pmc Microarray profiling of microRNAs reveals frequent coexpression with neighboring miRNAs and host genes
    Scott Baskerville
    Whitehead Institute for Biomedical Research, Massachusetts Institute of Technology, 9 Cambridge Center, Cambridge, MA 02142, USA
    RNA 11:241-7. 2005
    ....
  58. ncbi request reprint Compact and ordered collapse of randomly generated RNA sequences
    Erik A Schultes
    Whitehead Institute for Biomedical Research, 9 Cambridge Center, Cambridge, Massachusetts 02142, USA
    Nat Struct Mol Biol 12:1130-6. 2005
    ..Thus, for RNAs the size of small ribozymes, natural selection seems necessary to achieve uniquely folding sequences, but not to account for the well-ordered secondary structures and overall compactness observed in nature...
  59. ncbi request reprint MicroRNAS and their regulatory roles in plants
    Matthew W Jones-Rhoades
    Whitehead Institute for Biomedical Research, Department of Biology, Massachusetts Institute of Technology, and Howard Hughes Medical Institute, Cambridge, Massachusetts 02142, USA
    Annu Rev Plant Biol 57:19-53. 2006
    ....
  60. pmc A biochemical framework for RNA silencing in plants
    Guiliang Tang
    Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, Massachusetts 01605, USA
    Genes Dev 17:49-63. 2003
    ..Thus, endonuclease complexes guided by small RNAs are a common feature of RNA silencing in both animals and plants...
  61. ncbi request reprint MicroRNAs regulate brain morphogenesis in zebrafish
    Antonio J Giraldez
    Developmental Genetics Program, Skirball Institute of Biomolecular Medicine and Department of Cell Biology, New York University School of Medicine, New York, NY 10016, USA
    Science 308:833-8. 2005
    ..Injection of miR-430 miRNAs rescues the brain defects in MZdicer mutants, revealing essential roles for miRNAs during morphogenesis...
  62. ncbi request reprint Partially redundant functions of Arabidopsis DICER-like enzymes and a role for DCL4 in producing trans-acting siRNAs
    Virginie Gasciolli
    Laboratoire de Biologie Cellulaire, Institut Jean Pierre Bourgin, Institut National de la Recherche Agronomique, 78026 Versailles Cedex, France
    Curr Biol 15:1494-500. 2005
    ....
  63. ncbi request reprint The let-7 MicroRNA family members mir-48, mir-84, and mir-241 function together to regulate developmental timing in Caenorhabditis elegans
    Allison L Abbott
    Department of Genetics, Dartmouth Medical School, Hanover, New Hampshire 03755, USA
    Dev Cell 9:403-14. 2005
    ..These results indicate that let-7 family microRNAs function in combination to affect both early and late developmental timing decisions...
  64. ncbi request reprint Regulatory mutations of mir-48, a C. elegans let-7 family MicroRNA, cause developmental timing defects
    Ming Li
    Department of Genetics, Cell Biology and Development, University of Minnesota, Minneapolis, 55455, USA
    Dev Cell 9:415-22. 2005
    ..These results suggest that lin-58 alleles disrupt a repressor binding site that restricts the time of miR-48 action in wild-type animals...
  65. ncbi request reprint Passenger-strand cleavage facilitates assembly of siRNA into Ago2-containing RNAi enzyme complexes
    Christian Matranga
    Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, Massachusetts 01605, USA
    Cell 123:607-20. 2005
    ..For siRNAs, virtually all RISC is assembled through this cleavage-assisted mechanism. In contrast, passenger-strand cleavage is not important for the incorporation of miRNAs that derive from mismatched duplexes...
  66. pmc MicroRNAs: at the root of plant development?
    Bonnie Bartel
    Department Biochemistry, Rice University, Houston, Texas 77005, USA
    Plant Physiol 132:709-17. 2003
  67. ncbi request reprint Characterization of the piRNA complex from rat testes
    Nelson C Lau
    Department of Molecular Biology, Massachusetts General Hospital, 185 Cambridge Street, Boston, MA 02114, USA
    Science 313:363-7. 2006
    ..Piwi has been genetically linked to TGS in flies, and slicer activity cofractionates with the purified complex. These results are consistent with a gene-silencing role for piRC in mammals...
  68. pmc PRG-1 and 21U-RNAs interact to form the piRNA complex required for fertility in C. elegans
    Pedro J Batista
    Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA 01605, USA
    Mol Cell 31:67-78. 2008
    ..Our findings demonstrate that 21U-RNAs are the piRNAs of C. elegans and link this class of small RNAs and their associated Piwi Argonaute to the maintenance of temperature-dependent fertility...
  69. ncbi request reprint The microRNA miR-196 acts upstream of Hoxb8 and Shh in limb development
    Eran Hornstein
    Department of Genetics, Harvard Medical School, 77 Avenue Louis Pasteur, Boston, Massachusetts 02115, USA
    Nature 438:671-4. 2005
    ....
  70. pmc Common functions for diverse small RNAs of land plants
    Michael J Axtell
    Department of Biology and Huck Institutes of the Life Sciences, Pensylvania State University, University Park, PA 16802, USA
    Plant Cell 19:1750-69. 2007
    ..Diverse, lineage-specific, small RNAs can therefore perform common biological functions in plants...
  71. ncbi request reprint Conserved seed pairing, often flanked by adenosines, indicates that thousands of human genes are microRNA targets
    Benjamin P Lewis
    Cell 120:15-20. 2005
    ..Targeting was also detected in open reading frames. In sum, well over one third of human genes appear to be conserved miRNA targets...
  72. ncbi request reprint Microarray analysis shows that some microRNAs downregulate large numbers of target mRNAs
    Lee P Lim
    Rosetta Inpharmatics, Merck and Co, 401 Terry Avenue N, Seattle, Washington 98109, USA
    Nature 433:769-73. 2005
    ..Moreover, miR-1 and miR-124, and presumably other tissue-specific miRNAs, seem to downregulate a far greater number of targets than previously appreciated, thereby helping to define tissue-specific gene expression in humans...
  73. pmc Combinatorial minimization and secondary structure determination of a nucleotide synthase ribozyme
    Kelly E Chapple
    Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, British Columbia V5A 1S6, Canada
    RNA 9:1208-20. 2003
    ....
  74. pmc Endogenous siRNA and miRNA targets identified by sequencing of the Arabidopsis degradome
    Charles Addo-Quaye
    Department of Computer Science and Engineering, Pennsylvania State University, University Park, PA 16802, USA
    Curr Biol 18:758-62. 2008
    ..This empirical method is broadly applicable to the discovery and quantification of cleaved targets of small RNAs without a priori predictions...
  75. pmc The action of ARGONAUTE1 in the miRNA pathway and its regulation by the miRNA pathway are crucial for plant development
    Herve Vaucheret
    Laboratoire de Biologie Cellulaire, Institut Jean Pierre Bourgin, INRA, 78026 Versailles Cedex, France
    Genes Dev 18:1187-97. 2004
    ....
  76. 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...
  77. pmc TRAMP-mediated RNA surveillance prevents spurious entry of RNAs into the Schizosaccharomyces pombe siRNA pathway
    Marc Buhler
    Department of Cell Biology, 240 Longwood Avenue, Harvard Medical School, Boston, Massachusetts 02115 USA
    Nat Struct Mol Biol 15:1015-23. 2008
    ..Thus, Cid14 prevents certain abundant RNAs from becoming substrates for the RNAi machinery, thereby freeing the RNAi machinery to act on its proper targets...
  78. ncbi request reprint Endogenous trans-acting siRNAs regulate the accumulation of Arabidopsis mRNAs
    Franck Vazquez
    Laboratoire de physiologie de la différenciation végétale, UPRES EA3569, IFR118, EPT1016, Universite des Sciences et Technologies de Lille, Bat SN2, Cite Scientifique, 59650 Villeneuve d Ascq Cedex, France
    Mol Cell 16:69-79. 2004
    ..The identification of this silencing pathway provides yet another dimension to posttranscriptional mRNA regulation in plants...
  79. pmc AGO1 homeostasis entails coexpression of MIR168 and AGO1 and preferential stabilization of miR168 by AGO1
    Herve Vaucheret
    Laboratoire de Biologie Cellulaire, Institut Jean Pierre Bourgin, INRA, 78026 Versailles Cedex, France
    Mol Cell 22:129-36. 2006
    ..We suggest that miR168 stabilization occurs at the level of silencing-complex assembly and that modulating the efficiency of assembling miRNA-programmed silencing complexes will also be important in other contexts...

Research Grants16

  1. RNA CONFORMATION AND CATALYSIS
    David Bartel; Fiscal Year: 2001
    ..abstract_text> ..
  2. The Roles of MicroRNAs in Plant Development
    David Bartel; Fiscal Year: 2007
    ....
  3. RNA CONFORMATION AND CATALYSIS
    David Bartel; Fiscal Year: 2006
    ....
  4. MicroRNA genes and their functions
    David P Bartel; Fiscal Year: 2010
    ..Achieving these goals will shed light on why microRNAs are needed for normal growth and development, and how their dysfunction can contribute to human diseases. ..
  5. MicroRNA genes and their functions
    David Bartel; Fiscal Year: 2005
    ..abstract_text> ..
  6. MicroRNA genes and their functions
    David Bartel; Fiscal Year: 2004
    ..abstract_text> ..
  7. RNA CONFORMATION AND CATALYSIS
    David Bartel; Fiscal Year: 2003
    ..abstract_text> ..
  8. MicroRNA genes and their functions
    David Bartel; Fiscal Year: 2002
    ..abstract_text> ..
  9. RNA CONFORMATION AND CATALYSIS
    David Bartel; Fiscal Year: 2002
    ..abstract_text> ..
  10. MicroRNA genes and their functions
    David Bartel; Fiscal Year: 2003
    ..abstract_text> ..
  11. MicroRNA genes and their functions
    David Bartel; Fiscal Year: 2009
    ..Achieving these goals will shed light on why microRNAs are needed for normal growth and development, and how their dysfunction can contribute to human diseases. ..
  12. RNA CONFORMATION AND CATALYSIS
    David Bartel; Fiscal Year: 2007
    ....
  13. MicroRNA genes and their functions
    David Bartel; Fiscal Year: 2004
    ..abstract_text> ..
  14. RNA CONFORMATION AND CATALYSIS
    David Bartel; Fiscal Year: 2005
    ....