JEF BOEKE

Summary

Affiliation: Johns Hopkins University
Country: USA

Publications

  1. pmc TE-array--a high throughput tool to study transposon transcription
    Veena P Gnanakkan
    The Institute of Genetic Medicine, The Johns Hopkins University School of Medicine, 733 North Broadway, Miller Research Building MRB Room 469, Baltimore, MD 21205, USA
    BMC Genomics 14:869. 2013
  2. pmc Conserved structure and inferred evolutionary history of long terminal repeats (LTRs)
    Farid Benachenhou
    Section of Virology, Department of Medical Sciences, Uppsala University, Uppsala, Sweden
    Mob DNA 4:5. 2013
  3. pmc Identifying related L1 retrotransposons by analyzing 3' transduced sequences
    Suzanne T Szak
    National Center for Biotechnology Information NCBI, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
    Genome Biol 4:R30. 2003
  4. pmc Transposon technology and vertebrate functional genomics
    Wenfeng An
    Department of Molecular Biology and Genetics and High Throughput Biology Center, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
    Genome Biol 6:361. 2005
  5. pmc Molecular archeology of L1 insertions in the human genome
    Suzanne T Szak
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
    Genome Biol 3:research0052. 2002
  6. pmc Effect of reverse transcriptase inhibitors on LINE-1 and Ty1 reverse transcriptase activities and on LINE-1 retrotransposition
    Lixin Dai
    Department of Molecular Biology and Genetics, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
    BMC Biochem 12:18. 2011
  7. ncbi request reprint The unusual phylogenetic distribution of retrotransposons: a hypothesis
    Jef D Boeke
    Department of Molecular Biology and Genetics, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, USA
    Genome Res 13:1975-83. 2003
  8. pmc Characterization of a synthetic human LINE-1 retrotransposon ORFeus-Hs
    Wenfeng An
    Department of Molecular Biology and Genetics, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
    Mob DNA 2:2. 2011
  9. pmc Domesticated DNA transposon proteins mediate retrotransposon control
    Kathryn A O'Donnell
    Department of Molecular Biology and Genetics, The Johns Hopkins University School of Medicine, 733 N Broadway, Baltimore, MD 21205, USA
    Cell Res 18:331-3. 2008
  10. pmc Great exaptations
    Kathleen H Burns
    Department of Pathology, The Johns Hopkins Hospital, 600 North Wolfe Street, Baltimore, MD 21287, USA
    J Biol 7:5. 2008

Research Grants

  1. TRANSPOSITION MECHANISMS
    JEF BOEKE; Fiscal Year: 2006
  2. TRANSCRIPTIONAL SILENCING MECHANISMS
    JEF BOEKE; Fiscal Year: 2005
  3. YEAST GENETIC INTERACTION MAP
    JEF BOEKE; Fiscal Year: 2006
  4. YEAST GENETIC INTERACTION MAP
    JEF BOEKE; Fiscal Year: 2007
  5. TRANSPOSITION MECHANISMS
    JEF BOEKE; Fiscal Year: 2007
  6. TRANSPOSITION MECHANISMS
    JEF BOEKE; Fiscal Year: 2002
  7. TRANSPOSITION MECHANISMS
    JEF BOEKE; Fiscal Year: 1990
  8. TRANSPOSITION MECHANISMS
    JEF BOEKE; Fiscal Year: 1993
  9. TRANSPOSITION MECHANISMS
    Jef D Boeke; Fiscal Year: 2010

Collaborators

Detail Information

Publications72

  1. pmc TE-array--a high throughput tool to study transposon transcription
    Veena P Gnanakkan
    The Institute of Genetic Medicine, The Johns Hopkins University School of Medicine, 733 North Broadway, Miller Research Building MRB Room 469, Baltimore, MD 21205, USA
    BMC Genomics 14:869. 2013
    ....
  2. pmc Conserved structure and inferred evolutionary history of long terminal repeats (LTRs)
    Farid Benachenhou
    Section of Virology, Department of Medical Sciences, Uppsala University, Uppsala, Sweden
    Mob DNA 4:5. 2013
    ..They are difficult to analyse due to their variability.The aim was to obtain a more comprehensive view of structure, diversity and phylogeny of LTRs than hitherto possible...
  3. pmc Identifying related L1 retrotransposons by analyzing 3' transduced sequences
    Suzanne T Szak
    National Center for Biotechnology Information NCBI, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
    Genome Biol 4:R30. 2003
    ..Using computational methods, we collected DNA sequences from the human genome for which we have high confidence of their mobilization through L1-mediated 3' transduction...
  4. pmc Transposon technology and vertebrate functional genomics
    Wenfeng An
    Department of Molecular Biology and Genetics and High Throughput Biology Center, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
    Genome Biol 6:361. 2005
    ..A report on the Third Annual International Conference on Transposition and Animal Biotechnology, Minneapolis, USA, 23-24 June 2005, and the FASEB Summer Research Conference 'Mammalian Mobile Elements', Tuscon, USA, 4-9 June, 2005...
  5. pmc Molecular archeology of L1 insertions in the human genome
    Suzanne T Szak
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
    Genome Biol 3:research0052. 2002
    ..We carried out a detailed analysis of the anatomy and distribution of L1 elements in the human genome using a new computer program, TSDfinder, designed to identify transposon boundaries precisely...
  6. pmc Effect of reverse transcriptase inhibitors on LINE-1 and Ty1 reverse transcriptase activities and on LINE-1 retrotransposition
    Lixin Dai
    Department of Molecular Biology and Genetics, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
    BMC Biochem 12:18. 2011
    ..Full-length L1 encodes two open reading frames (ORF1, ORF2) and ORF2 has reverse transcriptase activity...
  7. ncbi request reprint The unusual phylogenetic distribution of retrotransposons: a hypothesis
    Jef D Boeke
    Department of Molecular Biology and Genetics, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, USA
    Genome Res 13:1975-83. 2003
    ....
  8. pmc Characterization of a synthetic human LINE-1 retrotransposon ORFeus-Hs
    Wenfeng An
    Department of Molecular Biology and Genetics, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
    Mob DNA 2:2. 2011
    ..Owing to the elevated expression of the L1 RNA/protein and its high retrotransposition ability, ORFeus-Hs and its chimeric derivatives will be useful tools for mechanistic L1 studies and mammalian genome manipulation...
  9. pmc Domesticated DNA transposon proteins mediate retrotransposon control
    Kathryn A O'Donnell
    Department of Molecular Biology and Genetics, The Johns Hopkins University School of Medicine, 733 N Broadway, Baltimore, MD 21205, USA
    Cell Res 18:331-3. 2008
  10. pmc Great exaptations
    Kathleen H Burns
    Department of Pathology, The Johns Hopkins Hospital, 600 North Wolfe Street, Baltimore, MD 21287, USA
    J Biol 7:5. 2008
    ..Recent work has discovered many instances of LINE incorporation into exons, reminding us of the hazards they pose to genes in their vicinity as well as their potential to be co-opted for the host's purposes...
  11. pmc Local definition of Ty1 target preference by long terminal repeats and clustered tRNA genes
    Nurjana Bachman
    The Johns Hopkins University School of Medicine, Department of Molecular Biology and Genetics, Baltimore, Maryland 21205, USA
    Genome Res 14:1232-47. 2004
    ..We showed that the presence and relative position of additional tDNAs and LTRs surrounding the target tDNA dramatically influenced the frequency of insertion events upstream of that target...
  12. pmc GeneDesign 3.0 is an updated synthetic biology toolkit
    Sarah M Richardson
    McKusick Nathans Institute of Genetic Medicine, High Throughput Biology Center, Johns Hopkins University School of Medicine, 733 North Broadway, Baltimore, MD 21205, USA
    Nucleic Acids Res 38:2603-6. 2010
    ....
  13. pmc Improved microarray methods for profiling the Yeast Knockout strain collection
    Daniel S Yuan
    Department of Molecular Biology and Genetics, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
    Nucleic Acids Res 33:e103. 2005
    ..The materials, protocols, data and associated software described here comprise a suite of experimental resources that should facilitate the use of TAG microarrays for a wide variety of genetic screens...
  14. pmc Retrotransposon overdose and genome integrity
    Lisa Z Scheifele
    Department of Molecular Biology and Genetics and High Throughput Biology Center, The Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
    Proc Natl Acad Sci U S A 106:13927-32. 2009
    ..Abrogation of normal DNA replication leads to rampant genome instability primarily in the form of chromosomal aberrations and confirms the central role of DNA replication accuracy in the stabilization of repetitive DNA...
  15. pmc Transposon insertion site profiling chip (TIP-chip)
    Sarah J Wheelan
    High Throughput Biology Center and Department of Molecular Biology and Genetics, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
    Proc Natl Acad Sci U S A 103:17632-7. 2006
    ..In addition, we mapped many new transposon copies in the high-copy Ty1 strain and determined its Ty1 insertion pattern...
  16. ncbi request reprint A robust toolkit for functional profiling of the yeast genome
    Xuewen Pan
    Department of Molecular Biology and Genetics, The Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
    Mol Cell 16:487-96. 2004
    ..Direct comparison revealed that these techniques are more robust than existing methods in functional profiling of the yeast genome. Widespread application of these tools will elucidate a comprehensive yeast genetic network...
  17. ncbi request reprint LINE-1 retrotransposons: modulators of quantity and quality of mammalian gene expression?
    Jeffrey S Han
    Department of Molecular Biology and Genetics and High Throughput Biology Center, The Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
    Bioessays 27:775-84. 2005
    ..Here we provide a review of L1 replication and its potential functional consequences...
  18. pmc Improved statistical analysis of budding yeast TAG microarrays revealed by defined spike-in pools
    Brian D Peyser
    McKusick Nathans Institute of Genetic Medicine, School of Medicine, Johns Hopkins University, Baltimore, MD, USA
    Nucleic Acids Res 33:e140. 2005
    ....
  19. ncbi request reprint A DNA integrity network in the yeast Saccharomyces cerevisiae
    Xuewen Pan
    Department of Molecular Biology and Genetics, The Johns Hopkins University School of Medicine, 733 North Broadway, Baltimore, MD 21205, USA
    Cell 124:1069-81. 2006
    ..This network will guide more detailed characterization of mechanisms governing DNA integrity in yeast and other organisms...
  20. doi request reprint Analysis of genetic interactions on a genome-wide scale in budding yeast: diploid-based synthetic lethality analysis by microarray
    Pamela B Meluh
    Department of Molecular Biology and Genetics, The High Throughput Biology Center, The Johns Hopkins University School of Medicine, Baltimore, MD, USA
    Methods Mol Biol 416:221-47. 2008
    ..Analysis of double-mutant strains is of growing importance in defining the spectrum of essential cellular functionalities and in understanding how these functionalities interrelate...
  21. pmc Teaching synthetic biology, bioinformatics and engineering to undergraduates: the interdisciplinary Build-a-Genome course
    Jessica S Dymond
    Department of Biomedical Engineering, Johns Hopkins University, Baltimore, Maryland 21205, USA
    Genetics 181:13-21. 2009
    ..Regular "lab meeting" sessions help prepare them for future roles in laboratory science...
  22. pmc TFIIIB subunit Bdp1p is required for periodic integration of the Ty1 retrotransposon and targeting of Isw2p to S. cerevisiae tDNAs
    Nurjana Bachman
    The Johns Hopkins University School of Medicine, Department of Molecular Biology and Genetics, Baltimore, Maryland 21205, USA
    Genes Dev 19:955-64. 2005
    ..This study provides the first example for recruitment of an ATP-dependent chromatin-remodeling factor by a general transcription factor in vivo...
  23. ncbi request reprint Human l1 retrotransposition is associated with genetic instability in vivo
    David E Symer
    Department of Molecular Biology and Genetics, John Hopkins University School of Medicine, Baltimore, Maryland 21205, USA
    Cell 110:327-38. 2002
    ..In a striking number of integrants, short identical sequences were shared between the donor and the target site's 3' end, suggesting a mechanistic model that helps explain the structure of L1 insertions...
  24. ncbi request reprint Global synthetic-lethality analysis and yeast functional profiling
    Siew Loon Ooi
    High Throughput Biology Center, Institute of Genetic Medicine, Department of Biostatistics, Johns Hopkins University School of Medicine, 339 Broadway Research Building, 733 North Broadway, Baltimore, MD 21205, USA
    Trends Genet 22:56-63. 2006
    ....
  25. pmc Identification and characterization of critical cis-acting sequences within the yeast Ty1 retrotransposon
    Eric C Bolton
    Department of Molecular Biology and Genetics, Johns Hopkins University School of Medicine, 339 Broadway Research Building, 733 North Broadway, Baltimore, MD 21205, USA
    RNA 11:308-22. 2005
    ..Our results suggest that the intramolecular interaction between the 5'-GAGGAGA and UCUCCUC sequences stabilizes an RNA structure required for efficient initiation of reverse transcription...
  26. pmc Mn2+ suppressor mutations and biochemical communication between Ty1 reverse transcriptase and RNase H domains
    Robert M Yarrington
    Department of Molecular Biology and Genetics, The Johns Hopkins University School of Medicine, 733 N Broadway, Baltimore MD 21205, USA
    J Virol 81:9004-12. 2007
    ..These intriguing results reveal that the effect of these suppressor mutations is transmitted to the polymerase domain and suggest biochemical communication between these two domains during reverse transcription...
  27. ncbi request reprint The sirtuins hst3 and Hst4p preserve genome integrity by controlling histone h3 lysine 56 deacetylation
    Ivana Celic
    High Throughput Biology Center, Department of Pharmacology and Molecular Sciences, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, USA
    Curr Biol 16:1280-9. 2006
    ..Acetylation of histone H3 lysine 56 (K56Ac) occurs transiently in newly synthesized H3 during passage through S phase and is removed in G2. However, the physiologic roles and effectors of K56Ac turnover are unknown...
  28. ncbi request reprint Stacking the deck: double-tiled DNA microarrays
    Sarah J Wheelan
    The High Throughput Biology Center and Department of Molecular Biology and Genetics, The Johns Hopkins University School of Medicine, 733 North Broadway, BRB Suite 331 Baltimore, Maryland 21205, USA
    Nat Methods 3:903-7. 2006
    ....
  29. ncbi request reprint Tn7-mediated mutagenesis of Saccharomyces cerevisiae genomic DNA in vitro
    Nurjana Bachman
    Department of Molecular Biology and Genetics, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, USA
    Methods Enzymol 350:230-47. 2002
  30. pmc dSLAM analysis of genome-wide genetic interactions in Saccharomyces cerevisiae
    Xuewen Pan
    Department of Molecular Biology and Genetics, The Johns Hopkins University School of Medicine, 733 North Broadway, Baltimore, MD 21205, USA
    Methods 41:206-21. 2007
    ..This technology has been effectively adapted to study other types of genome-wide genetic interactions including gene-compound synthetic lethality, secondary mutation suppression, dosage-dependent synthetic lethality and suppression...
  31. ncbi request reprint Inhibition of reverse transcription in vivo by elevated manganese ion concentration
    Eric C Bolton
    Department of Molecular Biology and Genetics, The Johns Hopkins University School of Medicine, 725 North Wolfe Street, Baltimore, MD 21205, USA
    Mol Cell 9:879-89. 2002
    ..We propose that occupancy of the B site is the major determinant of catalytic activity and that Mn(2+) at this site greatly reduces catalytic activity...
  32. pmc Ty1 defect in proteolysis at high temperature
    Joseph F Lawler
    Department of Molecular Biology and Genetics, The Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, USA
    J Virol 76:4233-40. 2002
    ..Taken together, these results suggest that alterations in Ty1 proteins that occur at high temperature affect both protease activity and RT activity, such that Ty1 transposition is abolished...
  33. pmc Transcriptional interactions between yeast tRNA genes, flanking genes and Ty elements: a genomic point of view
    Eric C Bolton
    Department of Molecular Biology and Genetics, The Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, USA
    Genome Res 13:254-63. 2003
    ..Direct analysis of PTR3 transcription, promoted by sequences very close to a tRNA gene, shows that this tRNA position effect can operate on a native chromosomal gene...
  34. pmc GeneDesign: rapid, automated design of multikilobase synthetic genes
    Sarah M Richardson
    High Throughput Biology Center, The Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, USA
    Genome Res 16:550-6. 2006
    ..GeneDesign has been implemented as a publicly accessible Web-based resource and can be found at http://slam.bs.jhmi.edu/gd...
  35. ncbi request reprint DNA helicase gene interaction network defined using synthetic lethality analyzed by microarray
    Siew Loon Ooi
    Department of Molecular Biology and Genetics, The Johns Hopkins University School of Medicine, 617 Hunterian Building, 725 North Wolfe Street, Baltimore, Maryland 21205, USA
    Nat Genet 35:277-86. 2003
    ..SLAM detects synthetic lethality efficiently and ranks candidate genetic interactions, making it an especially useful method...
  36. ncbi request reprint Transcriptional disruption by the L1 retrotransposon and implications for mammalian transcriptomes
    Jeffrey S Han
    Department of Molecular Biology and Genetics and High Throughput Biology Center, The Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, USA
    Nature 429:268-74. 2004
    ..Bioinformatic data are consistent with the hypothesis that L1 can serve as an evolutionary fine-tuner of the human transcriptome...
  37. pmc Insights into the role of histone H3 and histone H4 core modifiable residues in Saccharomyces cerevisiae
    Edel M Hyland
    High Throughput Biology Center, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
    Mol Cell Biol 25:10060-70. 2005
    ..Finally, we allude to the possible molecular mechanisms underlying the effects of these modifications...
  38. pmc Mobile interspersed repeats are major structural variants in the human genome
    Cheng Ran Lisa Huang
    Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
    Cell 141:1171-82. 2010
    ..We have just begun to probe the universe of human L1(Ta) polymorphisms, and as TIP-chip is applied to other insertions such as Alu SINEs, it will expand the catalog of genomic variants even further...
  39. pmc Gene-breaking: a new paradigm for human retrotransposon-mediated gene evolution
    Sarah J Wheelan
    Department of Molecular Biology and Genetics, The Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, USA
    Genome Res 15:1073-8. 2005
    ..Gene-breaking represents a new mechanism through which L1 elements remodel mammalian genomes...
  40. pmc Conditional activation of a single-copy L1 transgene in mice by Cre
    Wenfeng An
    The High Throughput Biology Center, The Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, USA
    Genesis 46:373-83. 2008
    ..This conditional transgenic ORFeus mouse model should allow further exploration of posttranscriptional cellular requirements for L1 retrotransposition and facilitate the development of ORFeus mouse lines suitable for in vivo mutagenesis...
  41. pmc HistoneHits: a database for histone mutations and their phenotypes
    Hailiang Huang
    Department of Biomedical Engineering, Johns Hopkins University and School of Medicine, Baltimore, Maryland 21218, USA
    Genome Res 19:674-81. 2009
    ..All data sets are freely available for download...
  42. pmc Protein acetylation microarray reveals that NuA4 controls key metabolic target regulating gluconeogenesis
    Yu yi Lin
    High Throughput Biology Center, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
    Cell 136:1073-84. 2009
    ..Our findings demonstrate a regulatory function for the NuA4 complex in glucose metabolism and life span by acetylating a critical metabolic enzyme...
  43. pmc The incredible shrinking world of DNA microarrays
    Sarah J Wheelan
    Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
    Mol Biosyst 4:726-32. 2008
    ....
  44. pmc A comprehensive synthetic genetic interaction network governing yeast histone acetylation and deacetylation
    Yu yi Lin
    High Throughput Biology Center, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, USA
    Genes Dev 22:2062-74. 2008
    ..These new characterizations of the HDA and NuA4 complexes demonstrate how systematic analyses of genetic interactions may help illuminate the mechanisms of intricate cellular processes...
  45. pmc CLONEQC: lightweight sequence verification for synthetic biology
    Pablo A Lee
    Department of Computer Science, Johns Hopkins University, 3400 N Charles St, Baltimore, MD 21215, USA
    Nucleic Acids Res 38:2617-23. 2010
    ..This software will be useful to laboratories conducting in-house DNA synthesis and is available at http://cloneqc.thruhere.net/ and as Berkeley Software Distribution (BSD) licensed source...
  46. pmc From the shards of a shattered genome, diversity
    Lisa Z Scheifele
    Department of Molecular Biology and Genetics, High Throughput Biology Center, Johns Hopkins University School of Medicine, 733 North Broadway, Baltimore, MD 21205, USA
    Proc Natl Acad Sci U S A 105:11593-4. 2008
  47. pmc Probing nucleosome function: a highly versatile library of synthetic histone H3 and H4 mutants
    Junbiao Dai
    High Throughput Biology Center, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
    Cell 134:1066-78. 2008
    ....
  48. pmc Silent information regulator 3: the Goldilocks of the silencing complex
    Anne Norris
    Department of Molecular Biology and Genetics, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, USA
    Genes Dev 24:115-22. 2010
    ..Finally, we synthesize these ideas to revise the model for how Sir3p mediates silent chromatin formation in yeast, in part through its affinity for the LRS region of the nucleosome, which must be "just right."..
  49. pmc Compensatory interactions between Sir3p and the nucleosomal LRS surface imply their direct interaction
    Anne Norris
    Department of Molecular Biology and Genetics, Johns Hopkins University School of Medicine, Baltimore, MD, USA
    PLoS Genet 4:e1000301. 2008
    ..Based on these findings, we propose an electrostatic model for how an extensive surface on the Sir3p BAH domain may regulate docking onto the LRS surface...
  50. pmc Finding friends and enemies in an enemies-only network: a graph diffusion kernel for predicting novel genetic interactions and co-complex membership from yeast genetic interactions
    Yan Qi
    Department of Biomedical Engineering, Johns Hopkins University, Baltimore, Maryland 21218, USA
    Genome Res 18:1991-2004. 2008
    ..The kernels show significant improvement over previous best methods for predicting genetic interactions and protein co-complex membership from genetic interaction data...
  51. pmc An evaluation of detection methods for large lariat RNAs
    Candice E Coombes
    Department of Oncology, Johns Hopkins University School of Medicine, 339 Broadway Research Building, 733 North Broadway, Baltimore, MD 21205, USA
    RNA 11:323-31. 2005
    ..Thus, the role of the Dbr1 protein in Ty1 retrotransposition remains elusive...
  52. ncbi request reprint A core nucleosome surface crucial for transcriptional silencing
    Jeong Hyun Park
    Department of Molecular Biology and Genetics, Johns Hopkins University School of Medicine, 725 N Wolfe Street, Baltimore, Maryland 21205, USA
    Nat Genet 32:273-9. 2002
    ..These two clusters relieve distinct forms of transcriptional repression (silencing versus repression resulting from lack of Swi/Snf chromatin remodeling activity)...
  53. ncbi request reprint A highly active synthetic mammalian retrotransposon
    Jeffrey S Han
    Department of Molecular Biology and Genetics and High Throughput Biology Center, The Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, USA
    Nature 429:314-8. 2004
    ..These synthetic retrotransposons are also the most highly active L1 elements known so far and have potential as practical tools for manipulating mammalian genomes...
  54. pmc A nucleocapsid functionality contained within the amino terminus of the Ty1 protease that is distinct and separable from proteolytic activity
    Joseph F Lawler
    Department of Molecular Biology and Genetics, The Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, USA
    J Virol 76:346-54. 2002
    ..Remarkably, these mutants have distinct defects in reverse transcription...
  55. ncbi request reprint Mighty Piwis defend the germline against genome intruders
    Kathryn A O'Donnell
    Department of Molecular Biology and Genetics, The Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
    Cell 129:37-44. 2007
    ..2007; Houwing et al., 2007). This function may be conserved in mice as loss of Miwi2, a mouse Piwi homolog, leads to germline stem cell and meiotic defects correlated with increased transposon activity (Carmell et al., 2007)...
  56. pmc Active retrotransposition by a synthetic L1 element in mice
    Wenfeng An
    High Throughput Biology Center and Department of Molecular Biology and Genetics, Johns Hopkins University School of Medicine, 733 North Broadway, Baltimore, MD 21205, USA
    Proc Natl Acad Sci U S A 103:18662-7. 2006
    ..The results suggest that ORFeus may be developed into useful tools for in vivo mutagenesis...
  57. pmc Gene function prediction from congruent synthetic lethal interactions in yeast
    Ping Ye
    Department of Biomedical Engineering, The Johns Hopkins University, Baltimore, MD, USA
    Mol Syst Biol 1:2005.0026. 2005
    ..These in silico methods can predict phenotypes and gene functions and are applicable to genomic synthetic lethality screens in yeast and analogous RNA interference screens in metazoans...
  58. pmc Ty1 mobilizes subtelomeric Y' elements in telomerase-negative Saccharomyces cerevisiae survivors
    Patrick H Maxwell
    Laboratory of Developmental Genetics, Wadsworth Center, and Department of Biomedical Sciences, University at Albany School of Public Health, Albany, New York 12201 2002, USA
    Mol Cell Biol 24:9887-98. 2004
    ..We propose that Y'-oligo(A)-Ty1 cDNA recombines with Y' elements at eroding telomeres in survivors and may play a role in telomere maintenance in the absence of telomerase...
  59. pmc Genome-wide identification of Isw2 chromatin-remodeling targets by localization of a catalytically inactive mutant
    Marnie E Gelbart
    Division of Basic Sciences, Fred Hutchinson Cancer Research Center, Seattle, Washington 98109, USA
    Genes Dev 19:942-54. 2005
    ....
  60. pmc Functional genomics of genes with small open reading frames (sORFs) in S. cerevisiae
    James P Kastenmayer
    Genetics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland 20889, USA
    Genome Res 16:365-73. 2006
    ..Moreover, our analyses of the S. cerevisiae sORFs establish that sORFs are conserved across eukaryotes and have important biological functions...
  61. pmc Short-chain fatty acid activation by acyl-coenzyme A synthetases requires SIR2 protein function in Salmonella enterica and Saccharomyces cerevisiae
    Vincent J Starai
    Department of Bacteriology, University of Wisconsin, Madison, Wisconsin 53726 4087, USA
    Genetics 163:545-55. 2003
    ..The data suggest that the Hst3 and Hst4 proteins are the most important for allowing growth on these short-chain fatty acids...
  62. pmc FKBP12 controls aspartate pathway flux in Saccharomyces cerevisiae to prevent toxic intermediate accumulation
    Miguel Arevalo-Rodriguez
    Department of Molecular Genetics and Microbiology, Box 3546, 322 CARL Building, Research Dr, Duke University Medical Center, Durham, NC 27710, USA
    Eukaryot Cell 3:1287-96. 2004
    ..Because this pathway is conserved in fungi but not in mammals, our findings suggest a facile route to synergistic antifungal drug development via concomitant inhibition of FKBP12 and Hom6...
  63. ncbi request reprint Functional profiling of the Saccharomyces cerevisiae genome
    Guri Giaever
    Stanford Genome Technology Center, Stanford University, Palo Alto, California 94304, USA
    Nature 418:387-91. 2002
    ..Our results validate the yeast gene-deletion collection as a valuable resource for functional genomics...
  64. ncbi request reprint Molecular biology. Ring around the retroelement
    Philip S Perlman
    Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
    Science 303:182-4. 2004
  65. pmc Reconstitution of papillomavirus E2-mediated plasmid maintenance in Saccharomyces cerevisiae by the Brd4 bromodomain protein
    Angela R Brannon
    Laboratory of Viral Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892 0455, USA
    Proc Natl Acad Sci U S A 102:2998-3003. 2005
    ..The S. cerevisiae-based plasmid maintenance assays described here are invaluable tools for dissecting mechanisms of episomal viral genome replication and screening for additional host protein factors involved in plasmid maintenance...
  66. doi request reprint Plasmid-chromosome shuffling for non-deletion alleles in yeast
    Zhiwei Huang
    Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, One Baylor Plaza, Houston, Texas 77030, USA
    Nat Methods 5:167-9. 2008
    ..This simple method will facilitate characterization of essential gene functions and genome-wide investigation of protein structure-function relationships...
  67. ncbi request reprint Analysis of the human protein interactome and comparison with yeast, worm and fly interaction datasets
    T K B Gandhi
    Institute of Bioinformatics, International Technology Park, Bangalore 560 066, India
    Nat Genet 38:285-93. 2006
    ..The human interaction map constructed from our analysis should facilitate an integrative systems biology approach to elucidating the cellular networks that contribute to health and disease states...
  68. pmc The LRS and SIN domains: two structurally equivalent but functionally distinct nucleosomal surfaces required for transcriptional silencing
    Christopher J Fry
    Program in Molecular Medicine, University of Massachusetts Medical School, Biotech 2, Suite 210, Worcester, MA 01605, USA
    Mol Cell Biol 26:9045-59. 2006
    ..Our study shows that structurally similar nucleosomal surfaces provide distinct functionalities in vivo and in vitro...
  69. pmc Efficient Tor signaling requires a functional class C Vps protein complex in Saccharomyces cerevisiae
    Sara A Zurita-Martinez
    Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, NC 27710, USA
    Genetics 176:2139-50. 2007
    ....
  70. pmc Microarray-based genetic screen defines SAW1, a gene required for Rad1/Rad10-dependent processing of recombination intermediates
    Fuyang Li
    Department of Molecular Medicine and Institute of Biotechnology, University of Texas Health Science Center at San Antonio, 15355 Lambda Drive, San Antonio, TX 78245, USA
    Mol Cell 30:325-35. 2008
    ..Deletion of SAW1 abolished association of Rad1 at SSA intermediates in vivo. We propose that Saw1 targets Rad1/Rad10 to Rad52-coated recombination intermediates...
  71. doi request reprint Toward a comprehensive temperature-sensitive mutant repository of the essential genes of Saccharomyces cerevisiae
    Shay Ben-Aroya
    Michael Smith Laboratories, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
    Mol Cell 30:248-58. 2008
    ..The importance of this collection is demonstrated by biochemical and genetic screens that reveal essential genes involved in RNA processing and maintenance of chromosomal stability...
  72. pmc Telomeric and rDNA silencing in Saccharomyces cerevisiae are dependent on a nuclear NAD(+) salvage pathway
    Joseph J Sandmeier
    Department of Biochemistry and Molecular Genetics, University of Virginia Health Sciences Center, Charlottesville, Virginia 22908, USA
    Genetics 160:877-89. 2002
    ..We propose a model in which two components of the NAD(+) salvage pathway, Pnc1p and Npt1p, function together in recycling the nuclear nicotinamide generated by Sir2p deacetylase activity back into NAD(+)...

Research Grants38

  1. TRANSPOSITION MECHANISMS
    JEF BOEKE; Fiscal Year: 2006
    ..Based on the results of these experiments, we will pursue the isolation of compounds that raise intracellular Mn+2 in human cells by interfering with the human Pmr1p protein. ..
  2. TRANSCRIPTIONAL SILENCING MECHANISMS
    JEF BOEKE; Fiscal Year: 2005
    ..We will use the tools of molecular genetics, biochemistry and structural biology to carry out a comprehensive analysis of the molecular mechanisms involved in silencing. ..
  3. YEAST GENETIC INTERACTION MAP
    JEF BOEKE; Fiscal Year: 2006
    ..Because yeast and human genes are often conserved in structure and function, many parts of this wiring diagram will be directly applicable to studies of human gene function and dysfunction. ..
  4. YEAST GENETIC INTERACTION MAP
    JEF BOEKE; Fiscal Year: 2007
    ..The method we developed during the initial funding period is in production and can be applied genome scale. Thus, to our knowledge, we are the only group that can complete the remaining 98% of the yeast synthetic lethal interaction map. ..
  5. TRANSPOSITION MECHANISMS
    JEF BOEKE; Fiscal Year: 2007
    ..Based on the results of these experiments, we will pursue the isolation of compounds that raise intracellular Mn+2 in human cells by interfering with the human Pmrlp protein. ..
  6. TRANSPOSITION MECHANISMS
    JEF BOEKE; Fiscal Year: 2002
    ..We will examine the transcriptional interactions between Ty1 elements and the pol III genes that often lie adjacent to them. ..
  7. TRANSPOSITION MECHANISMS
    JEF BOEKE; Fiscal Year: 1990
    ..4) To identify and characterize DNA intermediates in Ty element transposition. 5) To examine the factors influencing target specificity of Ty insertion...
  8. TRANSPOSITION MECHANISMS
    JEF BOEKE; Fiscal Year: 1993
    ....
  9. TRANSPOSITION MECHANISMS
    Jef D Boeke; Fiscal Year: 2010
    ..Additionally, we study how the jumping genes interact with the machinery that protects our DNA from damage, a process that can lead to cancer. ..