David J Garfinkel

Summary

Affiliation: National Cancer Institute
Country: USA

Publications

  1. ncbi 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
  2. ncbi Post-transcriptional cosuppression of Ty1 retrotransposition
    David J Garfinkel
    Gene Regulation and Chromosome Biology Laboratory, National Cancer Institute, Frederick, Maryland 21702 1201, USA
    Genetics 165:83-99. 2003
  3. ncbi Ty1 copy number dynamics in Saccharomyces
    David J Garfinkel
    Gene Regulation and Chromosome Biology Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, Maryland 21701 1201, USA
    Genetics 169:1845-57. 2005
  4. ncbi Retrotransposon suicide: formation of Ty1 circles and autointegration via a central DNA flap
    David J Garfinkel
    National Cancer Institute, P O Box B, Frederick, MD 21702 1201, USA
    J Virol 80:11920-34. 2006
  5. ncbi Chromatin-associated genes protect the yeast genome from Ty1 insertional mutagenesis
    Katherine M Nyswaner
    Gene Regulation and Chromosome Biology Laboratory, Center for Cancer Research, Science Applications International Corporation, National Cancer Institute, Frederick, Maryland 21702 1201, USA
    Genetics 178:197-214. 2008
  6. ncbi P-body components are required for Ty1 retrotransposition during assembly of retrotransposition-competent virus-like particles
    Mary Ann Checkley
    Gene Regulation and Chromosome Biology Laboratory, National Cancer Institute Frederick, P O Box B, Frederick, MD 21702 1201, USA
    Mol Cell Biol 30:382-98. 2010
  7. ncbi Posttranslational interference of Ty1 retrotransposition by antisense RNAs
    Emiko Matsuda
    Gene Regulation and Chromosome Biology Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, MD 21702 1201, USA
    Proc Natl Acad Sci U S A 106:15657-62. 2009
  8. ncbi Exploring Ty1 retrotransposon RNA structure within virus-like particles
    Katarzyna J Purzycka
    RT Biochemistry Section, HIV Drug Resistance Program, Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA
    Nucleic Acids Res 41:463-73. 2013
  9. ncbi BUD22 affects Ty1 retrotransposition and ribosome biogenesis in Saccharomyces cerevisiae
    Arun Dakshinamurthy
    Gene Regulation and Chromosome Biology Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, Maryland 21702, USA
    Genetics 185:1193-205. 2010
  10. ncbi Functional analysis of N-terminal residues of ty1 integrase
    Sharon P Moore
    Gene Regulation and Chromosome Biology Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, Maryland 21702, USA
    J Virol 83:9502-11. 2009

Collaborators

Detail Information

Publications16

  1. ncbi 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...
  2. ncbi Post-transcriptional cosuppression of Ty1 retrotransposition
    David J Garfinkel
    Gene Regulation and Chromosome Biology Laboratory, National Cancer Institute, Frederick, Maryland 21702 1201, USA
    Genetics 165:83-99. 2003
    ..Furthermore, a decrease in the synthesis of Ty1 cDNA is strongly associated with Ty1 CNC. Together our results suggest that Ty1 cosuppression can occur post-transcriptionally, either prior to or during reverse transcription...
  3. ncbi Ty1 copy number dynamics in Saccharomyces
    David J Garfinkel
    Gene Regulation and Chromosome Biology Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, Maryland 21701 1201, USA
    Genetics 169:1845-57. 2005
    ..Ty1 gain/loss ratios obtained under different conditions suggest that copy number oscillates over time by altering the rate of retrotransposition, resulting in the diverse copy numbers observed in Saccharomyces...
  4. ncbi Retrotransposon suicide: formation of Ty1 circles and autointegration via a central DNA flap
    David J Garfinkel
    National Cancer Institute, P O Box B, Frederick, MD 21702 1201, USA
    J Virol 80:11920-34. 2006
    ..These results suggest that Ty1-specific mechanisms minimize copy number and raise the possibility that special DNA structures are a targeting determinant...
  5. ncbi Chromatin-associated genes protect the yeast genome from Ty1 insertional mutagenesis
    Katherine M Nyswaner
    Gene Regulation and Chromosome Biology Laboratory, Center for Cancer Research, Science Applications International Corporation, National Cancer Institute, Frederick, Maryland 21702 1201, USA
    Genetics 178:197-214. 2008
    ..Our results indicate that multiple pathways restrict Ty1 mobility and histone modifications may protect coding regions from insertional mutagenesis...
  6. ncbi P-body components are required for Ty1 retrotransposition during assembly of retrotransposition-competent virus-like particles
    Mary Ann Checkley
    Gene Regulation and Chromosome Biology Laboratory, National Cancer Institute Frederick, P O Box B, Frederick, MD 21702 1201, USA
    Mol Cell Biol 30:382-98. 2010
    ..Therefore, Kem1p may prevent the aggregation of Ty1 antisense and mRNAs. Overall, our results suggest that P-body components enhance the formation of retrotransposition-competent Ty1 VLPs...
  7. ncbi Posttranslational interference of Ty1 retrotransposition by antisense RNAs
    Emiko Matsuda
    Gene Regulation and Chromosome Biology Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, MD 21702 1201, USA
    Proc Natl Acad Sci U S A 106:15657-62. 2009
    ..Thus, Ty1AS RNAs are part of an intrinsic mechanism that limits retrotransposition by reducing the level of proteins required for replication and integration...
  8. ncbi Exploring Ty1 retrotransposon RNA structure within virus-like particles
    Katarzyna J Purzycka
    RT Biochemistry Section, HIV Drug Resistance Program, Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA
    Nucleic Acids Res 41:463-73. 2013
    ..Our results support the idea that antisense RNAs inhibit retrotransposition by targeting Ty1 protein function rather than annealing with the RNA genome...
  9. ncbi BUD22 affects Ty1 retrotransposition and ribosome biogenesis in Saccharomyces cerevisiae
    Arun Dakshinamurthy
    Gene Regulation and Chromosome Biology Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, Maryland 21702, USA
    Genetics 185:1193-205. 2010
    ..Together our results suggest that BUD22 is involved in a step in ribosome biogenesis that not only affects general translation, but also may alter the frameshifting efficiency of ribosomes, an event central to Ty1 retrotransposition...
  10. ncbi Functional analysis of N-terminal residues of ty1 integrase
    Sharon P Moore
    Gene Regulation and Chromosome Biology Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, Maryland 21702, USA
    J Virol 83:9502-11. 2009
    ..Our results suggest that the histidine/cysteine residues are important for steps in transposition prior to integration, while the hydrophobic residues function in IN multimerization...
  11. ncbi Ty1 gag enhances the stability and nuclear export of Ty1 mRNA
    Mary Ann Checkley
    Gene Regulation and Chromosome Biology Laboratory, Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA
    Traffic 14:57-69. 2013
    ..Endogenously expressed Gag also localized to the nuclear periphery independent of RNA export. These results suggest that Gag is required for Ty1 mRNA stability, efficient nuclear export and localization into cytoplasmic foci...
  12. ncbi Sensitive phenotypic detection of minor drug-resistant human immunodeficiency virus type 1 reverse transcriptase variants
    Dwight V Nissley
    Basic Research Program, SAIC Frederick, NCI Frederick, P O Box B, Frederick, MD 21702, USA
    J Clin Microbiol 43:5696-704. 2005
    ....
  13. ncbi Analysis of a Ty1-less variant of Saccharomyces paradoxus: the gain and loss of Ty1 elements
    Sharon P Moore
    Gene Regulation and Chromosome Biology Laboratory, National Cancer Institute, PO Box B, Frederick, MD 21702 1201, USA
    Yeast 21:649-60. 2004
    ..The results indicate that Ty1 retrotransposition occurs at a much higher rate than elimination, suggesting that copy-number-dependent co-factors or environmental conditions contribute to the loss of Ty elements in this genome...
  14. ncbi The Rad27 (Fen-1) nuclease inhibits Ty1 mobility in Saccharomyces cerevisiae
    Anuradha Sundararajan
    Gene Regulation and Chromosome Biology Laboratory, National Cancer Institute, Frederick, Maryland 21702, USA
    Genetics 163:55-67. 2003
    ..Our results suggest that Rad27 inhibits Ty1 mobility by destabilizing unincorporated Ty1 cDNA and preventing the formation of Ty1 multimers...
  15. ncbi S-phase checkpoint pathways stimulate the mobility of the retrovirus-like transposon Ty1
    M Joan Curcio
    Laboratory of Developmental Genetics, Wadsworth Center, Albany, New York 12201, USA
    Mol Cell Biol 27:8874-85. 2007
    ..We propose that DNA lesions created in the absence of Rtt/genome caretakers trigger S-phase checkpoint pathways to stimulate Ty1 reverse transcriptase activity...
  16. ncbi Survival strategies for transposons and genomes
    Sandra L Martin
    Department of Cellular and Structural Biology, University of Colorado School of Medicine, Box B111, 4200 E, Ninth Avenue, Denver, CO 80262, USA
    Genome Biol 4:313. 2003
    ..A report on the Keystone Symposium "Transposition and other genome rearrangements", Santa Fe, USA, 8-14 February 2003...