David J Garfinkel

Summary

Affiliation: National Cancer Institute
Country: USA

Publications

  1. ncbi request reprint Genome evolution mediated by Ty elements in Saccharomyces
    D J Garfinkel
    National Cancer Institute, Frederick, MD 21702 1201, USA
    Cytogenet Genome Res 110:63-9. 2005
  2. pmc 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
  3. pmc 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. pmc 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
  5. ncbi request reprint 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
  6. pmc 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
  7. pmc 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
  8. pmc 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
  9. pmc 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
  10. pmc Nucleotide excision repair/TFIIH helicases RAD3 and SSL2 inhibit short-sequence recombination and Ty1 retrotransposition by similar mechanisms
    B S Lee
    Gene Regulation and Chromosome Biology Laboratory, National Cancer Institute Frederick Cancer Research and Development Center, National Institutes of Health, Frederick, Maryland 21702 1201, USA
    Mol Cell Biol 20:2436-45. 2000

Collaborators

Detail Information

Publications25

  1. ncbi request reprint Genome evolution mediated by Ty elements in Saccharomyces
    D J Garfinkel
    National Cancer Institute, Frederick, MD 21702 1201, USA
    Cytogenet Genome Res 110:63-9. 2005
    ..In this review I present key experiments from both the pre- and current genomic sequencing eras suggesting how Ty elements mediate genome evolution...
  2. pmc 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...
  3. pmc 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. pmc 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...
  5. ncbi request reprint 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...
  6. pmc 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...
  7. pmc 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...
  8. pmc 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...
  9. pmc 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...
  10. pmc Nucleotide excision repair/TFIIH helicases RAD3 and SSL2 inhibit short-sequence recombination and Ty1 retrotransposition by similar mechanisms
    B S Lee
    Gene Regulation and Chromosome Biology Laboratory, National Cancer Institute Frederick Cancer Research and Development Center, National Institutes of Health, Frederick, Maryland 21702 1201, USA
    Mol Cell Biol 20:2436-45. 2000
    ..Our results link components of the core NER/TFIIH complex with genome stability, homologous recombination, and host defense against Ty1 retrotransposition via a mechanism that involves DNA degradation...
  11. pmc 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...
  12. pmc 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...
  13. pmc The Saccharomyces cerevisiae DNA recombination and repair functions of the RAD52 epistasis group inhibit Ty1 transposition
    A J Rattray
    Gene Regulation and Chromosome Biology Laboratory, ABL Basic Research Program, NCI FCRDC, Frederick, Maryland 21702, USA
    Genetics 154:543-56. 2000
    ..However, unincorporated Ty1 cDNA levels are markedly elevated. These results suggest that members of the RAD52 recombinational repair pathway inhibit Ty1 post-translationally by influencing the fate of Ty1 cDNA...
  14. pmc Hybrid Ty1/HIV-1 elements used to detect inhibitors and monitor the activity of HIV-1 reverse transcriptase
    D V Nissley
    Gene Regulation and Chromosome Biology Laboratory, National Cancer Institute Frederick Cancer Research and Development Center, ABL Basic Research Program, Frederick, MD 21702 1201, USA
    Proc Natl Acad Sci U S A 95:13905-10. 1998
    ..HART elements carrying NNRTI-resistant variants of HIV-1 RT can be used to identify compounds that are active against drug-resistant viruses...
  15. pmc Correct integration of model substrates by Ty1 integrase
    S P Moore
    Gene Regulation and Chromosome Biology Laboratory, National Cancer Institute Frederick Cancer Research and Development Center, National Institutes of Health, Frederick, Maryland 21702 1201, USA
    J Virol 74:11522-30. 2000
    ..Together, our results suggest that IN is sufficient for Ty1 integration in vitro and IN interacts with exogenous donors less stringently than with endogenous elements...
  16. ncbi request reprint Chemical cleavage at aspartyl residues for protein identification
    A Li
    Protein Chemistry Laboratory, AIDS Vaccine Program, SAIC Frederick, NCI at Frederick, Maryland 21702 1201, USA
    Anal Chem 73:5395-402. 2001
    ..Parallel digestions using trypsin were also performed. The formic acid cleavage method generated comparable or better results than tryptic digestion for protein identification...
  17. pmc Posttranslational inhibition of Ty1 retrotransposition by nucleotide excision repair/transcription factor TFIIH subunits Ssl2p and Rad3p
    B S Lee
    Gene Regulation and Chromosome Biology Laboratory, Advanced BioScience Laboratories Basic Research Program, National Cancer Institute Frederick Cancer Research and Development Center, Maryland 21702 1201, USA
    Genetics 148:1743-61. 1998
    ..Our work suggests that NER/TFIIH subunits antagonize Ty1 transposition posttranslationally by inhibiting reverse transcription or destabilizing Ty1 cDNA...
  18. pmc 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...
  19. pmc MGA2 or SPT23 is required for transcription of the delta9 fatty acid desaturase gene, OLE1, and nuclear membrane integrity in Saccharomyces cerevisiae
    S Zhang
    Movable Genetic Elements Section, Gene Regulation and Chromosome Biology Laboratory, Advanced BioScience Laboratories Basic Research Program, National Cancer Institute Frederick Cancer Research and Development Center, Frederick, Maryland 21702, USA
    Genetics 151:473-83. 1999
    ..Furthermore, the level of the OLE1 transcript decreases more than 15-fold in the absence of wild-type Mga2p and Spt23p. Our results suggest that Mga2p/Spt23p control cell viability by stimulating OLE1 transcription...
  20. pmc 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
    ....
  21. pmc 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...
  22. ncbi request reprint Presence of Ty1-copia group retrotransposon sequences in the potato late blight pathogen Phytophthora infestans
    P W Tooley
    USDA ARS, Foreign Disease Weed Science Research, Ft Detrick, Frederick, MD 21701, USA
    Mol Plant Microbe Interact 9:305-9. 1996
    ..infestans isolates show restriction site polymorphisms. Some contain complete open reading frames while others do not, indicating the presence of potentially active as well as inactive elements...
  23. 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...
  24. pmc 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...
  25. pmc 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...