Voytas Lab: Publications

Data from Publications

Cover Articles

 

2005. Plant J. Nov;44:693-705

High-frequency homologous recombination in plants mediated by zinc-finger nucleases.

 

2007

Dai, J., Xie, W., Brady, T.L., Gao, J. and Voytas, D.F. (2007). Phosphorylation regulates integration of the yeast Ty5 retrotransposon into heterochromatin.Mol. Cell 27:289-299..

Preview: Mol. Cell 27:180-181. Stress management: how cells take control of their transposons. E. Hirotaka and H.L. Levin.

Sander, J.D., Zaback, P., Joung, J.K., Voytas, D.F. and Dobbs, D. (2007). Zinc Finger Targeter (ZiFiT): an engineered zinc finger/target site design tool. Nucleic Acids Res. 2007 May 25; [Epub ahead of print]

2006

Wright, D.A., Thibodeau—Beganny, S., Sander, J., Winfrey, R.J., Hirsh, A.S., Eichtinger, M., Fu, F., Porteus, M.H., Dobbs, D., Voytas, D.F. and Joung, J.K.  (2006). Standardized reagents and protocols for engineering zinc finger nucleases by modular design.  Nature Protocols.  1:1637-1652.

2005

Wright DA, Townsend FA, Winfrey RJ Jr, Irwin PA, Rajagopal J, Lonosky PM, Hall BD, Jondle MD, Voytas DF (2005). High-frequency homologous recombination in plants mediated by zinc-finger nucleases. Plant J. 44:693-705.

Review: Trends in Plant Science. 11:159-161. Gene targeting in plants: fingers on the move . Kumar, Allen, and Thompson.

Havecker ER, Gao X, Voytas DF (2005). The Sireviruses, a plant-specific lineage of the Ty1/copia retrotransposons, ineract with a family of proteins to dynein light chain 8. Plant Physiol. 139:857-68.

Gao X, Vander Velden KA, Voytas DF, Gu X (2005). SplitTester: software to identify domains responsible for functional divergence in protein family. BMC Bioinformatics. 6:137.

Gao X, Voytas DF (2005). A eukaryotic gene family related to retroelement integrases. Trends Genet. 21:133-7.

2004

Peterson-Burch BD, Nettleton D, Voytas DF (2004). Genomic neighborhoods for Arabidopsis retrotransposons: a role for targeted integration in the distribution of the Metaviridae. Genome Biology. 5:R78.

Havecker ER, Gao X, Voytas DF (2004).  The diversity of LTR retrotransposons.  Genome Biology. 5:225.

2003

Gao X, Havecker ER, Baranov PV, Atkins JF, Voytas DF (2003).  Translational recoding signals between gag and pol in diverse LTR retrotransposons.  RNA. 9:1422-30.

Fuerst PG and Voytas DF (2003).  CEN plasmid segregation is destabilized by tethered determinants of Ty 5 integration specificity: a role for double-strand breaks in CEN antagonism.  Chromosoma. 2003 112:58-65.

Laten HM, Havecker ER, Farmer LM, Voytas DF (2003).  SIRE1, an endogenous retrovirus family from Glycine max, is highly homogeneous and evolutionarily young.  Mol Biol Evol. 2003 20:1222-30.

Zhu Y, Dai J, Fuerst PG, Voytas DF (2003).  From the Cover: Controlling integration specificity of a yeast retrotransposon.   Proc Natl Acad Sci U S A. 100:5891-5.

Review: Proc Natl Acad Sci U S A. 100:5586-8. Integration by design. Sandmeyer S.. 

Review: Cell 115:135-138. Targeting Survival: Integration Site Selection by Retroviruses and LTR-Retrotransposons. Bushman.

Havecker ER and Voytas DF (2003).  The soybean retroelement SIRE1 uses stop codon suppression to express its envelope-like protein.  EMBO Rep. 2003 4:274-7.

2002

Peterson-Burch BD, Voytas DF. Books, LinkOut Genes of the Pseudoviridae (Ty1/copia Retrotransposons). Mol Biol Evol. 2002 19:1832-1845.

Vigdal T, Kaufman C, Izsvak Z, Voytas D, Ivics Z. Related Articles, Books, LinkOut Common Physical Properties of DNA Affecting Target Site Selection of Sleeping Beauty and other Tc1/mariner Transposable Elements. J Mol Biol. 2002 323:441. 

Gao X, Rowley DJ, Gai X, Voytas DF(2002). Ty5 gag Mutations Increase Retrotransposition and Suggest a Role for Hydrogen Bonding in the Function of the Nucleocapsid Zinc Finger. J Virol 76:3240-7.

Wright DA, Voytas DF(2002). Athila4 of Arabidopsis and Calypso of soybean define a lineage of endogenous plant retroviruses. Genome Res. 12:122-31.

2000-2001

Xie W, Gai X, Zhu Y, Zappulla DC, Sternglanz R and Voytas DF (2001). Targeting of the Yeast Ty5 Retrotransposon to Silent Chromatin Is Mediated by Interactions between Integrase and Sir4p. Mol. Cell. Biol. 21: 6606-6614.

Irwin PA and Voytas DF(2001). Expression and Processing of Proteins Encoded by the Saccharomyces Retrotransposon Ty5. J. Virol. 75:1790-97.

Chen M, Choi Y, Voytas DF, Rodermel S (2000). Mutations in the Arabidopsis VAR2 locus cause leaf variegation due to the loss of a chloroplast FtsH protease. Plant J. 22:303-13.

Peterson-Burch BD, Wright DA, Laten HM, Voytas DF (2000). Retroviruses in plants? Trends Genet.16:151-2.

1999

Zhu Y, Zou S, Wright DA, Voytas DF (1999). Tagging chromatin with retrotransposons: target specificity of the Saccharomyces Ty5 retrotransposon changes with the chromosomal localization of Sir3p and Sir4p. Genes Dev. 13:2738-49.

Wu, D., Wright, D. A., Wetzel, C., Voytas, D. F., and S. Rodermel (1999). The IMMUTANS variegation locus of Arabidopsis defines a mitochondrial alternative oxidase homolog that functions during early chloroplast biogenesis. Plant Cell 11:43-55.

Review: Plant Cell 11:1-4 Photosynthetic Pigmentation-- Variegations on a Theme. Smith, H. B.

Ke, N., X. Gao, J. B. Keeney, J. D. Broeke, and D. F. Voytas (1999). The yeast retrotransposon Ty5 uses the anticondon stem-loop of the initiator methionine tRNA as a primer for reverse transcription. RNA 5:929-38. 

Ke, N., and D. F. Voytas (1999). cDNA of the Yeast retrotransposon Ty5 Preferentially Recombines with substrates in Silent Chromatin. Mol. Cell. Biol. 19:484-494. 

1998

Voytas, D. F., and G. J. P. Naylor (1998). Rapid flux in plant genomes. Nature Genetics 20: 6-7. 

Gai, X., and D. F. Voytas (1998). A single amino acid change identifies a Ty5 retrotransposon domain that targets integration to silent chromatin. Molecular Cell 1:1051-55.

Review: Cell 93:1087-89. Yeast retrotransposons: finding a nice quiet neighborhood. Boeke J. D., and S. E. Devine. 

Wright, D. A, and D. F. Voytas. (1998). Potential retroviruses in plants: Tat1 belongs to a lineage of Arabidopsis thaliana retrotransposons that encode envelope-like proteins. Genetics149:703-15.

Review: Trends in Plant Sciences 3:371-74 The evolution of plant retroviruses: moving to green pastures. Kumar, A. 

Kim, J. M., S. Vanguri, J. D. Boeke, A. Gabriel, and D. F. Voytas. (1998). Transposable elements and genome organization: a comprehensive survey of retrotransposons revealed by the complete Saccharomyces cerevisiae genome sequence. Genome Res. 8:464-78.

Review: Genome Res. 8:416-18. Targeting transposition: At home in the genome. Sandmeyer, S.

1997

Ke, N., and D. F. Voytas. (1997) High frequency cDNA recombination of the saccharomyces retrotransposon Ty5: The LTR mediates formation of tandem elements. Genetics147:545-56. 

Ke, N., P. A. Irwin, and D. F. Voytas. (1997) The pheromone response pathway activates transcription of Ty5 retrotransposons located within silent chromatin of Saccharomyces cerevisiae. EMBO J 16:6272-80. 

Zou, S., and D. F. Voytas. (1997) Silent chromatin determines target preference of the Saccharomyces retrotransposon Ty5. Proc Natl Acad Sci U S A 94:7412-16. 

Wright, D. A., S. K. Park, D. Wu, G. J. Phillips, S. R. Rodermel, and D. F. Voytas. (1997) Recovery of YAC-end sequences through complementation of an Escherichia coli pyrF mutation. Nucleic Acids Res 25:2679-80. 

1996

Zou, S., J. M. Kim, and D. F. Voytas. (1996). The Saccharomyces retrotransposon Ty5 influences the structure of chromosome ends. Nucleic Acids Res 24:4825-31. 

Voytas, D. F. (1996) Retroelements in genome organization. Science 274:737-38. 

Zou, S., N. Ke, J. M. Kim, and D. F. Voytas. (1996) The Saccharomyces retrotransposon Ty5 integrates preferentially into regions of silent chromatin at the telomeres and mating loci. Genes Dev. 10:634-45. 

Wright, D. A., N. Ke, J. Smalle, B. Hauge, H. M. Goodman, and D.F. Voytas. (1996) Multiple non-LTR retrotransposons in the streamlined genome of Arabidopsis thaliana. Genetics 142:569-78. 

1988-1995

Zou, S., D. A. Wright and D. F. Voytas. (1995) The Saccharomyces Ty5 retrotransposon family is associated with origins of DNA replication at the telomeres and the silent mating locus HMR. Proc Natl Acad Sci U.S.A. 92:920-24. 

Keeney, J. B., K. B. Chapman, V. Lauermann, D. F. Voytas, S. U. strm, U. von Pawel-Rammingen, A. Bystrm, and J. D. Boeke. (1995) Multiple molecular determinants for retrotransposition in a primer tRNA. Mol. Cell. Biol. 15:217-26. 

Wetzel, C. M., C.-Z. Jiang, L. J. Meehan, D. F. Voytas, and S. R. Rodermel. (1994) Nuclear-organelle interactions: the immutans variegation mutant of Arabidopsis is plastid autonomous and impaired in carotenoid biosynthesis. Plant J. 6:161-75. 

Voytas, D. F., and J. D. Boeke. Yeast retrotransposons and tRNAs. (1993) Trends Genet. 9:421-27. 

Ji, H., D. P. Moore, M. A. Blomberg, L. T. Braiterman, D. F. Voytas, G. Natsoulis, and J.D. Boeke. (1993). Hotspots for unselected Ty1 transposition events on yeast chromosome III are near tRNA genes and LTR sequences. Cell 73:1007-18. 

VanderWiel, P. L., D. F. Voytas, and J. F. Wendel. (1993). Copia-like retrotransposable element evolution in diploid and polyploid cotton (Gossypium L.). J. Mol. Evol. 36:429-47. 

Voytas, D. F., and J. D. Boeke. (1992). Yeast retrotransposon revealed. Nature 358:717. 

Voytas, D. F., M. P. Cummings, A. Konieczny, F. M. Ausubel, and S. R. Rodermel. (1992). Copia-like retrotransposons are ubiquitous among plants. Proc. Natl Acad Sci U S A 89:7124-28. 

Konieczny, A., D. F. Voytas, M. P. Cummings, and F. M. Ausubel. (1991). A superfamily of retrotransposable elements in Arabidopsis thaliana. Genetics 127:801-09. 

Voytas, D. F., A. Konieczny, M. P. Cummings, and F. M. Ausubel. (1990). The structure, distribution and evolution of the Ta1 retrotransposable element family of Arabidopsis thaliana. Genetics 126:713-21. 

Voytas, D. F., and F. M. Ausubel. (1988)."A copia-like transposable element family in Arabidopsis thaliana. Nature 336:242-44.