Thomas H Eickbush

Summary

Affiliation: University of Rochester
Country: USA

Publications

  1. pmc A population genetic model for the maintenance of R2 retrotransposons in rRNA gene loci
    Jun Zhou
    Department of Biology, University of Rochester, Rochester, New York, United States of America
    PLoS Genet 9:e1003179. 2013
  2. pmc Reviewer acknowledgement 2013
    Nancy L Craig
    Johns Hopkins School of Medicine, 725 N, Wolfe Street, 502 PCTB, Baltimore, MD 21205, USA
    Mob DNA 4:4. 2013
  3. pmc R2 and R2/R1 hybrid non-autonomous retrotransposons derived by internal deletions of full-length elements
    Danna G Eickbush
    Department of Biology, University of Rochester, Rochester, NY, 14627, USA
    Mob DNA 3:10. 2012
  4. pmc Role of the Bombyx mori R2 element N-terminal domain in the target-primed reverse transcription (TPRT) reaction
    Shawn M Christensen
    Department of Biology, University of Rochester, Rochester, NY 14627 0211, USA
    Nucleic Acids Res 33:6461-8. 2005
  5. pmc RNA from the 5' end of the R2 retrotransposon controls R2 protein binding to and cleavage of its DNA target site
    Shawn M Christensen
    Department of Biology, University of Rochester, Rochester, NY 14627 0211, USA
    Proc Natl Acad Sci U S A 103:17602-7. 2006
  6. pmc The R2 retrotransposon RNA families
    Walter N Moss
    Department of Chemistry, University of Rochester, Rochester, NY, USA
    RNA Biol 8:714-8. 2011
  7. pmc Epigenetic regulation of retrotransposons within the nucleolus of Drosophila
    Danna G Eickbush
    Department of Biology, University of Rochester, Rochester, NY 14627, USA
    Mol Cell Biol 28:6452-61. 2008
  8. pmc Sequence variation within the rRNA gene loci of 12 Drosophila species
    Deborah E Stage
    University of Rochester, Department of Biology, Rochester, New York 14627, USA
    Genome Res 17:1888-97. 2007
  9. pmc Isoenergetic penta- and hexanucleotide microarray probing and chemical mapping provide a secondary structure model for an RNA element orchestrating R2 retrotransposon protein function
    Elzbieta Kierzek
    Department of Chemistry, University of Rochester, RC Box 270216, Rochester, NY 14627 0216, USA
    Nucleic Acids Res 36:1770-82. 2008
  10. pmc Secondary structures for 5' regions of R2 retrotransposon RNAs reveal a novel conserved pseudoknot and regions that evolve under different constraints
    Elzbieta Kierzek
    Department of Chemistry, University of Rochester, NY 14627 0216, USA
    J Mol Biol 390:428-42. 2009

Collaborators

Detail Information

Publications35

  1. pmc A population genetic model for the maintenance of R2 retrotransposons in rRNA gene loci
    Jun Zhou
    Department of Biology, University of Rochester, Rochester, New York, United States of America
    PLoS Genet 9:e1003179. 2013
    ....
  2. pmc Reviewer acknowledgement 2013
    Nancy L Craig
    Johns Hopkins School of Medicine, 725 N, Wolfe Street, 502 PCTB, Baltimore, MD 21205, USA
    Mob DNA 4:4. 2013
    ..CONTRIBUTING REVIEWERS: The editors of Mobile DNA would like to thank all our reviewers who have contributed to the journal in volume 3 (2012)...
  3. pmc R2 and R2/R1 hybrid non-autonomous retrotransposons derived by internal deletions of full-length elements
    Danna G Eickbush
    Department of Biology, University of Rochester, Rochester, NY, 14627, USA
    Mob DNA 3:10. 2012
    ..abstract:..
  4. pmc Role of the Bombyx mori R2 element N-terminal domain in the target-primed reverse transcription (TPRT) reaction
    Shawn M Christensen
    Department of Biology, University of Rochester, Rochester, NY 14627 0211, USA
    Nucleic Acids Res 33:6461-8. 2005
    ..Mutations of the protein domain also affected binding of the upstream subunit but not its function, suggesting the primary path to DNA target recognition by R2 involves both upstream and downstream subunits...
  5. pmc RNA from the 5' end of the R2 retrotransposon controls R2 protein binding to and cleavage of its DNA target site
    Shawn M Christensen
    Department of Biology, University of Rochester, Rochester, NY 14627 0211, USA
    Proc Natl Acad Sci U S A 103:17602-7. 2006
    ..We postulate that the removal of the 5' RNA normally occurs during reverse transcription, and thus provides a critical temporal link to first- and second-strand DNA cleavage in the R2 retrotransposition reaction...
  6. pmc The R2 retrotransposon RNA families
    Walter N Moss
    Department of Chemistry, University of Rochester, Rochester, NY, USA
    RNA Biol 8:714-8. 2011
    ..Seed alignments for the 5' structure and the R2 ribozyme, containing representative sequences and consensus structures, have been submitted to the Rfam database...
  7. pmc Epigenetic regulation of retrotransposons within the nucleolus of Drosophila
    Danna G Eickbush
    Department of Biology, University of Rochester, Rochester, NY 14627, USA
    Mol Cell Biol 28:6452-61. 2008
    ..This silencing of entire rDNA loci represents an example of the large-scale epigenetic control of transposable elements and shares features with the nucleolar dominance frequently seen in interspecies hybrids...
  8. pmc Sequence variation within the rRNA gene loci of 12 Drosophila species
    Deborah E Stage
    University of Rochester, Department of Biology, Rochester, New York 14627, USA
    Genome Res 17:1888-97. 2007
    ..We postulate that the fewer variants in the 28S gene is due to localized gene conversion or DNA repair triggered by the activity of retrotransposable elements that are specialized for insertion into the 28S genes of these species...
  9. pmc Isoenergetic penta- and hexanucleotide microarray probing and chemical mapping provide a secondary structure model for an RNA element orchestrating R2 retrotransposon protein function
    Elzbieta Kierzek
    Department of Chemistry, University of Rochester, RC Box 270216, Rochester, NY 14627 0216, USA
    Nucleic Acids Res 36:1770-82. 2008
    ..The experimental results were used as constraints in a free energy minimization algorithm to provide an initial model for the secondary structure of the R2Bm 5' RNA...
  10. pmc Secondary structures for 5' regions of R2 retrotransposon RNAs reveal a novel conserved pseudoknot and regions that evolve under different constraints
    Elzbieta Kierzek
    Department of Chemistry, University of Rochester, NY 14627 0216, USA
    J Mol Biol 390:428-42. 2009
    ..This suggests that local regions evolved under separate functional constraints (structural, coding, or both)...
  11. pmc Secondary structure models of the 3' untranslated regions of diverse R2 RNAs
    Amy M Ruschak
    Department of Chemistry, University of Rochester, Rochester, New York 14627 0216, USA
    RNA 10:978-87. 2004
    ..The structures appear to have common helices that are likely important for function...
  12. pmc R1 and R2 retrotransposition and deletion in the rDNA loci on the X and Y chromosomes of Drosophila melanogaster
    César E Pérez-González
    Department of Biology, University of Rochester, Rochester, New York 14627, USA
    Genetics 165:675-85. 2003
    ..e., loop-out events) that involve multiple rDNA units. These findings are interpreted in light of the known abundance of R1 and R2 elements in the X and Y rDNA loci of D. melanogaster...
  13. pmc DNA-directed DNA polymerase and strand displacement activity of the reverse transcriptase encoded by the R2 retrotransposon
    Anna Kurzynska-Kokorniak
    Department of Biology, University of Rochester, Rochester, NY 14627 0211, USA
    J Mol Biol 374:322-33. 2007
    ..This activity suggests that second-strand cleavage of the target site may not be sequence specific, but rather is specified by a single-stranded region generated when the first DNA strand is used to prime reverse transcription...
  14. pmc Role of recombination in the long-term retention of transposable elements in rRNA gene loci
    Xian Zhang
    Department of Biology, University of Rochester, Rochester, New York 14627 0211, USA
    Genetics 180:1617-26. 2008
    ..These simulations suggest that the rDNA locus serves as an ideal niche for the long-term survival of transposable elements...
  15. pmc Chromatin structure and transcription of the R1- and R2-inserted rRNA genes of Drosophila melanogaster
    Junqiang Ye
    Department of Biology, University of Rochester, Rochester, NY 14627, USA
    Mol Cell Biol 26:8781-90. 2006
    ..The accumulating data suggest that all units within small regions of the rDNA loci are activated for transcription, with most control over R1 and R2 activity involving steps downstream of transcription initiation...
  16. pmc R2 retrotransposons encode a self-cleaving ribozyme for processing from an rRNA cotranscript
    Danna G Eickbush
    Department of Biology, University of Rochester, Rochester, NY 14627, USA
    Mol Cell Biol 30:3142-50. 2010
    ..Tracing their sequence evolution in the Drosophila lineage suggests that the extensive similarity of the R2 ribozyme from D. simulans to that of HDV was a result of convergent evolution, not common descent...
  17. pmc R2 target-primed reverse transcription: ordered cleavage and polymerization steps by protein subunits asymmetrically bound to the target DNA
    Shawn M Christensen
    Department of Biology, University of Rochester, Rochester, NY 14627, USA
    Mol Cell Biol 25:6617-28. 2005
    ..A complete model for the R2 integration reaction is presented, which with minor modifications is adaptable to other non-LTR retrotransposons...
  18. ncbi request reprint End-to-end template jumping by the reverse transcriptase encoded by the R2 retrotransposon
    Arkadiusz Bibillo
    Department of Biology, University of Rochester, Rochester, New York 14627, USA
    J Biol Chem 279:14945-53. 2004
    ..These end-to-end jumps are similar to steps proposed to be part of the integration reaction of non-long terminal repeat retrotransposons and can explain chimeric integration products derived from multiple RNA templates...
  19. pmc The pattern of R2 retrotransposon activity in natural populations of Drosophila simulans reflects the dynamic nature of the rDNA locus
    Jun Zhou
    Department of Biology, University of Rochester, Rochester, New York, United States of America
    PLoS Genet 5:e1000386. 2009
    ....
  20. pmc The diversity of retrotransposons and the properties of their reverse transcriptases
    Thomas H Eickbush
    Department of Biology, University of Rochester, Rochester, NY 14627, USA
    Virus Res 134:221-34. 2008
    ..The RTs of the non-LTR retrotransposons have several unique properties reflecting their adaptation to a different mechanism of retrotransposition...
  21. ncbi request reprint Rapid R2 retrotransposition leads to the loss of previously inserted copies via large deletions of the rDNA locus
    Xian Zhang
    Department of Biology, University of Rochester, USA
    Mol Biol Evol 25:229-37. 2008
    ..These findings suggest that high rates of R2 retrotransposition do not necessarily lead to dramatic increases in the level of R2 insertions in the rDNA locus but can lead to a more rapid turnover of rDNA units...
  22. pmc Evolution of the R2 retrotransposon ribozyme and its self-cleavage site
    Danna G Eickbush
    Department of Biology, University of Rochester, Rochester, New York, United States of America
    PLoS ONE 8:e66441. 2013
    ..Finally, features of R2 ribozyme evolution, especially changes in cleavage site and convergence on the same active site sequences, are discussed. ..
  23. pmc Monitoring the mode and tempo of concerted evolution in the Drosophila melanogaster rDNA locus
    Karin Tetzlaff Averbeck
    Department of Biology, University of Rochester, Rochester, NY 14627 0211, USA
    Genetics 171:1837-46. 2005
    ....
  24. pmc Characterization of active R2 retrotransposition in the rDNA locus of Drosophila simulans
    Xian Zhang
    Department of Biology, University of Rochester, New York 14627, USA
    Genetics 170:195-205. 2005
    ..Retrotransposition activity was correlated with the number of full-length R2 elements but not with the size of the rDNA locus or the number of uninserted units...
  25. ncbi request reprint Footprint of the retrotransposon R2Bm protein on its target site before and after cleavage
    Shawn Christensen
    Department of Biology, University of Rochester, Hutchinson Hall 334, Rochester, NY 14627 0211, USA
    J Mol Biol 336:1035-45. 2004
    ..We suggest that this increased protection after cleavage is the RT domain that is positioned over the free DNA end to begin reverse transcription on the nicked DNA substrate...
  26. ncbi request reprint R5 retrotransposons insert into a family of infrequently transcribed 28S rRNA genes of planaria
    William D Burke
    Department of Biology, University of Rochester, USA
    Mol Biol Evol 20:1260-70. 2003
    ..Attempts to trace the phylogeny of R5 did not offer sufficient resolution to determine whether R2, R4, and R5 represent the same lineage or whether they represent independent specializations for the 28S gene...
  27. pmc Origin of nascent lineages and the mechanisms used to prime second-strand DNA synthesis in the R1 and R2 retrotransposons of Drosophila
    Deborah E Stage
    Biology Department, University of Rochester, Rochester NY 14627 0211, USA
    Genome Biol 10:R49. 2009
    ..subject to the concerted evolution process that is responsible for sequence homogeneity among the different copies of rRNA genes? Second, how precise are the target DNA cleavages and priming of DNA synthesis used by these elements?..
  28. pmc Finely orchestrated movements: evolution of the ribosomal RNA genes
    Thomas H Eickbush
    Department of Biology, University of Rochester, Rochester, New York 14627, USA
    Genetics 175:477-85. 2007
    ..Finally, we summarize data that suggest that recombination in the rDNA locus of higher eukaryotes is sufficiently frequent to monitor changes within a few generations...
  29. pmc Transcription of endogenous and exogenous R2 elements in the rRNA gene locus of Drosophila melanogaster
    Danna G Eickbush
    Department of Biology, University of Rochester, Rochester, New York 146270 0211, USA
    Mol Cell Biol 23:3825-36. 2003
    ..These results suggest that transcription of the rDNA units can be tightly regulated, but this regulation gradually breaks down as the cell approaches the minimum number of uninserted genes needed for survival...
  30. pmc Heterochromatin formation promotes longevity and represses ribosomal RNA synthesis
    Kimberly Larson
    Department of Biomedical Genetics, University of Rochester Medical Center, Rochester, New York, USA
    PLoS Genet 8:e1002473. 2012
    ..Taken together, these results suggest that epigenetic preservation of genome stability, especially at the rDNA locus, and repression of unnecessary rRNA synthesis, might be an evolutionarily conserved mechanism for prolonging lifespan...
  31. pmc The reverse transcriptase encoded by the non-LTR retrotransposon R2 is as error-prone as that encoded by HIV-1
    Varuni K Jamburuthugoda
    Department of Biology, University of Rochester, Rochester, NY 14627 0211, USA
    J Mol Biol 407:661-72. 2011
    ....
  32. ncbi request reprint Fruit flies and humans respond differently to retrotransposons
    Thomas H Eickbush
    Department of Biology, University of Rochester, Rochester, New York 14627, USA
    Curr Opin Genet Dev 12:669-74. 2002
    ....
  33. pmc Retrotransposition of R2 elements in somatic nuclei during the early development of Drosophila
    Michael T Eickbush
    Department of Biology, University of Rochester, Rochester, NY, USA
    Mob DNA 2:11. 2011
    ..abstract:..
  34. pmc R2 retrotransposition on assembled nucleosomes depends on the translational position of the target site
    Junqiang Ye
    University of Rochester, Department of Biology, Rochester, NY 14627, USA
    EMBO J 21:6853-64. 2002
    ..Interaction of the R2 protein with the nucleosome disrupted the histone:DNA contacts in the 50 bp region directly bound by R2, but did not modify the remainder of the nucleosome structure...
  35. pmc Rates of R1 and R2 retrotransposition and elimination from the rDNA locus of Drosophila melanogaster
    César E Pérez-González
    Department of Biology, University of Rochester, New York 14627, USA
    Genetics 162:799-811. 2002
    ..The high rates of R1 and R2 elimination from the rDNA locus confirm that these elements must maintain relatively high rates of retrotransposition to ensure their continued presence in this locus...