Publications

Evolution of the r2 retrotransposon ribozyme and its self-cleavage site. Eickbush DG, Burke WD, Eickbush TH.PLoS One. 2013 Sep 16;8(9):e66441.doi:10.1371/journal.pone.0066441.PMID:24066021 Free PMC Article

 A population genetic model for the maintenance of R2 retrotransposons in rRNA gene loci. Zhou J, Eickbush MT, Eickbush TH. PLoS Genet. 2013 Jan;9(1):e1003179. doi: 10.1371/journal.pgen.1003179. Epub 2013 Jan 10. PMID: 23326244 [PubMed] 

Y chromosome mediates ribosomal DNA silencing and modulates the chromatin state in Drosophila. Zhou J, Sackton TB, Martinsen L, Lemos B, Eickbush TH, Hartl DL.Proc Natl Acad Sci U S A. 2012 Jun 19;109(25):9941-6. Epub 2012 Jun 4.PMID: 22665801 (PubMed)

R2 and R2/R1 hybrid non-autonomous retrotransposons derived by internal deletions of full-length elements.
Eickbush DG, Eickbush TH.Mob DNA. 2012 May 23;3(1):10. doi: 10.1186/1759-8753-3-10.PMID: 22621441 [PubMed]

Heterochromatin formation promotes longevity and represses ribosomal RNA synthesis.
Larson K, Yan SJ, Tsurumi A, Liu J, Zhou J, Gaur K, Guo D, Eickbush TH, Li WX.PLoS Genet. 2012 Jan;8(1):e1002473. Epub 2012 Jan 26.PMID: 22291607 [PubMed - indexed for MEDLINE]

Retrotransposition of R2 elements in somatic nuclei during the early development of Drosophila.
Eickbush MT, Eickbush TH.Mob DNA. 2011 Sep 29;2(1):11. doi: 10.1186/1759-8753-2-11.PMID: 21958913 [PubMed]

The R2 retrotransposon RNA families
. Moss WN, Eickbush DG, Lopez MJ, Eickbush TH, Turner DH.RNA Biol. 2011 Sep-Oct;8(5):714-8. Epub 2011 Jul 7.PMID: 21734471 [PubMed]

The reverse transcriptase encoded by the non-LTR retrotransposon R2 is as error-prone as that encoded by HIV-1.
Jamburuthugoda VK, Eickbush TH.J Mol Biol. 2011 Apr 15;407(5):661-72. Epub 2011 Feb 12.PMID: 21320510 [PubMed]

R2 retrotransposons encode a self-cleaving ribozyme for processing from an rRNA cotranscript. 
Eickbush DG, Eickbush TH.Mol Cell Biol. 2010 Jul;30(13):3142-50. Epub 2010 Apr 26.PMID: 20421411 [PubMed - indexed for MEDLINE]

Welcome to mobile DNA.
Craig NL, Eickbush TH, Voytas DF.Mob DNA. 2010 Jan 25;1(1):1. No abstract available.PMID: 20226071 [PubMed]

Maintenance of multiple lineages of R1 and R2 retrotransposable elements in the ribosomal RNA gene loci of Nasonia. 
Stage DE, Eickbush TH.Insect Mol Biol. 2010 Feb;19 Suppl 1:37-48.PMID: 20167016 [PubMed - indexed for MEDLINE]

Origin of nascent lineages and the mechanisms used to prime second-strand DNA synthesis in the R1 and R2 retrotransposons of Drosophila
. Stage DE, Eickbush TH.Genome Biol. 2009;10(5):R49. Epub 2009 May 5.PMID: 19416522 [PubMed - indexed for MEDLINE]

Secondary structures for 5′ regions of R2 retrotransposon RNAs reveal a novel conserved pseudoknot and regions that evolve under different constraints.
Kierzek E, Christensen SM, Eickbush TH, Kierzek R, Turner DH, Moss WN.J Mol Biol. 2009 Jul 17;390(3):428-42. Epub 2009 May 3.PMID: 19397915 [PubMed - indexed for MEDLINE]

The pattern of R2 retrotransposon activity in natural populations of Drosophila simulans reflects the dynamic nature of the rDNA locus.
Zhou J, Eickbush TH.PLoS Genet. 2009 Feb;5(2):e1000386. Epub 2009 Feb 20.PMID: 19229317 [PubMed - indexed for MEDLINE]

Role of recombination in the long-term retention of transposable elements in rRNA gene loci 
.Zhang X, Eickbush MT, Eickbush TH.Genetics. 2008 Nov;180(3):1617-26. Epub 2008 Sep 14.PMID: 18791229 [PubMed - indexed for MEDLINE]

Epigenetic regulation of retrotransposons within the nucleolus of Drosophila.
Eickbush DG, Ye J, Zhang X, Burke WD, Eickbush TH.Mol Cell Biol. 2008 Oct;28(20):6452-61. Epub 2008 Aug 4.PMID: 18678644 [PubMed - indexed for MEDLINE]

The diversity of retrotransposons and the properties of their reverse transcriptases
. Eickbush TH, Jamburuthugoda VK.Virus Res. 2008 Jun;134(1-2):221-34. Epub 2008 Feb 7. Review.PMID: 18261821 [PubMed - indexed for MEDLINE]

Isoenergetic penta- and hexanucleotide microarray probing and chemical mapping provide a secondary structure model for an RNA element orchestrating R2 retrotransposon protein function
. Kierzek E, Kierzek R, Moss WN, Christensen SM, Eickbush TH, Turner DH.Nucleic Acids Res. 2008 Apr;36(6):1770-82. Epub 2008 Feb 5.PMID: 18252773 [PubMed - indexed for MEDLINE]

Rapid R2 retrotransposition leads to the loss of previously inserted copies via large deletions of the rDNA locus.
Zhang X, Zhou J, Eickbush TH.Mol Biol Evol. 2008 Jan;25(1):229-37. Epub 2007 Nov 13.PMID: 18003600 [PubMed - indexed for MEDLINE] 

Evolution of genes and genomes on the Drosophila phylogeny.
Drosophila 12 Genomes Consortium, multiple authors. Nature. 2007 Nov 8;450(7167):203-18.PMID: 17994087 [PubMed - indexed for MEDLINE]

Sequence variation within the rRNA gene loci of 12 Drosophila species.
Stage DE, Eickbush TH.Genome Res. 2007 Dec;17(12):1888-97. Epub 2007 Nov 7.PMID: 17989256 [PubMed - indexed for MEDLINE]

DNA-directed DNA polymerase and strand displacement activity of the reverse transcriptase encoded by the R2 retrotransposon.
Kurzynska-Kokorniak A, Jamburuthugoda VK, Bibillo A, Eickbush TH.J Mol Biol. 2007 Nov 23;374(2):322-33. Epub 2007 Sep 20.PMID: 17936300 [PubMed - indexed for MEDLINE]

Finely orchestrated movements: evolution of the ribosomal RNA genes.
Eickbush TH, Eickbush DG.Genetics. 2007 Feb;175(2):477-85. Review.PMID: 17322354 [PubMed - indexed for MEDLINE]

RNA from the 5′ end of the R2 retrotransposon controls R2 protein binding to and cleavage of its DNA target site
. Christensen, S.M., J.Ye,, and T.H. Eichbush. 2006. . PNAS PMID: 17105809 [PubMed - indexed for MEDLINE]

Chromatin structure and transcription of the R1- and R2-inserted rRNA genes of Drosophila melanogaste
r. Ye J, Eickbush TH.Mol Cell Biol. 2006 Dec;26(23):8781-90. Epub 2006 Sep 25.PMID: 17000772 [PubMed - indexed for MEDLINE]

Role of the Bombyx mori R2 element N-terminal domain in the target-primed reverse transcription (TPRT) reaction.
 Christensen, S.M., A. Bibillo and T.H. Eickbush. 2005. Nucleic Acids Res. 33(20):6461-8. (PubMed)

Monitoring the mode and tempo of concerted evolution in the Drosophila melanogaster rDNA locus.
 Averbeck, K.T. and T.H. Eickbush. 2005.  Genetics 171:1837-46.  (PubMed)


Characterization of active R2 retrotransposition in the rDNA locus of Drosophila simulans.
 Zhang, X. and T.H. Eickbush. 2005.  Genetics 170:195-205. (PubMed)

R2 target primed reverse transcription: ordered cleavage and polymerization steps by protein subunits asymmetrically bound to the target DNA. Christensen, S.M. and T.H. Eickbush. 2005.  Mol. Cell. Biol. 25:6617-6628.  (PubMed)

Competition between R1 and R2 retrotransposable elements in the 28S rRNA genes of insects. Ye, J., C.E. Perez-Gonzalez, D.G. Eickbush and T.H. Eickbush. 2005.  Cytogenet. Genome Res. 110:299-306.  (PubMed)

Secondary Structure models of the 3′ untranslated regions of diverse R2 RNAs. Ruschak, A.M., D.H. Mathews, A. Bibillo, S.L. Spinelli, J.L. Childs, T.H. Eickbush and D.H. Turner. 2004.  RNA 10:978-987.  (PubMed)

Footprint of the R2Bm protein on its target site before and after cleavage in the presence and absence of RNA. Christensen, S. and Eickbush, T. H. 2004. J. Mol. Biol. 336:1035-1045. (PubMed)

End-to-end template jumping by the reverse transcriptase encoded by the R2 retrotransposon. Bibillo, A. and T.H. Eickbush. 2004.  J. Biol. Chem. 279:14945-14953.  (PubMed)

R1 and R2 retrotransposition and deletion in the rDNA loci on the X and Y chromosomes of Drosophila melanogaster. Perez-Gonzalez, C.E., W.D. Burke and T.H. Eickbush. 2003. Genetics 165:675-685.  (PubMed)

R5 retrotransposons insert into a family of infrequently transcribed 28S rRNA genes of planaria. Burke, W.D., D. Singh and T.H. Eickbush. 2003.  Mol. Biol. Evol. 20:1260-1270.  (PubMed)

Transcription of endogenous and exogenous R2 elements in the rRNA gene locus of Drosophila melanogaster. Eickbush, D.G. and T.H. Eickbush. 2003.  Mol. Cell Biol. 23:3825-3836.  (PubMed)

R2 retrotransposition on assembled nucleosomes depends upon the translational position of the target site. Ye, J., Yang, Z, Hayes, J. J. and Eickbush, T. H. 2002.  EMBO J. 21: 6853-6864. (PubMed)

Rates of R1 and R2 retrotransposition and elimination from the rDNA locus of Drosophila melanogaster. Perez-Gonzalez, C. E. and Eickbush, T. H. 2002. Genetics 162: 799-811. (PubMed) 

High processivity of the reverse transcriptase from a non-Long Terminal repeat retrotransposon. Bibillo, A. and Eickbush, T. H. 2002.  J. Biol. Chem. 277: 34836-34845. (PubMed)

Fruit flies and humans respond differently to retrotransposons. Eickbush, T. H. and Furano A. V. 2002.  Current Opinion in Genetics & Development 12: 669-674.  (PubMed)

Repair by retrotransposition. Eickbush, T. H. 2002.  Nature Genetics 31:126-127. (PubMed)

Ancient lineages of non-LTR retrotransposons in the primitive eukaryote, Giardia lamblia. Burke, W. D, Malik, H. S., Rich, S. M and Eickbush, T. H. 2002.  Mol. Biol. Evol. 19: 619-630. (PubMed)

The reverse transcriptase of the R2 non-LTR retrotransposon: Continuous Synthesis of cDNA on Non-Continuous RNA Templates. Bibillo, A. and Eickbush, T. H. 2002.  J. Mol. Biol. 316:459-473. (PubMed)

Evolution of retrotransposons. Eickbush, T.H. and Malik, H. S. 2002.  pp. 1111-1144. In Mobile DNA II, N. Craig, R. Craigie, M. Gellert, and A. Lambowitz, eds. American Society of Microbiology Press. Washington D.C.

R2 and Related Site-specific non-LTR Retrotransposons. Eickbush, T.H. 2002.  pp. 813-835. In Mobile DNA II, N. Craig, R. Craigie, M. Gellert, and A. Lambowitz, eds. American Society of Microbiology Press. Washington D.C.

Phylogenetic analysis of Ribonuclease H domains suggests a late, chimeric origin of LTR retrotransposable elements and retroviruses. Malik, H.S. and Eickbush, T. H. 2001. Genome Research 11:1187-1197.  (PubMed)

Dynamics of R1 and R2 Elements in the rDNA locus of Drosophila. Perez-Gonzalez, C. E. and Eickbush, T. H. 2001.  Genetics 158:1557-1567. (PubMed)

A 10 kilodalton domain in the Ty3 gag-pol3p between PR and RT is dispensable for Ty3 transposition. Claypool, J. A., Malik, H. S., Eickbush, T. H. and Sandmeyer, S. B. 2001.  J. Virol. 75:1557-1560.  (PubMed)

Multiple lineages of R1 retrotransposable elements can coexist in the rDNA loci of Drosophila. Gentile, K., Burke, W. D. Lathe, W.C. and Eickbush, T.H. 2001. Mol. Biol. Evol. 18: 235-245. (PubMed)

Poised for contagion: evolutionary origins of the infectious abilities of insect errantiviruses and nematode retroviruses. Malik, H. S., Henikoff, S., and Eickbush, T. H. 2000.  2000. Genome Research 10: 1307-1318. (PubMed)

Putative telomerase catalytic subunits from Giardia lamblia and Caenorhabditis elegans. Malik, H.S. Burke, W. D. and Eickbush, T. H. 2000.  Gene 251:101-108. (PubMed)

 Introns gain ground. Eickbush, T.H. 2000. Nature 404:940-943.  (PubMed)

NeSL-1, an ancient lineage of site-specific non-LTR retrotransposons from Caenorhabditis elegans. Malik, H.S. and Eickbush, T. H. 2000.  Genetics 154: 193-203. (PubMed)

Integration of Bombyx mori R2 sequences into the 28S ribosomal DNA loci of Drosophila melanogaster. Eickbush D.G., Luan, D.D., and Eickbush, T. H. 2000.  Mol. Cell. Biol. 20:213-223. (PubMed)

Identification of the endonuclease domain encoded by R2 and other site-specific non-long terminal repeat retrotransposable elements. Yang, J., Malik, H. S., and Eickbush, T. H. 1999.  Proc. Natl. Acad. Sci. USA 96: 7847-7852. (PubMed))

The age and evolution of non-LTR retrotransposons. Malik, H. S., Burke, W. D., and Eickbush, T. H. 1999.  Mol. Biol. Evol. 16: 793-805. (PubMed)

The domain structure and retrotransposition mechanism of R2 elements are conserved throughout arthropods. Burke, W. D., Malik, H. S., Jones, J. P., and Eickbush, T. H. 1999. Mol. Biol. Evol. 16: 502-11.  (PubMed)

Modular evolution of the integrase domain in the Ty3/Gypsy class of LTR-retrotransposons. Malik, H.S., and Eickbush, T.H. 1999.  J. Virology. 73: 5186-5190. (PubMed)

 Exon shuffling in Retrospect. Eickbush, T.H. 1999. Science 283: 1465-1467. (PubMed)

 Mobile introns : Retrohoming by complete reverse splicing. Eickbush, T.H. 1999. Curr. Biol. 9 : R11-R14. (PubMed)

Conserved features at the 5′ end of Drosophila R2 retrotransposable elements: implications for transcription and translation. George, J.A. and Eickbush, T.H. 1999.  Insect Mol. Biol. 8: 3-10. (PubMed)

Retrotransposable elements R1 and R2 in the rDNA units of Drosophila mercatorum:abnormal abdomen revisited. Malik, H.S. and Eickbush, T.H. 1999.  Genetics 151 (2) : 653-665. (PubMed)

Metaviridae, in Virus Taxonomy: ICTV VIIth Report, edited by F. A. Murphy. Boeke, J.D., Eickbush, T. H., Sandmeyer, S.B. and Voytas, D. F. 1999.  Springer-Verlag, New York.Boeke, J.D.,

Pseudoviridae, in Virus Taxonomy: ICTV VIIth Report, edited by F. A. Murphy. Eickbush, T. H., Sandmeyer, S.B. and Voytas, D. F. 1999.  Springer-Verlag, New York.

The RTE class of non-LTR retrotransposons is widely distributed in animals and is the origin of many SINE elements. Malik, H. S. and Eickbush, T. H. 1998.  Mol. Biol. Evol. 15 (9) : 1123-1134. (PubMed)

RNA-induced changes in the activity of the endonuclease encoded by the R2 retrotransposable element. Yang, J. and Eickbush, T. H. 1998.  Mol. Cell. Biol. 18(16) : 3455-3465. (PubMed)

Are retrotransposons long-term hitchhikers? Burke, W.D., Malik, H. S., Lathe III, W. C. and Eickbush, T.H. 1998.  Nature 392(6672) : 141-142. (PubMed)

Evolutionary specialization of the nuclear targeting apparatus. Malik, H. S., Eickbush, T. H. and Goldfarb, D. S. 1997.  Proc. Natl. Acad. Sci. USA 94: 13738-13742. (PubMed)

A single lineage of R2 retrotransposable elements is an active, evolutionarily stable component of the Drosophila rDNA locus. Lathe III, W.C. and Eickbush, T.H. 1997.  Mol. Biol. Evol. 14(12) : 1232-1241. (PubMed)

Telomerase and retrotransposons: which came first? Eickbush, T.H. 1997.  Science 277(5328) : 911-912. (PubMed))

Evolution of R1 and R2 in the rDNA units of the genus Drosophila Eickbush, T.H., Burke, W.D., Eickbush, D.G. and Lathe III, W.C. 1997.  Genetica 100 (1-3) : 49-61. (PubMed)

Secondary structure model of the RNA recognized by the reverse transcriptase from the R2 retrotransposable element. Mathews, D.H., Banerjee, A.R., Luan, D.D., Eickbush, T.H. and Turner, D.H. 1997.  RNA 3(1) : 1-16. (PubMed)

Downstream 28S gene sequences on the RNA template affect the choice of primer and the accuracy of initiation by the R2 reverse transcriptase. Luan, D.D. and Eickbush, T.H. 1996.  Mol. Cell. Biol. 16(9) : 4726-4734. (PubMed)

Analysis of the 5′ junctions of R2 insertions with the 28S gene: implications for non-LTR retrotransposition. George, J.A., Burke, W.D. and Eickbush, T.H. 1996.  Genetics 142(3) : 853-863. (PubMed)

R4, a non-LTR retrotransposon specific to the large subunit rRNA gene of nematodes. Burke, W.D., Müller, F. and Eickbush, T.H. 1995.  Nucleic Acids Res. 23(22) : 4628-4634.  (PubMed))

Evolutionary stability of the R1 retrotransposable element in the genus Drosophila. Lathe, W.C., Burke, W.D. and Eickbush, T.H. 1995.  Mol. Biol. Evol. 12(6) :1094-1105. (PubMed)

RNA template requirements for target DNA-primed reverse transcription by the R2 retrotransposable element. Luan, D.D. and Eickbush, T.H. 1995.  Mol. Cell. Biol. 15(7) : 3882-3891. (PubMed))

R1 and R2 retrotransposable elements of Drosophila evolve at rates similar to those of nuclear genes. Eickbush, D.G., Lathe, W.D., Francino, M.P. and Eickbush, T.H. 1995.  Genetics 139(2) : 685-695. (PubMed)

Vertical transmission of the retrotransposable elements R1 and R2 during the evolution of the Drosophila melanogaster species subgroup. Eickbush, D.G. and Eickbush, T.H. 1995.  Genetics 139(2) : 671-684. (PubMed)

Mobile elements of Lepidopteran genomes.  Eickbush, T.H.  1995. In The Molecular Genetics and Molecular Biology of Lepidoptera, M.R. Goldsmith and A.S. Wilkins, eds. Cambridge University Press. pp. 77-106.

Chorion genes: molecular models of evolution. Eickbush, T.H., and Izzo, J.A.  1995. The Molecular Genetics and Molecular Biology of Lepidoptera, M.R. Goldsmith and A.S. Wilkins, eds. Cambridge University Press. pp. 217-248.

Origin and evolutionary relationship of retroelements. Eickbush, T.H. 1994.  Evolutionary Biology of Viruses, S.S. Morse ed., Raven Press. pp 121-157.

Pao, a highly divergent retrotransposable element from Bombyx mori containing long terminal repeats with tandem copies of the putative R region. Xiong, Y., Burke, W.D., and Eickbush, T.E. 1993.  Nucleic Acids Res. 21(9) : 2117-2123. (PubMed))

Dong, a non-long terminal repeat (non-LTR) retrotransposable element from Bombyx mori. Xiong, Y. and Eickbush, T.H. 1993.  Nucleic Acids Res. 21(5) : 1318. (PubMed)

Reverse transcription of R2Bm RNA is primed by a nick at the chromosomal target site: a mechanism for non-LTR retrotransposition. Luan, D., Korman, M.H., Jakubczak, J.L. and Eickbush, T.H. 1993.  Cell 72(4) : 595-605. (PubMed)

Sequence relationship of retrotransposable elements R1 and R2 within and between divergent insect species. Burke, W.D., Eickbush, D.G., Xiong, Y., Jakubczak, J.L. and Eickbush, T.H. 1993.  Mol. Biol. Evol 10(1) : 163-185. (PubMed) 

Molecular characterization of repetitive DNA sequences from a B chromosome. Eickbush, D.G., Eickbush, T.H. and Werren, J.H. 1992.  Chromosoma 101(9) : 575-590. (PubMed)

Organization and evolution of the human epidermal keratinocyte transglutaminase I gene. Polakowska, R.R., Eickbush, T.H., Falciano, V., Razvi, F. and Goldsmith, L.A. 1992.  Proc. Natl. Acad. Sci. 89(10) : 4476-4480. (PubMed)

Transposing without ends: the non-LTR retrotransposable elements. Eickbush, T.H. 1992.  New Biologist 4(5) : 430-440. (PubMed))

Turnover of R1 (Type I) and R2 (Type II) retrotransposable elements in the ribosomal DNA of Drosophila melanogaster. Jakubczak, J.L., Zenni, M.K., Woodruff, R.C. and Eickbush, T.H. 1992.  Genetics 131(1) :129-142. (PubMed))

Retrotransposable elements R1 and R2 interrupt the rDNA genes of most insects. Jakubczak, J., Burke, W.D. and Eickbush, T.H. 1991.  Proc. Natl. Acad. Sci. 88(8) : 3295-3299. (PubMed)

Origin and evolution of retroelements based upon their reverse transcriptase sequences. Xiong, Y. and Eickbush, T.H. 1990.  EMBO J. 9(10) : 3353-3362.  (PubMed)