Department of Biology

Research Overview

The Eickbush laboratory studies the molecular biology and evolution of two retrotransposable elements, R1 and R2. These elements insert specifically into the 28S rRNA genes of their arthropod hosts. Studies of the integration reaction of R2 has revealed a new retrotransposition mechanism, in which the element's RNA transcript is directly reverse transcribed into the DNA target site (see Figure). This Target Primed Reverse Transcription (TPRT) mechanism is believed to be used by all non-LTR retrotransposons, and has similarity to the mechanism used by group II introns and telomerase. Non-LTR retrotransposable elements are arguably the most abundant genomic parasites in eukaryotes and appear responsible for much of the useless DNA occupying the genomes. For example, the TPRT mechanism has recently been estimated to account for 40% of the human genome. Current efforts focus on characterizing the various enzymatic steps of the TPRT reaction, as well as the protein:DNA, protein:RNA and protein:protein interactions.

R1 and R2 elements are present in the rDNA units of every lineage of arthropods analyzed to date. Phylogenetic analysis suggest that this broad distribution is because these elements have been vertically propagated since the origin of the arthropod phylum (est. 600 million years). Current research is focused on population genetic studies of the concerted evolution of the rDNA loci themselves. These studies involve the analysis of variation within populations, the utilization of the sequence data generated by genome sequencing projects, and the analysis of the changes that occur in laboratory strains over time.

Finally, developmental genetic studies of the control over R1 and R2 expression. We have identified stable Drosophila lines with active or only inactive R2 elements which are allowing us to conduct developmental genetic studies of the control over R2 expression. Control over the rates of RNA transcription and retrotransposition appears to lie predominantly within the rDNA locus itself. When a chromosome with an rDNA locus containing "active" R2 elements is paired with a chromosome with a rDNA locus containing "inactive" R2 elements (i.e. heterozygous flies), only the rDNA locus with the inactive elements is expressed. This regulation appears similar to a phenomenon observed in both plants and animals and is referred to as nucleolar dominance. We are currently attempting to identify the epigenetic factors that are common to those rDNA loci that contain active R2 elements but not found in those loci with inactive elements. The chromatin structure of the units and/or the distribution of inserted units in the locus appear to be important factors rather than the number of R2 elements within the locus.

Selected Publications

• Kurzynska-Kokorniak, A., V. Jamburuthugoda, A. Bibillo and T.H. Eickbush. 2007. DNA-directed DNA polymerase and strand displacement activity of the reverse transcriptase encoded by the R2 retrotransposon. J. Mol. Biol. (in press).
• Eickbush, T.H. and D.G. Eickbush, D.G. 2007. Finely orchestrated movements: evolution of the ribosomal RNA genes. Genetics. 175: 477-485.
• Ye, J. and T.H. Eickbush. 2006. Chromatin structure and transcription of the R1- and R2-inserted rRNA genes of Drosophila melanogaster. Mol Cell Biol. 23: 8781-8790.
• Christensen, S.M., J. Ye and T.H. Eickbush. 2006. RNA from the 5' end of the R2 retrotransposon controls R2 protein binding to and cleavage of its DNA target site. Proc. Natl. Acad. Sci. USA, 104: 17602-17607.
• Christensen, S.M., A. Bibillo and T.H. Eickbush. 2005. Role of the R2 element amino-terminal domain in the target-primed reverse transcription reaction. Nucleic Acids Res. 33: 6461-6468.
• Averbeck, K.T. and T.H. Eickbush. 2005. Monitoring the mode and tempo of concerted evolution in the Drosophila melanogaster rDNA locus. Genetics 171: 1837-1846.
• Zhang, X. and Eickbush, T.H.. 2005. Characterization of active R2 retrotransposition in the rDNA locus of Drosophila simulans. Genetics 170: 195-205.
• Christensen, S.M. and T.H. Eickbush. 2005. R2 target primed reverse transcription: ordered cleavage and polymerization steps by protein subunits asymmetrically bound to the target DNA. Mol. Cell. Biol. 25: 6617-6628.
• Ye, J., C.E. Perez-Gonzalez, D.G. Eickbush and T.H. Eickbush. 2005. Competition between R1 and R2 retrotransposable elements in the 28S rRNA genes of insects. Cytogenetic Genome Res. 110: 299-306.
• Ruschak, A.M., D.H. Mathews, A. Bibillo, S.L. Spinelli, J.L. Childs, T.H. Eickbush and D.H. Turne. 2004. Secondary Structure models of the 3' untranslated regions of diverse R2 RNAs. RNA 10: 978-987.
• Christensen, S. and Eickbush, T. H.. 2004. Footprint of the R2Bm protein on its target site before and after cleavage in the presence and absence of RNA. J. Mol. Biol. 336: 1035-1045.
• Bibillo, A. and T.H. Eickbush. 2004. End-to-end template jumping by the reverse transcriptase encoded by the R2 retrotransposon. J. Biol. Chem. 279: 14945-14953.
• Perez-Gonzalez, C.E., W.D. Burke and T.H. Eickbush. 2003. R1 and R2 retrotransposition and deletion in the rDNA loci on the X and Y chromosomes of Drosophila melanogaster. Genetics 165: 675-685.
• Burke, W.D., D. Singh and T.H. Eickbush. 2003. R5 retrotransposons insert into a family of infrequently transcribed 28S rRNA genes of planaria. Mol. Biol. Evol. 20: 1260-1270.
• Eickush, D.G. and T.H. Eickbush. 2003. Transcription of endogenous and exogenous R2 elements in the rRNA gene locus of Drosophila melanogaster. Mol. Biol. Evol. 23: 3825-3836.
• Ye, J., Z. Yang, J.J. Hayes and T.H. Eickbush. 2002. R2 retrotransposition on assembled nucleosomes depends on the translational position of the target site. EMBO J. 21: 6853-6864.
• Perez-Gonzalez, C.E. and T.H. Eickbush. 2002. Rates of R1 and R2 retrotransposition and elimination from the rDNA locus of Drosophila melanogaster. Genetics 162: 799-811.
• Bibillo, A. and T.H. Eickbush. 2002. High processivity of the reverse transcriptase from a non-long terminal repeat retrotransposon. J. Biol. Chem. 277: 34836-34845.
• Eickbush, T.H. and A.V. Furano. 2002. Fruit flies and humans respond differently to retrotransposons. Curr. Opin. Genet. Dev. 12: 669-674.
• Eickbush, T.H.. 2002. Repair by retrotransposition. Nat. Genet. 31: 126-127.
• Burke, W.D., H.S. Malik, S.M. Rich and T.H. Eickbush. 2002. Ancient lineages of non-LTR retrotransposons in the primitive eukaryote, Giardia lamblia. Mol. Biol. Evol. 19: 619-630.
• Bibillo, A. and T.H. Eickbush. 2002. The reverse transcriptase of the R2 non-LTR retrotransposon: continuous synthesis of cDNA on non-continuous RNA templates. J. Mol. Biol. 316: 459-473.