Protein-DNA interactions of the RLE LINE R2Bm
Abstract
Long interspersed elements (LINEs) are a major group of non-long terminal repeat (non-LTR) retrotransposable elements that are ubiquitous in eukaryotic genomes. These selfish genetic elements influence the structure and function of the host genome. R2 elements are site-specific LINEs that insert at a specific target site in the 28S rRNA genes of the host. R2 elements encode a single open reading frame which makes a multifunctional protein containing reverse transcriptase, DNA endonuclease, and nucleic acid-binding domains. The R2 RNP reverse transcribes its mRNA to DNA at the site of insertion in order to integrate into the host genome. The first half of the integration reaction involves cleavage of the host DNA by the element encoded DNA endonuclease and priming of first strand cDNA by the free 3’-OH generated by the DNA endonuclease, a process called Target Primed Reverse Transcription (TPRT). The second half of the reaction, second strand cleavage and second strand DNA synthesis are accomplished with a second round of DNA cleavage / DNA polymerization events. The N terminal domain of the R2 encoded protein contains from 1-3 zinc fingers and a Myb domain. The first chapter of my thesis briefly reviews what is known about the R2 integration reaction. In chapter 2, I investigate the DNA binding potential of the zinc fingers. In the third chapter, I investigate the sequences of the DNA target required for binding to the R2 protein.