Garfinkel_Lab_Life Cycle.jpg
Our research concerns the mechanism of Ty1 element retrotransposition and copy number control in the budding yeast Saccharomyces. Ty elements comprise five related families of long terminal repeat (LTR) retrotransposons that transpose through an RNA intermediate. The Ty life cycle resembles that of retroviruses except Ty transposition is not infectious. Ty element GAG and POL genes encode the structural and enzymatic proteins required for retrotransposition. The retrotransposon is transcribed from LTR to LTR to form a genome-length RNA, which is the template for reverse transcription by Ty reverse transcriptase and for protein synthesis. Ty RNA and proteins accumulate in cytoplasmic foci termed retrosomes, which mark the sites for assembly of virus-like particles (VLPs). Reverse transcription takes place within VLPs following protein maturation by an element-encoded protease. A preintegration complex minimally containing Ty cDNA and integrase transits the nuclear membrane and mediates integration at preferred chromosomal locations.

We study Ty1 because these elements are competent for retrotransposition, can act as insertional mutagens and take part in genome rearrangements. Despite the synthesis of a highly abundant mRNA and the presence of retrosomes, there is a low level of mature Ty1 proteins, VLPs and transposition events. S. cerevisiae and its closest relative S. paradoxus also lack innate defense pathways used in other eukaryotes to limit retroelement propagation. Therefore, we are particularly interested in discovering novel host and element-based pathways responsible for modulating Ty1 retrotransposition.
 
Information gained from studying Ty elements has contributed to several areas of research. For example, understanding the mechanism and consequences of Ty retrotransposition can be applied to retroelements in other organisms, including humans, because these elements are evolutionarily related. Almost 50% of the human genome is comprised of retroelement sequences, such as LINE, SINE and endogenous retroviruses because utilizing RNA as a replication template can give rise to massive amplifications if left unchecked. Indeed, there are at least 50-fold more transposable element sequences than protein coding sequences in our genome. Chromosomal rearrangements and insertional events involving these elements have been implicated in human disease and cancer. In addition, since the retrotransposon and retroviral replication cycles are closely related, the process of retrotransposition can be compared and contrasted with propagation of retroviruses such as HIV to help illuminate areas of research more difficult to approach in humans.