Garfinkel

Our research concerns the mechanism and consequences of Ty1 retrotransposition in the budding yeast Saccharomyces. The Ty1 life cycle resembles that of retroviruses except transposition is not infectious. Ty1 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 Ty1 reverse transcriptase and for protein synthesis. Ty1 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 Ty1 cDNA and integrase transits the nuclear membrane and mediates integration at preferred chromosomal locations.



Of the several groups of Ty retrotransposons present in budding yeast, 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. We discovered a truncated form of  the Gag capsid protein that inhibits VLP assembly and function in a dose dependent manner. This self-encoded restriction factor expands the repertoire of defense proteins targeting capsid.

 

Information gained from studying Ty elements has contributed to several areas of research. For example, understanding 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. Chromosomal rearrangements and insertional events involving these elements have been implicated in human disease and cancer. 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. Interestingly, recent work shows that the neuronal gene Arc encodes a domesticated Ty3-like capsid protein that facilitates synaptic communication by transmission of Arc VLPs containing Arc and perhaps additional cellular transcripts.

More information on our work can be found at Google Scholar (https://scholar.google.com/citations?user=cNCwDoIAAAAJ&hl=en) or Pubmed (https://www.ncbi.nlm.nih.gov/pubmed/?term=Garfinkel+dj).