We have learned an enormous amount in the past budget period about the mechanism and biology of one of the major components of the human genome, the LI (LINE) retrotransposon. This remarkable element is responsible, directly or indirectly, for about one third of our genome by weight;its reverse transcriptase ORF (ORF2) is the most abundant ORF in the human genome. Recent gains in understanding how this element works result from technical breakthroughs. We conceived of, developed and exploited a new synthetic retrotransposon that is approximately 200-fold more efficient than a native element. We will use human tissue culture cell, in vitro and in silico systems to analyze the molecular mechanisms by which the LI element replicates and inserts itself into new sites. We will also investigate the mechanism and consequences of a newly discovered expression regulatory phenomenon we discovered in LI, namely that its ORF sequences block transcriptional elongation. In the opposite orientation they lead to premature polyadenylation. These combined effects may affect the expression of many human genes and the responsible insertion polymorphisms may well underlie complex traits such as cancer susceptibility. These hypotheses will be tested. Finally, we are building a transgenic synthetic retrotransposon mouse model that should provide technology for a) making genome wide knockout mutation collections and b) discovery of tumor suppressor genes in leukemia and other cancers.
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