(PROJECT 1) Retrotransposable elements (RTEs) comprise ~45% of the human genome. RTEs are mobile DNA elements that can insert into new genomic positions using a copy and paste mechanism. This process, termed retro- transposition, can be deleterious at multiple levels by causing mutagenesis and genome structural instability, triggering epigenetic changes, and disrupting normal patterns of gene regulation. Organisms have evolved multiple transcriptional and post-transcriptional silencing mechanisms to protect their genomes. Until recently RTEs were thought to be silent in the soma, however, new evidence points to activity in the brain and in cancer cells. Indeed, initial indications are that somatic retrotransposition is much more frequent than previously anticipated. Our group has reported that retrotransposition is activated during aging and cellular senescence, and hypothesized that it may represent a hitherto unappreciated molecular aging process. These findings however raise important new questions: what is the magnitude of the 'retrotransposition problem', and to what extent is this process damaging to our somatic cells? What are the mechanisms that hold RTEs in check in somatic tissues, and how do they fail with age? Our lack of knowledge in these areas is a key barrier to under- standing the role of RTEs in aging and disease. To break new ground in these efforts our research seeks to elucidate what we broadly refer to as 'the landscape of somatic retrotransposition'.
In Aim 1 we will perform a genome-wide quantitative analysis of novel transpositions. The frequency of these events in the genomes of senescent or aged cells, their structures, and their locations are completely unknown. With Jef Boeke and Core B we will apply high-throughput DNA sequencing, including TIP-seq and single-cell whole genome sequencing to comprehensively profile novel transposition events. As an independent method we will use retrotransposon reporters.
Aim 2 is based on our preliminary data that occupancy of pRb on the L1 promoter decreases in senescent human cells and aging mouse tissues, that overexpression of pRb antagonizes the activation of L1 in senescent cells, and knockdown in normal cells promotes L1 activation. We hypothesize that pRb, a known regulator heterochromatin, represses L1 in normal cells and that this mechanism fails during senescence and aging. We will therefore examine the composition of pRb-containing complexes and their interaction with L1s, observe their behavior during cellular senescence and mouse aging, and perturb specific components to test effects on L1 activity.
In Aim 3 we will modulate RTE activity using genetic and pharmaceutical interventions and investigate the consequences on cellular function. We will use engineered regulatable L1 elements to drive increased retrotransposition activity, develop shRNA or CRISPR interventions to block the transcription of endogenous L1s, and treat cells and mice with reverse transcriptase inhibitors to determine whether age- associated phenotypes can be ameliorated. Our long-term goal is to assess the extent to which RTEs contribute to aging or age-associated disorders, and hence are potential targets for therapeutic interventions.
