Retrotransposable elements (RTEs) comprise approximately 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 retrotransposition, can be deleterious at multiple levels by causing mutagenesis and genome structural instability, triggering epigenetic changes, and disrupting normal patterns of gene regulation. Numerous single- gene mutations in humans have been documented to result from germline retrotransposition. Organisms have evolved multiple transcriptional and post-transcriptional silencing mechanisms to protect their genomes against RTEs. 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. We have reported that retrotransposition is activated during aging and cellular senescence, and hypothesized that it may represent a hitherto unappreciated molecular aging process. The long-term goal of our research is to determine the impact of retrotransposition on our genomes and transcriptomes during aging. As a first step, our objective in this proposal is to study, using high-throughput DNA and RNA sequencing methods, the mobilization of RTEs during cellular senescence and aging, and their impact on the transcriptome.
In Aim 1 we will perform genome-wide high-throughput DNA sequencing of in senescent cells to determine where new insertions occur and to evaluate whether these events have the potential to exert deleterious effects by disrupting regions of the genome important for cell function. We have evidence that many new insertions likely occur in individual post-mitotic cells after they have ceased dividing. To comprehensively profile the spectrum and frequency of these events we will use single-cell whole genome DNA sequencing.
In Aim 2 we will perform these same studies in the mouse to investigate to what degree different tissues are affected by increased retrotransposition with age.
In Aim 3 we will investigate the effects of RTEs derepression and transposition on the transcriptome of senescent cells and in the aging mouse. Throughout our research plan we will apply interventive methods to modulate RTE activity to investigate the consequences on the landscape of somatic transposition as well as on the physiological function of the cells. Our research will employ innovative state-of-the-art high-throughput sequencing strategies, and we will develop new bioinformatic tools to integrate and validate the output from multiple algorithms. The information obtained will address the question: To what extent is retrotransposition damaging to the genomes of somatic cells in our bodies, and is this a plausible mechanism of aging? The experience gained and tools developed will be highly informative for future studies aimed at examining these processes directly in aging human tissues. Our efforts will also inform us whether proof-of-principle studies using interventions that inhibit retrotransposition should be investigated as potential therapeutics for age-associated diseases.
Retrotransposable element (RTE) DNA sequences are parasitic, mobile, and normally repressed DNA elements that can insert into new genomic positions using a ?copy and paste? mechanism. Recently, it was discovered that retrotransposable elements become active in cellular senescence and aging. The goal of this proposal is to characterize the detrimental consequences of RTE derepression in cellular senescence and to assess whether RTEs may be damaging to the genome of somatic cells during aging.
