Understanding the regulation and impact of transposable elements in Vertebrate health and disease

Project summary
The overarching goal of my lab is to understand understudied mechanisms of genomic regulation, and how
they influence lifelong Vertebrate health and disease. In multi-cellular organisms, diverse cell types are
characterized by specific genomic regulation patterns, and the precise control of these patterns is key not only
for development, but also for cell/tissue homeostasis in adults. Indeed, loss of fine control in genomic regulation
has been linked to disease (e.g. cancer, neurodegeneration) and age-related functional decline. An interesting
and understudied family of genomic elements lies in dormant genetic parasites (e.g. transposons, also called
“jumping genes”). Although transposons can represent up to 80% of some eukaryotic genomes, they remain
critically understudied, since they were historically dismissed as unimportant (i.e. “junk DNA”), and their high
copy numbers and repetitive nature pose unique technical challenges. Consistent with their potential impact in
health and disease, the ability of cells to suppress transposon activity is disrupted with disease and with aging.
In addition, accumulating evidence suggests that many aspects of biology and genomic regulation differ between
males and females, including emerging data suggesting potential sex-dimorphism in transposon activity.
However, how transposable elements are regulated throughout life in healthy somatic tissues and
across biological sexes, and how they influence vertebrate health, remains largely unknown. Thus, we
propose to decipher how transposons are controlled in healthy somatic cells (including in male vs. female cells),
and how loss of that control could influence Vertebrate health and disease. To explore this question, my group
will use a unique combination of ‘omics’ approaches, machine-learning, and experimental validation in animal
models. We use two vertebrate models for their respective strengths: the laboratory mouse (e.g. powerful
genetics, validated antibodies, etc.) and the African turquoise killifish, a naturally short-lived model organism I
have helped develop (e.g. short generation time/lifespan, strain diversity, cost-effectiveness, etc.). First, we will
decipher sex-dimorphic regulation of transposon activity, determining the impact of gonadal hormones vs. sex-
chromosomes on such regulation. Second, we will use functional genomics to identify new regulators of
transposon activity in somatic cells. Finally, we will evaluate the impact of transposon control in key somatic
tissues and across sexes on lifelong vertebrate health using the naturally short-lived African turquoise killifish as
a model. Ultimately, understanding the fine control of transposon in healthy cells will help devise strategies to
prevent their misregulation in disease, by allowing us to maintain youthful and healthy genomic regulation
landscapes.
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Grant Number: 5R35GM142395-05
NIH Institute/Center: NIH
Principal Investigator: Berenice Benayoun