John Templeton Foundation awards $836,000 for genomics project, with Drs. Karl Cottenie and Ryan Gregory as co-PIs

The John Templeton Foundation has awarded an $836,000 grant for a project that takes a novel approach to the study of genomics. Transposable Genetic Elements as Ecological Agents is led by Dr. Stefan Linquist from the Department of Philosophy, in collaboration with Drs. Karl Cottenie and Ryan Gregory from Integrative Biology. 

Transposable Genetic Elements as Ecological Agents

Instead of classifying DNA as either functional (if it encodes information for building an organism) or junk (if it has no informational relevance for the organism), the researchers view the genome as a miniature ecosystem. 

This idea makes sense once you appreciate the roles of transposable elements (TEs) in generating most of the DNA in plant and animal cells. Also called jumping genes, TEs are independent strands of DNA capable of self-replicating and inserting into new chromosomal locations. In this respect, they behave much like organisms. For instance, TEs “invade” a host genome in similar fashion to an introduced species radiating throughout a new habitat. In addition, particular families of TE are known to inhabit specific genomic regions just as particular species inhabit niches.

Our proposal is to borrow concepts, models, and methods from the science of ecology to explain patterns in the abundance and distribution of TEs among genomes. This project brings together science and philosophy.  Scientifically, we will be analyzing genomic data using ecological tools (a novel approach in itself) while also constructing computer simulations of TE behaviour. Philosophically, we will be exploring the conceptual foundations of genomics and ecology, outlining what it means to think of the genome as a literal ecosystem and the implications for biomedical science.

This approach could revolutionize the study of genomics. For instance, it will shed light on the so called “C-value paradox”: why are some genomes are so much larger than others? Genome-level ecology will also supply new functional categories for classifying DNA. For example, our research group has already identified the potential for TEs to function as ecosystem engineers. Other possible roles for TES include keystone elements, mutualists, and competitive exclusion among TE families.

This enriched conceptual framework will facilitate new research avenues within science of genomics, enabling this discipline to transcend the unhelpful dichotomy between functional versus junk DNA.