Genomic time machine: Revealing DNA secrets

Fresh insights into human evolution and health.

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Recent research suggests transposable elements (TEs) are crucial for evolution, contributing coding and non-coding sequences to genomes. However, identifying TE-derived functional elements has been limited to intact sequences within individual species. A recent study introduces an innovative method, probing ancestral genomes from hundreds of species to discover previously unannotated degenerate TEs (degTEs).

EPFL researchers present this novel approach, unveiling fragments of our genetic blueprint from ancient genetic parasites. This provides valuable insights into human evolution and health.

Half of human DNA consists of transposable elements (TEs), but these elements change over time due to movement and aging, making it challenging for scientists to recognize their original form. TEs undergo “degeneration,” becoming less identifiable over time, complicating tracking in our genetic code.

In a recent study by Didier Trono’s group at EPFL, researchers enhanced TE detection in the human genome. They achieved this by utilizing reconstructed ancestral genomes from different species, enabling the identification of previously unnoticed degenerate TEs in the human genome.

Scientists employed a genomic “time machine” by utilizing a database of reconstructed ancestral genomes from various species. This database served as a comparison tool with the human genome, enabling the identification of transposable elements (TEs) that have become degenerate over millions of years. This approach, comparing the human genome with ancestral genomes, allowed scientists to discover more TEs than previously known.

The findings indicated that a larger portion of our DNA is contributed by TEs than previously recognized. Moreover, the newly uncovered TE sequences were shown to perform the same regulatory roles as their already identified counterparts, demonstrating their significance in genetic regulation.

Didier Trono said“The potential applications are vast: Better understanding TEs and their regulators could lead to insights into human diseases, many of which are believed to be influenced by genetic factors. First and foremost, cancer, but also auto-immune and metabolic disorders, and more generally our body’s response to environmental stresses and aging.”

Journal Reference:

  1. Wayo Matsushima, Evarist Planet, Didier Trono. Ancestral genome reconstruction enhances transposable element annotation by identifying degenerate integrants. Cell Genomics 30 January 2024. DOI: 10.1016/j.xgen.2024.100497
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