Ancient genomes unearth degenerate transposable elements in human DNA

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The human genome, a complex tapestry of genetic information for life, has proven to be a treasure trove of unique traits. They include segments of DNA that can “jump around” and move between genomes, known as “transposable elements” (TEs).

Because they change their location within the genome, TEs can potentially cause mutations and alter the genetic profile of cells, but they are also the master orchestrators of our genome’s organization and expression. For example, TEs contribute to the creation of regulatory elements, transcription factor binding sites, and chimeric transcripts—the genetic sequence created when two different genes or parts of a genome join together to form a new, hybrid RNA molecule.

In keeping with their functional importance, TEs have been recognized as half of human DNA. However, as they move and age, TEs undergo changes that mask their true form. Over time, TEs “decline” and become less recognized, making it harder for scientists to identify and track them in our genetic blueprint.

In a new study, researchers from EPFL’s Didier Trono group have found a way to improve TE detection in the human genome by using reconstructed ancestral genomes from different species, allowing them to identify previously undetected degenerate TEs in the human genome. .. The research is published Cell Genomics.

Scientists have used a database of reconstructed ancestral genomes from a wide variety of species as a genomic “time machine.” By comparing the human genome with the reconstructed ancestral genome, they were able to subsequently identify TEs that, over millions of years, had become decayed (worn out) in humans.

This comparison allows them to identify (“annotated”) TEs that may have been missed in previous studies that only used data from the human genome.

Using this approach, scientists uncovered a much greater number of TEs than previously known, adding significantly to the portion of our DNA contributed by TEs. Moreover, they could show that these newly discovered TE sequences played the same regulatory role as their more recent, already identified relatives.

The potential applications are vast.

A better understanding of TEs and their regulators may lead to insights into human diseases, many of which are thought 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 stress and aging.”


Didier Trono at EPFL

Source:

Journal Reference:

Matsushima, W., etc. (2024). Ancestral genome reconstruction enhances annotation of transposable elements by identifying degraded integrants. Cell Genomics. doi.org/10.1016/j.xgen.2024.100497.



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