The “dark genome” — including transposons, repetitive DNA sequences, and long non-coding RNAs — accounts for much of mammalian DNA. For many years, these sequences were thought to be mostly inactive or non-functional. More recently, however, scientists have discovered that some of these elements can influence how the genome is organized inside the nucleus and how genes are switched on and off.

These discoveries have raised new questions about the role of the dark genome during the earliest stages of mammalian development, when cells rapidly change identity and developmental potential.

To address these questions, IMBA Group Leader Joanna Jachowicz has been awarded an FWF Principal Investigator Project grant from the Austrian Science Fund (FWF). Together with her team, she will investigate how RNA molecules produced from LINE-1 elements help control gene activity during early mammalian development.

LINE-1 elements are repetitive DNA sequences scattered throughout mammalian genomes that make up almost one fifth of mouse and human DNA. Once considered largely inactive “junk DNA,” LINE-1 elements are now increasingly recognized as important regulators of cellular processes.

To study their function, the Jachowicz lab will combine stem cell biology with advanced genomic and biochemical approaches. Using mouse embryonic stem cells as a model system, the researchers will follow LINE-1 RNAs as cells transition between different developmental states. The team aims to discover how these RNA molecules help organize the genome and influence changes in cell identity.

In the long term, this research could fundamentally reshape how we understand cancer, aging, and other diseases linked to disrupted genome regulation. By uncovering the normal functions of LINE-1 during early development, the project may reveal entirely new strategies to prevent or control its harmful activation in disease.

About the FWF

The Austrian Science Fund (FWF) is Austria's central funding organization for basic research. Stand-alone grants are allocated to fund individual research in the area of non-profit oriented basic research. They are assigned solely based on their high quality, assessed by international referees on a competitive basis.