31. Oct. 2023

The idea of creating a user-friendly tool for biologists to discover novel non-coding RNAs (ncRNA) was born in Agata Kilar’s head, a researcher in Jiří Fajkus research group based at CEITEC Masaryk University in Brno. She developed GERONIMO, a bioinformatics tool that simplifies the identification of ncRNA homologs (genes inherited in two species from a common ancestor) across a wide range of organisms. It enables researchers to uncover previously unknown ncRNAs, and can potentially lead to significant discoveries in various fields, including medicine and genetics. Agata continues her scientific career at the Harvard University in a team developing computational methods for RNA structure prediction.

Non-coding RNAs (ncRNA), pieces of genetic information that do not control protein production but play a role in various biological processes, have diverse sequences and structures that present significant challenges for researchers. Classes of ncRNAs significantly vary in terms of sequence length, functions, biological occurrence, structure, and distribution across species. A notable challenging example of ncRNA with a highly heterogeneous sequence is telomerase RNA (TR), which provides the template for DNA synthesis at the ends of chromosomes – the telomere that play a role in cellular ageing or development of serious human diseases including cancer.

Unlike conserved genes (genes that have remained unchanged through evolution), ncRNAs often exhibit low sequence conservation due to genetic variations. This complexity has made it difficult to identify them using traditional tools. GERONIMO (GEnomic RNA hOmology aNd evolutIonary MOdeling), an innovative tool, allows researchers, including biologists without a background in bioinformatics, to conduct searches on various evolutionary scales. This democratization of advanced computational tools empowers a broader range of scientists to engage in cutting-edge genomic research.

The scalability of GERONIMO is noteworthy. The possibility to scale GERONIMO on many processors and perform more homology sequences searches simultaneously accelerates the pace of scientific discovery, enabling researchers to explore larger datasets and test hypotheses more efficiently. Besides, it allows to process an extension of an experiment that has already been performed in the past without having to re-process the entire experiment.

“The impact of GERONIMO extends far beyond telomerase research. By enabling researchers to explore both narrow and broad evolutionary scales, the tool opens avenues for studying a wide range of biological phenomena. Scientists can utilize GERONIMO to investigate various RNA families, regulatory elements, and evolutionary relationships, potentially leading to numerous ground-breaking discoveries in genetics, medicine, and ecology”, says Agata Kilar.

Although GERONIMO was primarily an independent initiative, the supervision and consultancy provided by Jiří and Petr Fajkus highlight the importance of teamwork and mentorship in scientific research leading to a successful development of such a powerful bioinformatics tool that accelerates scientific discovery, allowing researchers to explore larger datasets and test hypotheses more efficiently.

The development of GERONIMO was made possible thanks to the Visegrad Fund, which awarded Agata Kilar a scholarship for post-master students. This study was a part of GAČR-EXPRO project, a collaborative project between Masaryk University and the Institute of Biophysics, CAS. It has been published in GigaScience Journal.