New Software Tool Helps Scientists Design and Analyze Gene Regulation

A research team led by Prof. Stein Aerts from VIB (Vlaams Instituut voor Biotechnologie) and KU Leuven (Katholieke Universiteit Leuven) has developed a new software tool that makes it easier to study how genes are switched on and off in different cell types. The tool, called CREsted, aims to simplify the analysis and design of gene regulatory elements, known as enhancers, which control when and where genes are active.

CREsted combines several steps, including data processing, model training, interpretation, and DNA sequence design, into a single, streamlined workflow. “CREsted allows researchers to systematically study enhancer logic across biological systems, starting from cell-by-cell maps of accessible regulatory DNA and going all the way to sequence design,” said PhD student Niklas Kempynck.

The team applied CREsted on various systems, including human immune cells, cancer cell states, and zebrafish development, where designed enhancers were successfully validated. The findings of the study, published in Nature Methods, show that the tool can help scientists not only understand gene regulation but also design new DNA sequences.

For more information, read the article from VIB.