New technologies to determine genome structure and regulation

The activity of our genes is controlled by a complex network of physical contacts with a multitude of regulatory sequences scattered throughout the genome. The proper execution of these interactions is of vital importance; in fact, errors or malfunctions are reflected in diseases such as congenital disorders or cancer. For this reason, important technologies, such as Hi-C, SPRITE and GAM, have been developed that harness the power of current DNA sequencing techniques to monitor the network of contacts between genes and regulators. However, it remained unclear how closely they mirrored the structure of these interactions, and what the accuracy of one over the other was under different conditions.

A research team from the University of Naples Federico II formed by Luca Fiorillo, Francesco Musella and Mattia Conte, and led by Professor Mario Nicodemi of the Department of Physics "Ettore Pancini," has developed a new computational technology to determine genome structure and regulation.

The discovery has just been published in the journal Nature Methods and captured in the journal's News&Views. In addition, Professor Nicodemi was selected by Nature Methods for its Author of the Month column.

The Federico II team developed a new computational method based on polymer physics and the combined analysis of Hi-C, SPRITE, GAM and high-resolution microscopy data, which allowed for the first time to provide a comprehensive benchmark of these technologies. The Neapolitan team, in collaboration with Professor Ana Pombo's research group at von Humboldt in Berlin, had already developed the GAM method in a paper published in Nature in 2017.

This new work paves the way for the concrete application of such technologies in biomedicine.