AI helps scientists decode DNA switches for targeted gene control

Researchers have used AI to understand patterns in DNA sequences that determine when and where genes are active. This work, from The Jackson Laboratory, MIT’s Broad Institute, and Yale University, introduces a new tool for precise gene editing. The focus of this study was on DNA regions called cis-regulatory elements (CREs). These are like on-off switches that ensure that specific genes are only active in the right cells. Although CREs cause genes to work in one cell type and not others, the rules (or ‘grammar’) for how CREs work are difficult to figure out.

To decipher these rules, the team analyzed large sets of DNA data using an AI model. This model identified CRE patterns that help activate or repress genes in certain cells. Researchers then used these insights to design synthetic DNA switches, targeting specific tissues.

Testing in live models

The team tested these synthetic switches, or CREs, in animal models to see how well they worked. They observed successful results, such as activating a fluorescent marker only in the liver cells of zebrafish embryos without affecting other tissues. This precise targeting shows the potential for future therapies that would activate genes in just one tissue or organ.

Using this AI approach, scientists have created thousands of new CREs, each with unique functions for targeted gene control. This development could lead to genetic treatments for conditions that require specific cell targeting.

Future use and medical potential

This tool can promote gene editing for research, but also opens doors for targeted treatments. With the ability to turn genes on or off in specific cell types, scientists see applications in treating genetic disorders or improving tissue repair. As lead researcher Ryan Tewhey noted, this approach could allow researchers to fine-tune gene activity in one tissue, paving the way for treatments with minimal side effects on other cells.