RNA editing is a crucial process that allows cells to make changes to RNA molecules after they’re created, helping fine-tune gene expression and increase protein diversity. One type of RNA editing, where cytosine (C) is changed to uracil (U), has been particularly hard to detect because of technical challenges like sequencing errors and interference from similar changes in DNA.

Researchers at the Shanghai Institute of Biological Products have developed a new analysis tool called CADRES, which stands for Calibrated Differential RNA Editing Scanner. CADRES helps researchers pinpoint these rare C>U RNA edits more accurately than previous methods.

Schematic for the Calibrated Differential RNA Editing Scanner (CADRES) analysis pipeline

What sets CADRES apart is its ability to filter out misleading data by combining advanced statistical analysis with information from both DNA and RNA sequencing. The team tested CADRES using both computer simulations and lab experiments involving cells engineered to express the APOBEC3B (A3B) enzyme, which is known to cause C>U edits.

The results showed that CADRES can effectively tell the difference between real RNA edits and sequencing errors or DNA-level mutations. This makes it a valuable tool for researchers studying how RNA editing affects cell behavior and disease. More precise detection of C>U RNA editing could lead to new discoveries in gene regulation and potential new targets for therapies.

Availability  – CADRES is coded by a combination of Python and Shell script languages, which is available at GitHub (https://github.com/junsun-hash/CADRES)