Expanded palette of RNA base editors for comprehensive RBP-RNA interactome studies

RNA binding proteins (RBPs) are key regulators of RNA processing and cellular function. Several methods have been established to identify RNA targets of RBPs including antibody-free methods that use RNA base-editors (rBEs) fused to RBPs.
Hugo Medina-Muñoz, PhD and Gene Yeo, PhD, MBA (University of California, San Diego) highlight the work published in Nature Communications describing an experimental and computational framework called PRINTER (protein-RNA-interaction-based triaging of enzymes that edit RNA). This framework expands the repertoire of available base editors and provides a rapid means to characterize these enzymes before their application in RBP-mediated editing. It also enables the identification of DNA editors, addressing a critical aspect of the field's current limitations.
The study emphasizes the importance of acknowledging and addressing enzyme bias when designing experiments and interpreting their outcomes. Relying solely on one enzyme can lead to false negatives and an incomplete understanding of protein-RNA interactions.
Access the full, free text of the Nature Communications publication www.ncbi.nlm.n...
Code Availability
The software utilized and code generated for the analyses in this study can be obtained by accessing the following repositories:
snakemake.read...
PRINTER github.com/Yeo...
FLARE github.com/Yeo...
Visit the Gene Yeo Lab yeolab.com/
This work was partially supported by an NHGRI Opportunity Fund to Gene W. Yeo and Rahul M. Kohli. Opportunity Funds are administered by the TDCC and provided as a subcontract from NIH grant U24HG011735.
Learn more about the TDCC and other NHGRI-funded projects:
genometdcc.org/