An improved SNAP-ADAR tool enables efficient RNA base editing to interfere with post-translational protein modification

Authors:
Karthika Devi Kiran Kumar , Shubhangi Singh , Stella Maria Schmelzle , Paul Vogel , Carolin Fruhner, Alfred Hanswillemenke  Adrian Brun , Jacqueline Wettengel , Yvonne Füll , Lukas Funk , Valentin Mast , J Josephine Botsch , Philipp Reautschnig , Jin Billy Li , Thorsten Stafforst 
In:
Source: Nature
Publication Date: (2024)
Issue: :
Cells used in publication:
Epithelial, retinal pigment (RPE), human
Species: human
Tissue Origin: eye
Experiment

Cell culture
Flp-In T-REx 293 cells (cat. no. R78007, Thermo Fisher scientific) stably expressing SA1Q were cultured and used for editing experiments as
previously described12. Ad293 cells (Cat. No. 240085, Agilent Technologies) were cultured in DMEM with 10% FBS and 1% AntibioticAntimycotic. A549 and HeLa cell lines (ACC 107 and ACC 57, DSMZ, Braunschweig, Germany) were cultured in DMEM with 10% FBS and 1% Penicillin/Streptomycin (P/S). Primary cells, NHA (Normal Human
Astrocytes, Cat.no. CC-2565) and H-RPE (Human Retinal Pigment Epithelial Cells, Cat. no. 00194987), were purchased from Lonza and
cultured in their respective commercially available medium and supplements from Lonza as instructed in the manual (AGM#- Astrocyte
Growth Medium BulletKit, Cat. no. CC-3186 for NHAs and RtEGM#- Retinal Pigment Epithelial Cell Growth Medium BulletKit Cat. no. 00195409 for H-RPE cells). HEK 293FT-cells (Cat. No. R70007, ThermoFisher Scientific) were cultured in DMEM with 10% FBS and 500 µg/ ml Geneticin. All cells were maintained at 37 °C with 5% CO2 in a watersaturated steam atmosphere. Authentication via STR profiling was performed by the commercial suppliers before purchase of the material. Cell lines were not additionally authenticated by us.

Abstract

RNA base editing relies on the introduction of adenosine-to-inosine changes into target RNAs in a highly programmable manner in order to repair disease-causing mutations. Here, we propose that RNA base editing could be broadly applied to perturb protein function by removal of regulatory phosphorylation and acetylation sites. We demonstrate the feasibility on more than 70 sites in various signaling proteins and identify key determinants for high editing efficiency and potent down-stream effects. For the JAK/STAT pathway, we demonstrate both, negative and positive regulation. To achieve high editing efficiency over a broad codon scope, we applied an improved version of the SNAP-ADAR tool. The transient nature of RNA base editing enables the comparably fast (hours to days), dose-dependent (thus partial) and reversible manipulation of regulatory sites, which is a key advantage over DNA (base) editing approaches. In summary, PTM interference might become a valuable field of application of RNA base editing.