Engineered domain swapping indicates context dependent functional role of RNA G-quadruplexes.

Area of Science:

• Molecular Biology
• RNA Biology
• Genetics

Background:

• RNA domain swapping usually preserves native function in new contexts.
• G-quadruplexes (GQs) are crucial RNA structures with diverse functions.
• Understanding GQ function context-dependency is key for RNA engineering.

Purpose of the Study:

• To investigate if RNA G-quadruplex (GQ) function deviates from its native role based on location.
• To demonstrate functional role reversal of GQs through RNA engineering.
• To establish the context-dependent modularity of RNA GQ structures.

Main Methods:

• Engineered known translation-repressing RNA GQs into the human VEGF IRES A.
• Replaced the endogenous GQ in VEGF IRES A with engineered GQs.
• Swapped translation-inhibitory GQs in MT3-MMP mRNA with known translation-essential GQs.

Main Results:

• Engineered GQs adopted stable structures in non-native environments.
• GQs exhibited a functional role reversal, adapting to the new genetic context.
• Demonstrated that GQ function is contingent upon its location within the RNA molecule.

Conclusions:

• RNA G-quadruplex function is not solely sequence-dependent but highly influenced by its genomic context.
• RNA engineering can achieve functional role reversals by relocating GQ motifs.
• RNA GQs are modular elements whose function can be predictably altered by their environment.