Structural basis for nucleolin recognition of MYC promoter G-quadruplex

Area of Science:

• Molecular Biology
• Structural Biology
• Epigenetics

Background:

• The MYC oncogene promoter G-quadruplex (MycG4) is a key regulator of transcription in immortal cells.
• Nucleolin is a protein that binds to MycG4 with high affinity, showing preference over RNA.

Purpose of the Study:

• To elucidate the structural basis of nucleolin's interaction with MycG4.
• To confirm nucleolin's binding to MycG4 in a cellular context.
• To understand the role of this interaction in epigenetic transcriptional regulation.

Main Methods:

• X-ray crystallography to determine the structure of the nucleolin-MycG4 complex.
• Nuclear Magnetic Resonance (NMR) spectroscopy to study interactions with specific loops.
• Cleavage under targets and tagmentation sequencing (CUT&Tag) to validate binding in cells.

Main Results:

• The crystal structure reveals a parallel three-tetrad G-quadruplex bound by nucleolin's RNA binding domains (RBDs) 1 and 2, and Linker12.
• Nucleolin's RBD3 and RBD4 were shown by NMR to bind to the 1-nt loops of MycG4.
• CUT&Tag confirmed that nucleolin binds to MycG4 within cells.

Conclusions:

• Nucleolin recognizes G-quadruplexes through multivalent interactions based on G4 conformation.
• G-quadruplexes are likely primary cellular substrates for nucleolin.
• This study provides insights into G-quadruplex-mediated epigenetic transcriptional regulation and aids in G4-targeted drug discovery.