Structural basis for nucleolin recognition of <i>MYC</i> promoter G-quadruplex
Luying Chen, Jonathan Dickerhoff, Ke‐wei Zheng, Satchal K. Erramilli, Hanqiao Feng, Guanhui Wu, Buket Onel, Yuwei Chen, Kai‐Bo Wang, Megan Carver, Clement Lin, Saburo Sakai, Jun Wan, Charles Vinson, Laurence H. Hurley, Anthony A. Kossiakoff, Nanjie Deng, Yawen Bai, Nicholas Noinaj, Danzhou Yang
Abstract
The MYC oncogene promoter G-quadruplex (MycG4) regulates transcription and is a prevalent G4 locus in immortal cells. Nucleolin, a major MycG4-binding protein, exhibits greater affinity for MycG4 than for nucleolin recognition element (NRE) RNA. Nucleolin’s four RNA binding domains (RBDs) are essential for high-affinity MycG4 binding. We present the 2.6-angstrom crystal structure of the nucleolin-MycG4 complex, revealing a folded parallel three-tetrad G-quadruplex with two coordinating potassium ions (K + ), interacting with RBD1, RBD2, and Linker12 through its 6–nucleotide (nt) central loop and 5′ flanking region. RBD3 and RBD4 bind MycG4’s 1-nt loops as demonstrated by nuclear magnetic resonance (NMR). Cleavage under targets and tagmentation sequencing confirmed nucleolin’s binding to MycG4 in cells. Our results revealed a G4 conformation-based recognition by a regulating protein through multivalent interactions, suggesting that G4s are nucleolin’s primary cellular substrates, indicating G4 epigenetic transcriptional regulation and helping G4-targeted drug discovery.