Structural basis for nucleolin recognition of MYC promoter G-quadruplex

• 成果类型: Article
• 署名作者: Chen, Luying; Dickerhoff, Jonathan; Zheng, Ke-wei; Erramilli, Satchal; Feng, Hanqiao; Wu, Guanhui; Onel, Buket; Chen, Yuwei; Wang, Kai-Bo; Carver, Megan; Lin, Clement; Sakai, Saburo; Wan, Jun; Vinson, Charles; Hurley, Laurence; Kossiakoff, Anthony A.; Deng, Nanjie; Bai, Yawen; Noinaj, Nicholas; Yang, Danzhou
• 署名单位: Purdue University System; Purdue University; Hunan University; University of Chicago; National Institutes of Health (NIH) - USA; NIH National Cancer Institute (NCI); University of Arizona; Indiana University System; Indiana University Bloomington; National Institutes of Health (NIH) - USA; NIH National Cancer Institute (NCI); Pace University; Purdue University System; Purdue University; Purdue University System; Purdue University; Purdue University System; Purdue University
• 刊物名称: SCIENCE
• ISSN/ISSBN: 0036-8096
• DOI: 10.1126/science.adr1752
• 发表日期: 2025-04-18
• 关键词: rna-binding proteins; pre-ribosomal-rna; identification; localization; domains; element; region

摘要

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.