Structural basis for nucleolin recognition of <i>MYC</i> promoter G-quadruplex
The <i>MYC</i> 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<sup>+</sup>), 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.
Authors
- Luying Chen (ORCID: https://orcid.org/0000-0001-5136-4945)
- Buket Onel
- Nicholas Noinaj (ORCID: https://orcid.org/0000-0001-6361-2336)
- Jonathan Dickerhoff
- Satchal K. Erramilli (ORCID: https://orcid.org/0000-0001-8694-7681)
- Danzhou Yang (ORCID: https://orcid.org/0000-0001-7489-7111)
- Saburo Sakai (ORCID: https://orcid.org/0000-0002-3809-0254)
- Ke‐wei Zheng (ORCID: https://orcid.org/0000-0002-4110-4776)
- Yuwei Chen
- Anthony A. Kossiakoff (ORCID: https://orcid.org/0000-0003-3174-9359)
- Laurence H. Hurley (ORCID: https://orcid.org/0000-0002-8522-450X)
- Guanhui Wu (ORCID: https://orcid.org/0000-0003-4659-8717)
- Clement Lin (ORCID: https://orcid.org/0000-0001-7054-3455)
- Yawen Bai (ORCID: https://orcid.org/0000-0003-3239-1109)
- Hanqiao Feng (ORCID: https://orcid.org/0000-0003-3488-0600)
- Nanjie Deng (ORCID: https://orcid.org/0000-0001-8805-3526)
- Megan Carver (ORCID: https://orcid.org/0000-0003-3637-5253)
- Kai‐Bo Wang (ORCID: https://orcid.org/0000-0002-2934-9906)
- Jun Wan (ORCID: https://orcid.org/0000-0001-9286-6562)
- Charles Vinson (ORCID: https://orcid.org/0000-0001-7453-1793)
Institutions
- Pace University (US)
- National Institutes of Health (US)
- Japan Agency for Marine-Earth Science and Technology (JP)
- University of Arizona (US)
- Hunan University (CN)
- Purdue University West Lafayette (US)
- University of Chicago (US)
- National Cancer Institute (US)
- Indiana University School of Medicine
- Indiana University – Purdue University Indianapolis (US)
Publication Details
- Journal
- Science
- Published
- 2025-04-17
- DOI
- https://doi.org/10.1126/science.adr1752
- Citations
- 30
- Primary Topic
- DNA and Nucleic Acid Chemistry
- Type
- article
- Field-Weighted Citation Impact
- 24.18