1. Detection of genomic G-quadruplexes in living cells using a small artificial protein
- Author
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Ke-wei Zheng, Jia-Yuan Gong, Juan-Nan Chen, Yong Zhao, Yu-hua Hao, Cui-Jiao Wen, Zheng Tan, Yi-de He, and Jia-yu Zhang
- Subjects
Transcription, Genetic ,AcademicSubjects/SCI00010 ,Chicken Cells ,Biology ,010402 general chemistry ,G-quadruplex ,01 natural sciences ,Cell Line ,DEAD-box RNA Helicases ,03 medical and health sciences ,chemistry.chemical_compound ,Mice ,Plasmid ,Transcription (biology) ,Structural Biology ,Genetics ,Animals ,Humans ,Gene ,030304 developmental biology ,0303 health sciences ,Genome ,DNA, Superhelical ,Promoter ,Recombinant Proteins ,0104 chemical sciences ,DNA-Binding Proteins ,G-Quadruplexes ,Biochemistry ,chemistry ,Nucleic acid ,DNA - Abstract
G-quadruplex (G4) structures formed by guanine-rich nucleic acids are implicated in essential physiological and pathological processes and serve as important drug targets. The genome-wide detection of G4s in living cells is important for exploring the functional role of G4s but has not yet been achieved due to the lack of a suitable G4 probe. Here we report an artificial 6.7 kDa G4 probe (G4P) protein that binds G4s with high affinity and specificity. We used it to capture G4s in living human, mouse, and chicken cells with the ChIP-Seq technique, yielding genome-wide landscape as well as details on the positions, frequencies, and sequence identities of G4 formation in these cells. Our results indicate that transcription is accompanied by a robust formation of G4s in genes. In human cells, we detected up to >123 000 G4P peaks, of which >1/3 had a fold increase of ≥5 and were present in >60% promoters and ∼70% genes. Being much smaller than a scFv antibody (27 kDa) or even a nanobody (12–15 kDa), we expect that the G4P may find diverse applications in biology, medicine, and molecular devices as a G4 affinity agent.
- Published
- 2020