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Genome-wide mapping of G-quadruplex structures with CUT&Tag
Jing Lyu1,2, Rui Shao1,2, Philip Yuk Kwong Yung1,2
1Science for Life Laboratory, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Tomtebodavägen 23, 17165 Stockholm, Sweden.
Nucleic Acids Research
|November 18, 2021
Summary
Researchers mapped G-quadruplex (G4) DNA structures using CUT&Tag, revealing their widespread presence at active gene regulatory elements in mouse cells. G4 structures were lost upon differentiation, highlighting their dynamic role in cellular processes.
Area of Science:
- Genomics and Molecular Biology
- Epigenetics and Gene Regulation
Background:
- Non-canonical DNA structures, including G-quadruplexes (G4) and DNA:RNA hybrids (R loops), influence critical genomic functions like gene expression and stability.
- The formation, resolution, and precise genomic localization of G4 structures remain poorly understood.
Purpose of the Study:
- To develop and apply a high-resolution method for mapping native G-quadruplex structures in mammalian genomes.
- To investigate the genomic landscape and dynamic changes of G4 structures during cellular differentiation.
Main Methods:
- Utilized Cleavage Under Targets and Tagmentation (CUT&Tag) under mild native conditions to map G4 structures with high resolution and low background.
- Applied R-loop CUT&Tag to assess the co-occurrence of G4s, R loops, and single-stranded DNA.
- Compared G4 landscapes in mouse embryonic stem cells (ESC) and neural progenitor cells (NPC).
Main Results:
- Widespread G4 formation was observed at active promoters and active/poised enhancers in mouse ESCs.
- G4 structures at enhancers were lost upon differentiation into NPCs.
- Demonstrated genome-wide co-occurrence of G4s, R loops, and single-stranded DNA at promoters and enhancers.
- Found evidence that G4 structures can exist independently of active transcription.
Conclusions:
- CUT&Tag provides a sensitive method for mapping native G4 structures, revealing their prevalence at key regulatory regions.
- Enhancer G4s are dynamic and cell-type/differentiation-dependent.
- G4s, R loops, and single-stranded DNA frequently co-localize, suggesting complex interplay in genome regulation.
