Artificially inserted strong promoter containing multiple G-quadruplexes induces long-range chromatin modification

Area of Science:

• Genomics
• Epigenetics
• Molecular Biology

Background:

• G-quadruplex (G4) DNA structures are implicated in chromosomal looping but direct causal evidence was lacking.
• Understanding G4 DNA's role is crucial for deciphering 3D genome organization and gene regulation.

Purpose of the Study:

• To experimentally test the causal role of G-quadruplex DNA structures in driving 3D chromatin looping and enhancer function.
• To investigate the molecular mechanisms by which G4 DNA influences genome topology and gene expression.

Main Methods:

• Insertion of G-quadruplex forming sequences and control sequences into cellular chromatin.
• Confirmation of in vivo G4 formation using a G4-selective antibody.
• Analysis of 3D chromatin looping interactions, enhancer histone marks, and gene activation using genomic and epigenomic techniques.

Main Results:

• G-quadruplex arrays, unlike control sequences, significantly increased 3D chromatin looping interactions genome-wide.
• G4 insertion led to local enrichment of enhancer marks and the coactivator p300/Acetylated-p300.
• Promoter-enhancer interactions and gene activation were observed up to 5 Mb away from the G4 insertion site.

Conclusions:

• G-quadruplex DNA structures play a causal role in mediating long-range chromatin interactions and enhancer function.
• This study highlights the intrinsic DNA sequence/structure, specifically G4s, as a novel mechanism for inducing or maintaining 3D genome topology.
• Findings challenge traditional models of 3D topology solely reliant on architectural proteins, offering new insights into genome organization.