G-quadruplexes regulate chromatin accessibility and gene expression in Bloom Syndrome

Bloom Syndrome (BS) is a recessive genetic disorder characterized by hyper-recombination and genome instability. It is caused by mutations in BLM, which encodes a conserved RecQ helicase that unwinds various aberrant DNA structures. One such structure is DNA G-quadruplexes (G4s), which have versatile regulatory potential in chromatin organization and gene expression. However, whether G4 profiles are altered in BS and how G4s contribute to disease-associated molecular changes remain unclear. Here, we profiled chromatin accessibility and gene expression using ATAC-seq and RNA-seq and mapped endogenous G4 by ChIP-seq in wild type (WT) and BS cell lines. We observed that in BS cell lines, differential G4 formation positively correlated with both differential chromatin accessibility and gene expression. To test the direct involvement of G4s in the molecular phenotypes in BS, we applied pyridostatin, a G4-stabilizing molecule, in WT cells and showed that G4 stabilization partially recapitulated BS-associated molecular phenotypes. Additionally, we found that regions with increased chromatin accessibility in BS individuals in a family were also enriched for G4-forming sequences. Together, our data substantiate a regulatory role for G4s in Bloom syndrome and support a molecular model in which unresolved G4s in BLM/-cells enhance chromatin accessibility, thereby promoting gene expression. These findings reveal an expanded regulatory function of BLM mediated through G4 structures and previously underappreciated role of G4s in the molecular etiology of BS.