TOP1α-mediated stabilization of CYP82C4 G-quadruplex DNA represses lateral root primordium initiation in Arabidopsis

Lateral roots are an indispensable part of the plant root system and influence nutrient uptake and environmental adaptability. Chromatin remodelling has a key regulatory role in lateral root development by modulating gene expression. However, how chromatin regulates this process remains largely unknown. Here we found that TOPOISOMERASE1 ALPHA (TOP1α), as an essential chromatin remodelling factor, significantly inhibited the density of lateral root primordium (LRP) in Arabidopsis thaliana. CUT&Tag analyses indicated that CYP82C4 was most upregulated in the loss-of-function mutant line top1α. Further biophysical study demonstrated that a 19-nt G-rich DNA (T19) was fold into an antiparallel G-quadruplex (G4) structure in the template strand of CYP82C4. In Arabidopsis root, the T19 was markedly enriched in top1α. Circular dichroism melting and surface plasmon resonance assays confirmed that TOP1α stabilized T19 DNA G-quadruplex with high affinity in vitro. G4-mutant lines and G4-destabilizing ligand treatment both showed that CYP82C4 expression increased when G4 structure failed to form properly, which promoted LRP initiation. These results demonstrated that TOP1α inhibited LRP initiation by suppressing CYP82C4 expression by stabilizing the T19 DNA G-quadruplex. Together, our findings identify a mechanism by which TOP1α drives chromatin remodelling to regulate LRP initiation through its action on G-quadruplex structures.