Molecular basis of UV lesion binding and repair inhibition by ETS-family transcription factors

ABSTRACT Mutation hotspots in melanoma frequently occur at DNA binding sites of ETS-family transcription factors, as ETS factors stimulate the formation of UV-induced cyclobutane pyrimidine dimers (CPDs) while suppressing repair at ETS-bound DNA sites. To elucidate the molecular mechanism by which ETS factors bind to damaged DNA sites and inhibit repair, we investigated the binding of members from the three major classes of the ETS superfamily (Ets1, ELF1 and PU.1) to cognate DNA containing a cis-syn TpT CPD. These site-specific CPDs modulated ETS recognition and repair by a model repair enzyme in a position-dependent manner, with a deaminated CPD located in a damage hotspot in the ETS binding motif consistently stimulating binding and repair inhibition by all three paralogs. Co-crystal structures of PU.1 reveal that CPDs and mismatches are recognized within the framework of canonical ETS/DNA complexes, but with highly differentiated thermodynamic and dynamic properties. Specifically, the CPD-bound complex exhibits unique dynamics that reveal a novel DNA-binding mode as well as inform how ETS domains navigate the DNA conformational landscape to predispose CPD induction. The results offer a molecular rationale for how ETS factors induce mutation hotspots in skin cancers and other UV-exposed tissues by promoting CPD induction and inhibiting repair. KEY POINTS ETS-family proteins from all major classes bind CPD-containing DNA sites. Engagement of CPD by ETS proteins inhibits DNA repair in a position-dependent manner. Structure and thermodynamics of ETS binding to damaged DNA differ from undamaged substrates.