A Balancing Act: Thymine DNA Glycosylase Combines Sequence and Rotational Preferences To Define Lesion Excision in the Nucleosome Core Particle

Thymine DNA glycosylase (TDG) is a DNA glycosylase involved in base excision repair (BER) with a specialized role in the regulation of transcription through the maintenance of 5'-CpG-3' sites via active demethylation. In this work, we investigate the ability of TDG to excise modified nucleobases from the simplest unit of compacted DNA, the nucleosome core particle (NCP). We measure TDG activity on a population of NCPs with uracil (U) at various geometric positions and report that <i>k</i>_obs for U excision from the NCP depends on positioning and dinucleotide sequence context. Specifically, TDG prefers solution accessible 5'-UpG-3' and 5'-UpA-3' sites. By coupling our findings with previous studies, we suggest that TDG's stringent substrate preferences facilitate its epigenetic role through the extensive contacts made with its DNA substrate.