Development of Substrate-Directed Activity-Based Probes via Disulfide-Trapping for Site-Specific Interrogation of Nucleosomal Deubiquitination
Abstract
nucleosome probe and applied it in the activity-based profiling of DUBs in nuclear lysates of DNA-damaged HeLa cells. Subsequent biochemical analyses confirmed USP3 as a bona fide DUB for H2AK15Ub nucleosomes. Cross-linking mass spectrometry (XL-MS) further delineated the spatial interaction network among USP3, Ub, and the nucleosome, providing mechanistic insights into H2AK15 deubiquitination. Furthermore, we extended this strategy to other nucleosomal ubiquitination sites (H2AK119Ub and H2BK120Ub), capturing their cognate DUBs (USP16 and Ubp10, respectively). The SD-NucDUB-ABP platform thus enables integrated proteomic discovery and mechanistic dissection of nucleosome-specific deubiquitination, providing a versatile chemical tool for epigenetic research at the intersection of chemical biology and chromatin biology.
Fields of Study & Subjects
Ubiquitin and proteasome pathways
Protein Degradation and Inhibitors
Histone Deacetylase Inhibitors Research
Publication details
- Journal / source
- Journal of the American Chemical Society
- Publisher
- American Chemical Society (ACS)
- Volume
- 148
- Issue
- 6
- Pages
- 6485–6497
- Publication date
- 7 February 2026
- Language
- EN