U.S. Department of Energy

Pacific Northwest National Laboratory

Multi-omic data integration links deleted in breast cancer 1 (DBC1) degradation to chromatin remodeling in inflammatory response.

TitleMulti-omic data integration links deleted in breast cancer 1 (DBC1) degradation to chromatin remodeling in inflammatory response.
Publication TypeJournal Article
Year of Publication2013
AuthorsNakayasu ES, Brown RN, Ansong C, Sydor MA, Imtiaz S, Mihai C, Sontag R, Hixson KK, Monroe ME, Sobreira TJP, Orr G, Petyuk VA, Yang F, Smith RD, Adkins JN
JournalMol Cell Proteomics
Abstract

This study investigated the dynamics of ubiquitinated proteins after the inflammatory stimulation of RAW 264.7 macrophage-like cells with bacterial lipopolysaccharide. Ubiquitination is a common protein post-translational modification that regulates many key cellular functions. We demonstrated that levels of global ubiquitination and K48 and K63 polyubiquitin chains change after lipopolysaccharide stimulation. Quantitative proteomic analysis identified 1199 ubiquitinated proteins, 78 of which exhibited significant changes in ubiquitination levels following stimulation. Integrating the ubiquitinome data with global proteomic and transcriptomic results allowed us to identify a subset of 88 proteins that were targeted for degradation after lipopolysaccharide stimulation. Using cellular assays and Western blot analyses, we biochemically validated DBC1 (a histone deacetylase inhibitor) as a degradation substrate that is targeted via an orchestrated mechanism utilizing caspases and the proteasome. The degradation of DBC1 releases histone deacetylase activity, linking lipopolysaccharide activation to chromatin remodeling in caspase- and proteasome-mediated signaling.

DOI10.1074/mcp.M112.026138
PubMed ID23639857
PubMed Central IDPMC3734575
Grant ListGM094623 / GM / NIGMS NIH HHS / United States
P41GM103493-10 / GM / NIGMS NIH HHS / United States
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