1 Multi-omic data integration links DBC1 degradation to chromatin remodeling in inflammatory response Ernesto S. Nakayasu¶, Roslyn N. Brown§, Charles Ansong¶, Michael A. Sydor¶, Sayed Imtiaz¶, Cosmin Mihai‡, Ryan Sontag¶, Kim K. Hixson‡, Matthew E. Monroe¶, Tiago J. P. Sobreira¥, Gayla Orr‡, Vladislav A. Petyuk¶, Feng Yang¶, Richard D. Smith¶ and Joshua N. Adkins¶ * From the ¶Biological Science Division and ‡Environmental and Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA 99352, USA. §Center for Bioproducts and Bioenergy, Washington State University, ¥National Laboratory for Biosciences (LNBio), National Center for Research in Energy and Materials, Campinas, SP 13083-970, Brazil. Running title: Ubiquitinome analysis of lipopolysaccharide-stimulated cells *To whom correspondence should be addressed: Joshua N. Adkins, Biological Science Division, Pacific Northwest National Laboratory, P. O. Box 999, MSIN K8-98, Richland, WA 99352, USA. Tel: (509) 371-6583, Fax: (509) 371-6564, e-mail: Joshua.Adkins@pnnl.gov Keywords: Ubiquitination, proteomics, lipopolysaccharide, DBC1, protein degradation, inflammation The used abbreviations are: DBC1, deleted in breast cancer 1; DAVID, Database for Annotation, Visualization and Integrated Discovery; DPBS, Dubelcco’s phosphate-buffered saline solution; DUB, deubiquitinase; FBS, fetal bovine serum; HAT, histone acetyltransferase; HDAC, histone deacetylase; IAP, inhibitor of apoptosis; IKK, iKB kinase; iTRAQ, isobaric tag for relative and absolute quantification; LPS, lipopolysaccharide; MonoUb, monoubiquitination; PAMPs, pathogen-associated molecular patterns; PolyUb, polyubiquitination; PTM, post-translational modification; TAK1, Tat-associated kinase 1; TLR, toll-like receptor. MCP Papers in Press. Published on May 2, 2013 as Manuscript M112.026138 Copyright 2013 by The American Society for Biochemistry and Molecular Biology, Inc.