Activity-based probes for proteomic profiling of histone deacetylase complexes
- 23 January 2007
- journal article
- research article
- Published by Proceedings of the National Academy of Sciences in Proceedings of the National Academy of Sciences of the United States of America
- Vol. 104 (4), 1171-1176
- https://doi.org/10.1073/pnas.0608659104
Abstract
Histone deacetylases (HDACs) are key regulators of gene expression that require assembly into larger protein complexes for activity. Efforts to understand how associated proteins modulate the function of HDACs would benefit from new technologies that evaluate HDAC activity in native biological systems. Here, we describe an active site-directed chemical probe for profiling HDACs in native proteomes and live cells. This probe, designated SAHA-BPyne, contains structural elements of the general HDAC inhibitor suberoylanilide hydroxamic acid (SAHA), as well as benzophenone and alkyne moieties to effect covalent modification and enrichment of HDACs, respectively. Both class I and II HDACs were identified as specific targets of SAHA-BPyne in proteomes. Interestingly, multiple HDAC-associated proteins were also enriched by SAHA-BPyne, even after denaturation of probe-labeled proteomes. These data indicate that certain HDAC-associated proteins are directly modified by SAHA-BPyne, placing them in close proximity to HDAC active sites where they would be primed to regulate substrate recognition and activity. We further show that SAHA-BPyne can be used to measure differences in HDAC content and complex assembly in human disease models. This chemical proteomics probe should thus prove valuable for profiling both the activity state of HDACs and the binding proteins that regulate their function.Keywords
This publication has 30 references indexed in Scilit:
- Proteomic profiling of metalloprotease activities with cocktails of active-site probesNature Chemical Biology, 2006
- p66 and p66 of the Mi-2/NuRD complex mediate MBD2 and histone interactionNucleic Acids Research, 2006
- A streamlined platform for high-content functional proteomics of primary human specimensNature Methods, 2005
- Drug Insight: histone deacetylase inhibitors—development of the new targeted anticancer agent suberoylanilide hydroxamic acidNature Clinical Practice Oncology, 2005
- Matrix Metalloproteinase Inhibitors and Cancer—Trials and TribulationsScience, 2002
- Functional organization of the yeast proteome by systematic analysis of protein complexesNature, 2002
- Histone Deacetylase 1 Phosphorylation Promotes Enzymatic Activity and Complex FormationJournal of Biological Chemistry, 2001
- Histone deacetylases and cancer: causes and therapiesNature Reviews Cancer, 2001
- CoREST is an integral component of the CoREST- human histone deacetylase complexProceedings of the National Academy of Sciences of the United States of America, 2001
- Activity-based protein profiling: The serine hydrolasesProceedings of the National Academy of Sciences of the United States of America, 1999