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Updated: Jul 17, 2026
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Extraction of Histones from Clinical Specimens for Epigenetic Profiling by Mass Spectrometry
Published on: November 21, 2025
Activity-based probes for proteomic profiling of histone deacetylase complexes
Cleo M Salisbury1, Benjamin F Cravatt
1The Skaggs Institute for Chemical Biology and Department of Cell Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA.
Summary
Researchers developed SAHA-BPyne, a chemical probe to profile histone deacetylase (HDAC) activity and associated proteins in cells. This tool aids in understanding how HDAC complexes regulate gene expression and disease states.
Area of Science:
- Biochemistry
- Molecular Biology
- Chemical Biology
Background:
- Histone deacetylases (HDACs) are crucial for gene expression, functioning within large protein complexes.
- Understanding how associated proteins influence HDAC activity requires advanced detection technologies in native biological settings.
Purpose of the Study:
- To develop and validate a novel chemical probe for profiling HDACs and their interacting proteins in native proteomes and live cells.
- To investigate the direct modification of HDAC-associated proteins by the chemical probe.
Main Methods:
- Design and synthesis of SAHA-BPyne, a chemical probe incorporating suberoylanilide hydroxamic acid (SAHA) features with benzophenone and alkyne tags.
- Application of SAHA-BPyne for chemical proteomics to identify HDAC targets and associated proteins in native proteomes.
- Utilizing the probe to analyze HDAC content and complex assembly in human disease models.
Main Results:
- SAHA-BPyne specifically targets and covalently modifies Class I and II HDACs in proteomes.
- The probe enriched multiple HDAC-associated proteins, suggesting direct modification near HDAC active sites.
- SAHA-BPyne effectively detected alterations in HDAC content and complex formation in disease models.
Conclusions:
- SAHA-BPyne is a valuable chemical proteomics tool for assessing HDAC activity and identifying regulatory binding proteins.
- The probe facilitates the study of HDAC function and regulation in native biological systems and disease contexts.
