Histone deacetylase inhibitor-based chromatin precipitation for identification of targeted genomic loci

Authors

  • Thomas W. Hanigan University of Illinois at Chicago
  • Jeanne M. Danes University of Illinois at Chicago
  • Taha Y. Taha University of Illinois at Chicago
  • Jonna Frasor University of Illinois at Chicago
  • Pavel A. Petukhov University of Illinois at Chicago

DOI:

https://doi.org/10.14440/jbm.2018.216

Keywords:

histone deacetylase, chromatin immunoprecipitation, photoreactive probes

Abstract

Histone deacetylase (HDAC) catalyzes the removal of acetyl marks from histones, effectively regulating gene expression. Genome wide chromatin immunoprecipitation (ChIP) studies have shown HDACs are present on numerous active and repressed genes. However, HDAC inhibitors (HDACi) only regulate a small subset of this population in a cell type dependent fashion. To determine genomic locations directly targeted by HDACi, we developed a chromatin precipitation method using a photoreactive HDAC inhibitor probe (photomate). We validate this method by analyzing several canonical HDACi regulated genes, CDKN1A and FOSL1, and compare it to traditional ChIP using HDAC1 antibodies. We show that HDACi target HDACs bound at the promoter regions but not gene bodies, differing from HDAC1 antibody-based ChIP in the case of CDKN1A. This approach is anticipated to be useful for genome wide studies to identify the subset of genes directly regulated by an HDACi in a given cell type.

Author Biographies

Thomas W. Hanigan, University of Illinois at Chicago

Department of Medicinal Chemistry and Pharmacognosy

Jeanne M. Danes, University of Illinois at Chicago

Department of Physiology and Biophysics

Taha Y. Taha, University of Illinois at Chicago

Department of Medicinal Chemistry and Pharmacognosy

Pavel A. Petukhov, University of Illinois at Chicago

Department of Medicinal Chemistry and Pharmacognosy

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Published

2018-03-30

How to Cite

1.
Hanigan TW, Danes JM, Taha TY, Frasor J, Petukhov PA. Histone deacetylase inhibitor-based chromatin precipitation for identification of targeted genomic loci. J Biol Methods [Internet]. 2018Mar.30 [cited 2021Oct.21];5(1):e88. Available from: https://jbmethods.org/jbm/article/view/216

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