Protocol to apply spike-in ChIP-seq to capture massive histone acetylation in human cells

STAR Protoc. 2021 Jul 17;2(3):100681. doi: 10.1016/j.xpro.2021.100681. eCollection 2021 Sep 17.


Inhibition of histone deacetylases causes rapid and robust acetylation of histones. In this case, histone acetylation is likely increased on nearly every nucleosome, and the per-cell DNA/chromatin yield in chromatin immunoprecipitation (ChIP) experiments is significantly increased. Spike-in controls are essential for normalizing ChIP sequencing (ChIP-seq) data to capture this massive effect. Here, we report a detailed protocol of H3K27-ac ChIP-seq in human cells with chromatin from an ancestral species as a spike-in control. For complete details on the use and execution of this protocol, please refer to Wu et al. (2021).

Keywords: Bioinformatics; Cell Biology; Cell-based Assays; ChIP-seq; Genomics; Sequence analysis.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't

MeSH terms

  • Acetylation / drug effects*
  • Chromatin
  • Chromatin Immunoprecipitation / methods*
  • Chromatin Immunoprecipitation Sequencing / methods*
  • DNA / metabolism
  • High-Throughput Nucleotide Sequencing / methods
  • Histone Deacetylases / metabolism
  • Histones / metabolism
  • Humans
  • Nucleosomes
  • Protein Processing, Post-Translational
  • Sequence Analysis, DNA / methods


  • Chromatin
  • Histones
  • Nucleosomes
  • DNA
  • Histone Deacetylases