PUB-NChIP-"in vivo biotinylation" approach to study chromatin in proximity to a protein of interest

Muhammad Shoaib, Arman Kulyyassov, Chloé Robin, Kinga Winczura, Pavel Tarlykov, Emmanuelle Despas, Patricia Kannouche, Erlan Ramanculov, Marc Lipinski, Vasily Ogryzko

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Abstract

We have developed an approach termed PUB-NChIP (proximity utilizing biotinylation with native ChIP) to purify and study the protein composition of chromatin in proximity to a nuclear protein of interest. It is based on coexpression of (1) a protein of interest, fused with the bacterial biotin ligase BirA, together with (2) a histone fused to a biotin acceptor peptide (BAP), which is specifically biotinylated by BirA-fusion in the proximity of the protein of interest. Using the RAD18 protein as a model, we demonstrate that the RAD18-proximal chromatin is enriched in some H4 acetylated species. Moreover, the RAD18-proximal chromatin containing a replacement histone H2AZ has a different pattern of H4 acetylation. Finally, biotin pulse-chase experiments show that the H4 acetylation pattern starts to resemble the acetylation pattern of total H4 after the proximity of chromatin to RAD18 has been lost.

Original languageEnglish
Pages (from-to)331-340
Number of pages10
JournalGenome Research
Volume23
Issue number2
DOIs
Publication statusPublished - Feb 1 2013
Externally publishedYes

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ASJC Scopus subject areas

  • Genetics
  • Genetics(clinical)

Cite this

Shoaib, M., Kulyyassov, A., Robin, C., Winczura, K., Tarlykov, P., Despas, E., Kannouche, P., Ramanculov, E., Lipinski, M., & Ogryzko, V. (2013). PUB-NChIP-"in vivo biotinylation" approach to study chromatin in proximity to a protein of interest. Genome Research, 23(2), 331-340. https://doi.org/10.1101/gr.134874.111