ChIPseq in Yeast Species: From Chromatin Immunoprecipitation to High-Throughput Sequencing and Bioinformatics Data Analyses

Methods Mol Biol. 2016;1361:185-202. doi: 10.1007/978-1-4939-3079-1_11.


Chromatin immunoprecipitation (ChIP) followed by high-throughput sequencing (ChIPseq) is a powerful technique for the genome-wide location of protein DNA-binding sites. The ChIP experiment consists in treating living cells with a cross-linking agent to bind proteins to their DNA substrates. After fragmentation of DNA, specific fractions associated with a particular protein of interest are purified by immunoaffinity. They are next sequenced and identified on the reference genome using dedicated bioinformatics programs. Several technical aspects are important to obtain high-quality ChIPseq results. This includes the quality of antibodies, the sequencing protocols, the use of accurate controls and the careful choice of bioinformatics tools. We present here a general protocol to perform ChIPseq analyses in yeast species. This protocol has been optimized to identify target genes of specific transcription factors but can be used for any other DNA binding proteins.

Keywords: Bioinformatics; Chromatin immunoprecipitation; DNA binding site s of proteins; High-throughput sequencing; Yeasts.

MeSH terms

  • Binding Sites / genetics
  • Chromatin Immunoprecipitation / methods*
  • Computational Biology / methods*
  • DNA-Binding Proteins / genetics
  • High-Throughput Nucleotide Sequencing / methods*
  • Saccharomyces cerevisiae / genetics
  • Transcription Factors / genetics


  • DNA-Binding Proteins
  • Transcription Factors