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

Gaëlle Lelandais (1) , Corinne Blugeon (2) , Jawad Merhej (3)

1 IJM (UMR_7592) - Institut Jacques Monod
2 Genomique ENS - GenomiqueENS
3 LCQB - Biologie Computationnelle et Quantitative = Laboratory of Computational and Quantitative Biology

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.

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

Domaines: Biochimie, Biologie Moléculaire; Microbiologie et Parasitologie

Gaëlle Lelandais, Corinne Blugeon, Jawad Merhej. ChIPseq in Yeast Species: From Chromatin Immunoprecipitation to High-Throughput Sequencing and Bioinformatics Data Analyses.. Methods in Molecular Biology, 2016, pp.185-202. ⟨10.1007/978-1-4939-3079-1_11⟩. ⟨hal-01400736⟩