Yeast Functional Genomics pp 185-202

Part of the Methods in Molecular Biology book series (MIMB, volume 1361) | Cite as

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

Abstract

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.

Key words

Chromatin immunoprecipitation High-throughput sequencing DNA binding sites of proteins Yeasts Bioinformatics 

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Copyright information

© Springer Science+Business Media New York 2016

Authors and Affiliations

  1. 1.Institut Jacques Monod, CNRS UMR 7592University of Paris DiderotParisFrance
  2. 2.Plateforme Génomique, Ecole Normale SupérieureInstitut de Biologie de l’ENS, IBENSParisFrance
  3. 3.Inserm, U1024ParisFrance
  4. 4.CNRS, UMR 8197ParisFrance
  5. 5.Laboratoire de Biologie Computationnelle et Quantitative, Sorbonne Universités, UPMC University of Paris 06, UMR 7238ParisFrance
  6. 6.Laboratoire de Biologie Computationnelle et QuantitativeCNRS, UMR 7238ParisFrance

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