Yeast Genetics pp 231-255 | Cite as

Global Analysis of Transcription Factor-Binding Sites in Yeast Using ChIP-Seq

  • Philippe Lefrançois
  • Jennifer E. G. Gallagher
  • Michael SnyderEmail author
Part of the Methods in Molecular Biology book series (MIMB, volume 1205)


Transcription factors influence gene expression through their ability to bind DNA at specific regulatory elements. Specific DNA-protein interactions can be isolated through the chromatin immunoprecipitation (ChIP) procedure, in which DNA fragments bound by the protein of interest are recovered. ChIP is followed by high-throughput DNA sequencing (Seq) to determine the genomic provenance of ChIP DNA fragments and their relative abundance in the sample. This chapter describes a ChIP-Seq strategy adapted for budding yeast to enable the genome-wide characterization of binding sites of transcription factors (TFs) and other DNA-binding proteins in an efficient and cost-effective way.

Yeast strains with epitope-tagged TFs are most commonly used for ChIP-Seq, along with their matching untagged control strains. The initial step of ChIP involves the cross-linking of DNA and proteins. Next, yeast cells are lysed and sonicated to shear chromatin into smaller fragments. An antibody against an epitope-tagged TF is used to pull down chromatin complexes containing DNA and the TF of interest. DNA is then purified and proteins degraded. Specific barcoded adapters for multiplex DNA sequencing are ligated to ChIP DNA. Short DNA sequence reads (28–36 base pairs) are parsed according to the barcode and aligned against the yeast reference genome, thus generating a nucleotide-resolution map of transcription factor-binding sites and their occupancy.

Key words

ChIP-Seq ChIP Yeast Chromatin Transcription factor Binding site Genomics Multiplex 


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Copyright information

© Springer Science+Business Media New York 2014

Authors and Affiliations

  • Philippe Lefrançois
    • 1
  • Jennifer E. G. Gallagher
    • 2
  • Michael Snyder
    • 3
    Email author
  1. 1.Department of Molecular, Cellular and Developmental BiologyYale UniversityNew HavenUSA
  2. 2.Department of BiologyWest Virginia UniversityMorgantownUSA
  3. 3.Department of Genetics, MC: 5120Stanford University School of MedicineStanfordUSA

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