Genome-Wide Chromatin Immunoprecipitation in Candida albicans and Other Yeasts.
Chromatin immunoprecipitation experiments are critical to investigating the interactions between DNA and a wide range of nuclear proteins within a cell or biological sample. In this chapter we outline an optimized protocol for genome-wide chromatin immunoprecipitation that has been used successfully for several distinct morphological forms of numerous yeast species, and include an optimized method for amplification of chromatin immunoprecipitated DNA samples and hybridization to a high-density oligonucleotide tiling microarray. We also provide detailed suggestions on how to analyze the complex data obtained from these experiments.
Department of Microbiology and Immunology, University of California, San Francisco, 600 16th Street, San Francisco, CA, 94158, USA.
Matthew B
MB
Lohse
Department of Molecular and Cell Biology, School of Natural Sciences, University of California, Merced, 5200 North Lake Road, Merced, CA, 95343, USA.
Pisiwat
P
Kongsomboonvech
Department of Molecular and Cell Biology, School of Natural Sciences, University of California, Merced, 5200 North Lake Road, Merced, CA, 95343, USA.
Maria
M
Madrigal
Department of Molecular and Cell Biology, School of Natural Sciences, University of California, Merced, 5200 North Lake Road, Merced, CA, 95343, USA. ahernday@ucmerced.edu.
Aaron D
AD
Hernday
Department of Molecular and Cell Biology, School of Natural Sciences, University of California, Merced, 5200 North Lake Road, Merced, CA, 95343, USA. cnobile@ucmerced.edu.
Clarissa J
CJ
Nobile
D002176:Candida albicans / Q000235:genetics*; D002843:Chromatin / Q000235:genetics; D047369:Chromatin Immunoprecipitation / Q000379:methods*; D004271:DNA, Fungal / Q000235:genetics*; D016681:Genome, Fungal; D009693:Nucleic Acid Hybridization / Q000379:methods*
D002843:Chromatin; D004271:DNA, Fungal
Candida albicans; ChIP -chip; ChIP -seq; Chromatin immunoprecipitation; Yeast