title: Characterization of in vivo DNA-binding events of plant transcription factors by ChIP-seq: experimental protocol and computational analysis.
abstract: Chromatin immunoprecipitation followed by next-generation sequencing (ChIP-seq) is a powerful technique for genome-wide identification of in vivo binding sites of DNA-binding proteins. The technique had been used to study many DNA-binding proteins in a broad variety of species. The basis of the ChIP-seq technique is the ability to covalently cross-link DNA and proteins that are located in very close proximity. This allows the use of an antibody against the (tagged) protein of interest to specifically enrich DNA-fragments bound by this protein. ChIP-seq can be performed using antibodies against the native protein or against tagged proteins. Using a specific antibody against a tag to immunoprecipitate tagged proteins eliminates the need for a specific antibody against the native protein and allows more experimental flexibility. In this chapter we present a complete workflow for experimental procedure and bioinformatic analysis that allows wet-lab biologists to perform and analyze ChIP-seq experiments.
authors.affiliation: Laboratory of Molecular Biology, Wageningen University, 6708PB, Wageningen, The Netherlands.
authors.forename: Hilda
authors.initials: H
authors.lastname: van Mourik
authors.forename: Jose M
authors.initials: JM
authors.lastname: Muiño
authors.forename: Alice
authors.initials: A
authors.lastname: Pajoro
authors.forename: Gerco C
authors.initials: GC
authors.lastname: Angenent
authors.forename: Kerstin
authors.initials: K
authors.lastname: Kaufmann
mesh_terms: D001665:Binding Sites; D047369:Chromatin Immunoprecipitation / Q000379:methods; D019295:Computational Biology / Q000379:methods; D018744:DNA, Plant / Q000235:genetics* / Q000378:metabolism*; D015698:Genomic Library; D023281:Genomics / Q000379:methods; D059014:High-Throughput Nucleotide Sequencing / Q000379:methods; D010944:Plants / Q000235:genetics* / Q000378:metabolism*; D016133:Polymerase Chain Reaction; D011485:Protein Binding; D011786:Quality Control; D015203:Reproducibility of Results; D014157:Transcription Factors / Q000378:metabolism*
chemical_list: D018744:DNA, Plant; D014157:Transcription Factors