Characterization of in vivo DNA-binding events of plant transcription factors by ChIP-seq: Experimental protocol and computational analysis

Hilda Van Mourik, J.M. Muiño, Alice Pajoro, G.C. Angenent, Kerstin Kaufmann

Research output: Chapter in Book/Report/Conference proceedingChapterAcademicpeer-review

5 Citations (Scopus)

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 DNAfragments 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.

Original languageEnglish
Title of host publicationPlant Functional Genomics: Methods and Protocols: Second Edition
PublisherSpringer New York LLC
Pages93-121
ISBN (Print)9781493924448, 9781493924431
DOIs
Publication statusPublished - 2015

Fingerprint

Transcription Factors
transcription factors
DNA
Proteins
proteins
Antibodies
DNA-Binding Proteins
antibodies
DNA-binding proteins
Workflow
Chromatin Immunoprecipitation
Computational Biology
bioinformatics
biologists
chromatin
Binding Sites
binding sites
Genome
methodology
genome

Keywords

  • ChIP-seq data analysis
  • Chromatin immunoprecipitation
  • Plant transcription factors
  • Transcription factor DNA-binding sites

Cite this

Van Mourik, H., Muiño, J. M., Pajoro, A., Angenent, G. C., & Kaufmann, K. (2015). Characterization of in vivo DNA-binding events of plant transcription factors by ChIP-seq: Experimental protocol and computational analysis. In Plant Functional Genomics: Methods and Protocols: Second Edition (pp. 93-121). Springer New York LLC. https://doi.org/10.1007/978-1-4939-2444-8_5
Van Mourik, Hilda ; Muiño, J.M. ; Pajoro, Alice ; Angenent, G.C. ; Kaufmann, Kerstin. / Characterization of in vivo DNA-binding events of plant transcription factors by ChIP-seq : Experimental protocol and computational analysis. Plant Functional Genomics: Methods and Protocols: Second Edition. Springer New York LLC, 2015. pp. 93-121
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Van Mourik, H, Muiño, JM, Pajoro, A, Angenent, GC & Kaufmann, K 2015, Characterization of in vivo DNA-binding events of plant transcription factors by ChIP-seq: Experimental protocol and computational analysis. in Plant Functional Genomics: Methods and Protocols: Second Edition. Springer New York LLC, pp. 93-121. https://doi.org/10.1007/978-1-4939-2444-8_5

Characterization of in vivo DNA-binding events of plant transcription factors by ChIP-seq : Experimental protocol and computational analysis. / Van Mourik, Hilda; Muiño, J.M.; Pajoro, Alice; Angenent, G.C.; Kaufmann, Kerstin.

Plant Functional Genomics: Methods and Protocols: Second Edition. Springer New York LLC, 2015. p. 93-121.

Research output: Chapter in Book/Report/Conference proceedingChapterAcademicpeer-review

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AU - Angenent, G.C.

AU - Kaufmann, Kerstin

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AB - 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 DNAfragments 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.

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Van Mourik H, Muiño JM, Pajoro A, Angenent GC, Kaufmann K. Characterization of in vivo DNA-binding events of plant transcription factors by ChIP-seq: Experimental protocol and computational analysis. In Plant Functional Genomics: Methods and Protocols: Second Edition. Springer New York LLC. 2015. p. 93-121 https://doi.org/10.1007/978-1-4939-2444-8_5