Mapping Protein-DNA Interactions Using ChIP-exo and Illumina-Based Sequencing

Stefan J Barfeld, Ian G Mills

Research output: Chapter in Book/Report/Conference proceedingChapter (peer-reviewed)

2 Citations (Scopus)
212 Downloads (Pure)

Abstract

Chromatin immunoprecipitation (ChIP) provides a means of enriching DNA associated with transcription factors, histone modifications, and indeed any other proteins for which suitably characterized antibodies are available. Over the years, sequence detection has progressed from quantitative real-time PCR and Southern blotting to microarrays (ChIP-chip) and now high-throughput sequencing (ChIP-seq). This progression has vastly increased the sequence coverage and data volumes generated. This in turn has enabled informaticians to predict the identity of multi-protein complexes on DNA based on the overrepresentation of sequence motifs in DNA enriched by ChIP with a single antibody against a single protein. In the course of the development of high-throughput sequencing, little has changed in the ChIP methodology until recently. In the last three years, a number of modifications have been made to the ChIP protocol with the goal of enhancing the sensitivity of the method and further reducing the levels of nonspecific background sequences in ChIPped samples. In this chapter, we provide a brief commentary on these methodological changes and describe a detailed ChIP-exo method able to generate narrower peaks and greater peak coverage from ChIPped material.

Original languageEnglish
Title of host publicationThe Nuclear Receptor Superfamily: methods and protocols Part III
EditorsIain J McEwan
Place of PublicationNew York
PublisherSpringer
Pages119-137
Number of pages19
Volume1443
ISBN (Electronic)978-1-4939-3724-0
ISBN (Print)978-1-4939-3722-6
DOIs
Publication statusPublished - 01 Jun 2016

Publication series

NameMethods in Molecular Biology
PublisherSpringer
Volume1443
ISSN (Electronic)1064-3745

Fingerprint

Protein Interaction Mapping
Chromatin Immunoprecipitation
DNA
Histone Code
Nucleotide Motifs
Proteins
Antibodies
Southern Blotting
Real-Time Polymerase Chain Reaction
Transcription Factors

Cite this

Barfeld, S. J., & Mills, I. G. (2016). Mapping Protein-DNA Interactions Using ChIP-exo and Illumina-Based Sequencing. In I. J. McEwan (Ed.), The Nuclear Receptor Superfamily: methods and protocols Part III (Vol. 1443, pp. 119-137). (Methods in Molecular Biology; Vol. 1443). New York: Springer. https://doi.org/10.1007/978-1-4939-3724-0_8
Barfeld, Stefan J ; Mills, Ian G. / Mapping Protein-DNA Interactions Using ChIP-exo and Illumina-Based Sequencing. The Nuclear Receptor Superfamily: methods and protocols Part III. editor / Iain J McEwan. Vol. 1443 New York : Springer, 2016. pp. 119-137 (Methods in Molecular Biology).
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Barfeld, SJ & Mills, IG 2016, Mapping Protein-DNA Interactions Using ChIP-exo and Illumina-Based Sequencing. in IJ McEwan (ed.), The Nuclear Receptor Superfamily: methods and protocols Part III. vol. 1443, Methods in Molecular Biology, vol. 1443, Springer, New York, pp. 119-137. https://doi.org/10.1007/978-1-4939-3724-0_8

Mapping Protein-DNA Interactions Using ChIP-exo and Illumina-Based Sequencing. / Barfeld, Stefan J; Mills, Ian G.

The Nuclear Receptor Superfamily: methods and protocols Part III. ed. / Iain J McEwan. Vol. 1443 New York : Springer, 2016. p. 119-137 (Methods in Molecular Biology; Vol. 1443).

Research output: Chapter in Book/Report/Conference proceedingChapter (peer-reviewed)

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Barfeld SJ, Mills IG. Mapping Protein-DNA Interactions Using ChIP-exo and Illumina-Based Sequencing. In McEwan IJ, editor, The Nuclear Receptor Superfamily: methods and protocols Part III. Vol. 1443. New York: Springer. 2016. p. 119-137. (Methods in Molecular Biology). https://doi.org/10.1007/978-1-4939-3724-0_8