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 language | English |
|---|---|
| Title of host publication | The Nuclear Receptor Superfamily: methods and protocols Part III |
| Editors | Iain J McEwan |
| Place of Publication | New York |
| Publisher | Springer |
| Pages | 119-137 |
| Number of pages | 19 |
| Volume | 1443 |
| ISBN (Electronic) | 978-1-4939-3724-0 |
| ISBN (Print) | 978-1-4939-3722-6 |
| DOIs | |
| Publication status | Published - 01 Jun 2016 |
Publication series
| Name | Methods in Molecular Biology |
|---|---|
| Publisher | Springer |
| Volume | 1443 |
| ISSN (Electronic) | 1064-3745 |
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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 proceeding › Chapter (peer-reviewed)
TY - CHAP
T1 - Mapping Protein-DNA Interactions Using ChIP-exo and Illumina-Based Sequencing
AU - Barfeld, Stefan J
AU - Mills, Ian G
PY - 2016/6/1
Y1 - 2016/6/1
N2 - 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.
AB - 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.
U2 - 10.1007/978-1-4939-3724-0_8
DO - 10.1007/978-1-4939-3724-0_8
M3 - Chapter (peer-reviewed)
C2 - 27246337
SN - 978-1-4939-3722-6
VL - 1443
T3 - Methods in Molecular Biology
SP - 119
EP - 137
BT - The Nuclear Receptor Superfamily: methods and protocols Part III
A2 - McEwan, Iain J
PB - Springer
CY - New York
ER -