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Author  |
Blecher-Gonen, R.; Barnett-Itzhaki, Z.; Jaitin, D.; Amann-Zalcenstein, D.; Lara-Astiaso, D.; Amit, I. |
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Title |
High-throughput chromatin immunoprecipitation for genome-wide mapping of in vivo protein-DNA interactions and epigenomic states |
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Journal Article |
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Year |
2013 |
Publication |
Nature Protocols |
Abbreviated Journal |
Nat Protoc |
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Volume |
8 |
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3 |
Pages |
539-554 |
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Abstract |
Dynamic protein binding to DNA elements regulates genome function and cell fate. Although methods for mapping in vivo protein-DNA interactions are becoming crucial for every aspect of genomic research, they are laborious and costly, thereby limiting progress. Here we present a protocol for mapping in vivo protein-DNA interactions using a high-throughput chromatin immunoprecipitation (HT-ChIP) approach. By using paramagnetic beads, we streamline the entire ChIP and indexed library construction process: sample transfer and loss is minimized and the need for manually labor-intensive procedures such as washes, gel extraction and DNA precipitation is eliminated. All of this allows for fully automated, cost effective and highly sensitive 96-well ChIP sequencing (ChIP-seq). Sample preparation takes 3 d from cultured cells to pooled libraries. Compared with previous methods, HT-ChIP is more suitable for large-scale in vivo studies, specifically those measuring the dynamics of a large number of different chromatin modifications/transcription factors or multiple perturbations. |
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Address |
Department of Immunology, Weizmann Institute of Science, Rehovot, Israel |
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English |
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ISSN |
1750-2799 |
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Notes |
PMID:23429716 |
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Call Number |
@ @ |
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38049 |
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