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High-throughput chromatin immunoprecipitation for genome-wide mapping of in vivo protein-DNA interactions and epigenomic states

Nature Protocols volume 8, pages 539554 (2013) | Download Citation

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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Acknowledgements

We thank H. Keren-Shaul for important comments and G. Brodsky for artwork. This project was supported by an excellence grant from the Weizmann institute (R.B.-G.), The Human Frontiers Science Program, Career Development Award; an Israel Science Foundation (ISF) Bikura Institutional Research Grant Program; ERC starting grant 309788; and the Center for Excellence in Genome Science from the National Human Genome Research Institute (NHGRI) 1P50HG006193 (I.A.).

Author information

Affiliations

  1. Department of Immunology, Weizmann Institute of Science, Rehovot, Israel.

    • Ronnie Blecher-Gonen
    • , Zohar Barnett-Itzhaki
    • , Diego Jaitin
    • , Daniela Amann-Zalcenstein
    • , David Lara-Astiaso
    •  & Ido Amit
  2. Broad Institute of Massachusetts Institute of Technology (MIT) and Harvard University, Cambridge, Massachusetts, USA.

    • Ido Amit

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Contributions

R.B.-G. and I.A. designed the experiments. R.B.-G., D.J., D.A.-Z., D.L.-A. and I.A. conducted the experimental work. Z.B.-I. performed the computational analysis. R.B.-G., D.J., Z.B.-I. and I.A. wrote the manuscript.

Competing interests

The authors declare no competing financial interests.

Corresponding author

Correspondence to Ido Amit.

Supplementary information

PDF files

  1. 1.

    Supplementary Table 1

    ChIP-grade antibodies used in this manuscript

  2. 2.

    Supplementary Table 2

    Sequencing library barcodes

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DOI

https://doi.org/10.1038/nprot.2013.023

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