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Systematic characterization of protein-DNA interactions

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Abstract

Sequence-specific protein-DNA interactions (PDIs) are critical for regulating many cellular processes, including transcription, DNA replication, repair, and rearrangement. We review recent experimental advances in high-throughput technologies designed to characterize PDIs and discuss recent studies that use these tools, including ChIP-chip/seq, SELEX-based approaches, yeast one-hybrid, bacterial one-hybrid, protein binding microarray, and protein microarray. The results of these studies have challenged some long-standing concepts of PDI and provide valuable insights into the complex transcriptional regulatory networks.

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Acknowledgments

We are grateful to NIH for funding support.

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Author notes

  1. Zhi Xie

    Present address: The Center for Human Immunology, National Institutes of Health, Bethesda, MD, USA

Authors and Affiliations

  1. Department of Ophthalmology, Johns Hopkins University School of Medicine, Baltimore, MD, USA

    Zhi Xie & Jiang Qian

  2. The Center for High-Throughput Biology, Johns Hopkins University School of Medicine, Baltimore, MD, USA

    Shaohui Hu, Seth Blackshaw & Heng Zhu

  3. Department of Pharmacology and Molecular Sciences, Johns Hopkins University School of Medicine, Baltimore, MD, USA

    Shaohui Hu & Heng Zhu

  4. The Solomon H. Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD, USA

    Seth Blackshaw

  5. The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD, USA

    Jiang Qian & Heng Zhu

  6. Room 333, BRB, 733 N. Broadway, 21205, Baltimore, MD, USA

    Heng Zhu

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Xie, Z., Hu, S., Qian, J. et al. Systematic characterization of protein-DNA interactions. Cell. Mol. Life Sci. 68, 1657–1668 (2011). https://doi.org/10.1007/s00018-010-0617-y

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