Abstract
Protein–DNA interactions play key roles in determining gene-expression programs during cellular development and differentiation. Chromatin immunoprecipitation (ChIP) is the most widely used assay for probing such interactions. With recent advances in sequencing technology, ChIP-Seq, an approach that combines ChIP and next-generation parallel sequencing is fast becoming the method of choice for mapping protein–DNA interactions on a genome-wide scale. Here, we briefly review the ChIP-Seq approach for mapping protein–DNA interactions and describe the use of the SISSRs peak-finder, a software tool for precise identification of protein–DNA binding sites from sequencing data generated using ChIP-Seq.
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Acknowledgments
This work was supported by the Intramural Research Program of the National Institutes of Health, National Institute of Environmental Health Sciences (Project number ES102625–02 to R.J.).
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Narlikar, L., Jothi, R. (2012). ChIP-Seq Data Analysis: Identification of Protein–DNA Binding Sites with SISSRs Peak-Finder. In: Wang, J., Tan, A., Tian, T. (eds) Next Generation Microarray Bioinformatics. Methods in Molecular Biology, vol 802. Humana Press. https://doi.org/10.1007/978-1-61779-400-1_20
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DOI: https://doi.org/10.1007/978-1-61779-400-1_20
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