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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Boyer LA, Lee TI, Cole MF et al (2005) Core transcriptional regulatory circuitry in human embryonic stem cells. Cell 122:947–956.
Chen X, Xu H, Yuan P et al (2008) Integration of external signaling pathways with the core transcriptional network in embryonic stem cells. Cell 133:1106–1117.
Ho L, Jothi R, Ronan JL et al (2009) An embryonic stem cell chromatin remodeling complex, esBAF, is an essential component of the core pluripotency transcriptional network. Proceedings of the National Academy of Sciences of the United States of America 106:5187–5191.
Molkentin JD (2000) The zinc finger-containing transcription factors GATA-4, -5, and −6. Ubiquitously expressed regulators of tissue-specific gene expression. J Biol Chem 275:38949–38952.
Hou C, Dale R, Dean A (2010) Cell type specificity of chromatin organization mediated by CTCF and cohesin. Proceedings of the National Academy of Sciences of the United States of America 107:3651–3656.
Rampakakis E, Gkogkas C, Di Paola D et al (2010) Replication initiation and DNA topology: The twisted life of the origin. J Cell Biochem 110:35–43.
Cohn MA, D’Andrea AD (2008) Chromatin recruitment of DNA repair proteins: lessons from the fanconi anemia and double-strand break repair pathways. Mol Cell 32:306–312.
Shivji MK, Venkitaraman AR (2004) DNA recombination, chromosomal stability and carcinogenesis: insights into the role of BRCA2. DNA Repair (Amst) 3:835–843.
Solomon MJ, Larsen PL, Varshavsky A (1988) Mapping protein-DNA interactions in vivo with formaldehyde: evidence that histone H4 is retained on a highly transcribed gene. Cell 53:937–947.
Ren B, Robert F, Wyrick JJ et al (2000) Genome-wide location and function of DNA binding proteins. Science 290:2306–2309.
Mardis ER (2007) ChIP-seq: welcome to the new frontier. Nat Methods 4:613–614.
Park PJ (2009) ChIP-seq: advantages and challenges of a maturing technology. Nat Rev Genet 10:669–680.
Barski A, Cuddapah S, Cui K et al (2007) High-resolution profiling of histone methylations in the human genome. Cell 129:823–837.
Johnson DS, Mortazavi A, Myers RM et al (2007) Genome-wide mapping of in vivo protein-DNA interactions. Science 316:1497–1502.
Robertson G, Hirst M, Bainbridge M et al (2007) Genome-wide profiles of STAT1 DNA association using chromatin immunoprecipitation and massively parallel sequencing. Nat Methods 4:651–657.
Barski A, Jothi R, Cuddapah S et al (2009) Chromatin poises miRNA- and protein-coding genes for expression. Genome Research 19:1742–1751.
Cuddapah S, Jothi R, Schones DE et al (2009) Global analysis of the insulator binding protein CTCF in chromatin barrier regions reveals demarcation of active and repressive domains. Genome Research 19:24–32.
Barski A, Zhao K (2009) Genomic location analysis by ChIP-Seq. J Cell Biochem 107:11–18.
Cuddapah S, Barski A, Cui K et al (2009) Native chromatin preparation and Illumina/Solexa library construction. Cold Spring Harb Protoc 2009:pdb prot5237.
Langmead B, Trapnell C, Pop M et al (2009) Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol 10:R25.
Li H, Ruan J, Durbin R (2008) Mapping short DNA sequencing reads and calling variants using mapping quality scores. Genome Research 18:1851–1858.
Jothi R, Cuddapah S, Barski A et al (2008) Genome-wide identification of in vivo protein-DNA binding sites from ChIP-Seq data. Nucleic Acids Research 36:5221–5231.
Narlikar L, Gordan R, Hartemink AJ (2007) A nucleosome-guided map of transcription factor binding sites in yeast. PLoS Comput Biol 3:e215.
Bailey TL, Elkan C (1994) Fitting a mixture model by expectation maximization to discover motifs in biopolymers. Proc Int Conf Intell Syst Mol Biol 2:28–36.
Li L (2009) GADEM: a genetic algorithm guided formation of spaced dyads coupled with an EM algorithm for motif discovery. J Comput Biol 16:317–329.
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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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