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In Cellulo DNA Analysis (LMPCR Footprinting)

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DNA-Protein Interactions

Part of the book series: Methods in Molecular Biology™ ((MIMB,volume 543))

Summary

The in cellulo analysis of DNA protein interactions and chromatin structure is very important to better understand the mechanisms involved in the regulation of gene expression. The nuclease-hypersensitive sites and sequences bound by transcription factors often correspond to genetic regulatory elements. Using the Ligation-mediated polymerase chain reaction (LMPCR) technology, it is possible to precisely analyze these DNA sequences to demonstrate the existence of DNA–protein interactions or unusual DNA structures directly in living cells. Indeed, the ideal chromatin substrate is, of course, found inside intact cells. LMPCR, a genomic-sequencing, technique that map DNA single-strand breaks at the sequence level of resolution, is the method of choice for in cellulo footprinting and DNA structure studies because it can be used to investigate any complex genomes, including human. The detailed conventional and automated LMPCR protocols are presented in this chapter.

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Acknowledgments

This work was supported by the Canadian Genetic Diseases Network (MRC/NSERC NCE program) and the Canada Research Chair. R. Drouin holds the Canada Research Chair in “Genetics, Mutagenesis and Cancer.”

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Authors and Affiliations

  1. Department of Pediatrics, Faculty of Medicine and Health Sciences, Université de Sherbrooke, 3001, 12th Avenue North, Sherbrooke, QC, Canada J1H 5N4

    Régen Drouin, Nathalie Bastien, Jean-François Millau, François Vigneault & Isabelle Paradis

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  1. Régen Drouin
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  2. Nathalie Bastien
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  3. Jean-François Millau
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  4. François Vigneault
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  5. Isabelle Paradis
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Correspondence to Régen Drouin .

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    © 2009 Humana Press, a part of Springer Science+Business Media, LLC

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    Drouin, R., Bastien, N., Millau, JF., Vigneault, F., Paradis, I. (2009). In Cellulo DNA Analysis (LMPCR Footprinting). In: Leblanc, B., Moss, T. (eds) DNA-Protein Interactions. Methods in Molecular Biology™, vol 543. Humana Press. https://doi.org/10.1007/978-1-60327-015-1_20

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    • DOI: https://doi.org/10.1007/978-1-60327-015-1_20

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    • Print ISBN: 978-1-60327-014-4

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